”.
2019-06-23
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2019-06-24
Mike Smith (05:34:33) (in thread): > Nice blog post, I don’t see much ONT data anymore, so I didn’t know they’d finally released a fast5 format that could contain multiple reads. It felt like a natural step to merge into one file for storage space, but I guess didn’t make a huge amount of sense when basecalling was carried out on a per-read basis and done immediately in the cloud.
Mike Smith (05:36:07) (in thread): > If you interested in taking IONiseR and updating or expanding its capabilities I’d be very happy to collaborate.
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2019-06-25
Aaron Lun (00:06:30): > It’s quiet… too quiet.
Mike Smith (03:35:32): > You should be on Twitter, it’s crazy on there#bioc2019(Is there a FOMO emoji?)
Federico Marini (03:36:40): > That’s my face now
Federico Marini (03:36:46): > :stuck_out_tongue:
FelixErnst (07:53:33): > Does anybody know a method forIRanges(List)objects, which can be used to scale the ranges to some arbitrary dimension? Likeshift, but with multiplication. I imagine something like this:scale(subject, query, width).subjectwould be aIRanges(List),querywould be like towidth()result andwidthwould be the target dimension, like a single numeric value or a list of numeric values along subject. > > So it should work like this or similar: > > x <- IRangesList(a = IRanges(5,10)) > scale(x,10L,100L) > > IRangesList object of length 1: > > $a > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 45 91 47 > > I didn’t find any solution by chaining the intra-range methods. Did I miss some option?
Elisabeth (09:07:29): > @Elisabeth has joined the channel
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Stephanie Hicks (14:06:26): > @Mike Smiththere is now!:fomo:
Stephanie Hicks (14:25:00): > and just for fun…. I’ve added:magic::parrot_aussie::carlton::cell::clippy::death_star::dr_evil::face_palm_star_trek::flashing_light::good_luck::happy_goat::jelly::power_up::preprint_posted::sad_file::seal_of_approval:and because#bioc2019is in NYC this year –>:bagel:
Gabriel J. Odom (15:33:28): > @Gabriel J. Odom has joined the channel
Federico Marini (15:37:09): > Oh welll… then:fomo:
Hervé Pagès (16:43:28) (in thread): > Sorry but I can’t figure out what you are trying to do e.g. I can’t link the desired output range (45-91) with the input range (5-10).
Aaron Lun (18:23:33): > Quiet again. Is everyone drunk?
Aaron Lun (18:23:38): > Still one day to go!
Luyi Tian (20:19:08) (in thread): > surprised that you are not on twitter.
Aaron Lun (20:19:44) (in thread): > Well, so many people are wrong there, I would spend too much time on it and it would be hard for me to get any work done.
Luyi Tian (20:32:34) (in thread): > ok I thought it was some minimalism philosophy.
Aaron Lun (20:32:45) (in thread): > also that.
Kevin Rue-Albrecht (23:16:06) (in thread): > Dont worry: if it’s silent here, it’s because everyone’s busy praising you at the conference:sunglasses:
2019-06-26
Hervé Pagès (00:38:07) (in thread): > and also because you are on the wrong channel
Aaron Lun (01:32:03) (in thread): > ah dammit.
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FelixErnst (09:45:45) (in thread): > Hmm. I made a mistake in the example. I mixed up the 1-based coordinate and 0-based coordinate systems. So the correct output would be > > x <- IRangesList(a = IRanges(5,10)) > scale(x,10L,100L) > > IRangesList object of length 1: > > $a > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 41 100 60 >
Hervé Pagès (09:54:25) (in thread): > “querywould be like towidth()result andwidthwould be the target dimension” Can you expand on that? In particular I don’t see that thedimension of the target range in your example (41-100) is 100. What is the dimension of a range?
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FelixErnst (10:18:24) (in thread): > The simple example assumes start coordinates of 1, since noIRangesobject is used as query or width. Therefore, the subject resides on a range1-10and is scaled to a range1-100. > A second option would be, that subject might be anIRangesobject with the range505-510and query could have the range501-510. The result would stay the same compared to the example above. > A third option would be that width might be anIRangesobject (alternative input nametarget). The output would be shifted to fit the target. For the example above and a target range of101-200, the output would have the range141-200
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Hervé Pagès (13:58:13) (in thread): > So it looks like you are after something like this: > > zoom <- function(x, z=1) > { > stopifnot(is(x, "Ranges"), is.numeric(z)) > if (length(z) > length(x) && length(z) != 1L) > stop("'z' longer than 'x'") > if (anyNA(z) || min(z) <= -1L) > stop("'z' contains NAs and/or negative values") > new_start <- as.integer(start(x) * z) > new_width <- as.integer(width(x) * z) > BiocGenerics:::replaceSlots(x, start=new_start, width=new_width) > } > > .normarg_scale <- function(scale) > { > if (is(scale, "IRanges")) > return(scale) > if (is.numeric(scale)) > return(IRanges(1L, scale)) > as(scale, "IRanges") > } > > ## 'oldscale' and 'newscale': integer vectors or IRanges > ## objects recycled to the length of 'x'. > rescale <- function(x, oldscale=1L, newscale=1L) > { > if (!is(x, "IRanges")) > x <- as(x, "IRanges") > oldscale <- .normarg_scale(oldscale) > newscale <- .normarg_scale(newscale) > ans <- shift(x, -start(oldscale)) > ans <- zoom(ans, width(newscale) / width(oldscale)) > shift(ans, start(newscale)) > } > > Then: > > > rescale("5-10", 10, 100) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 41 100 60 > > rescale("505-510", "501-510", 100) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 41 100 60 > > rescale("505-510", "501-510", "101-200") > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 141 200 60 > > This type of question should really be asked on the support site.
Tiphaine Martin (14:03:47): > Do we still have access after today to the talk slides and worshop presentations to still play and learn from them ?
Lori Shepherd (14:05:17): > We will have them posted on the bioconductor course materials page in the up coming weeks and a book down version should hopefully be coming out as well
Sean Davis (14:07:12): > The workshops will be up indefinitely in addition to the cleaned up book that is forthcoming. The location of the rendered material may change, but I’ll redirect if it does. Also, I’ll leave the Docker and packages in place, so anyone with docker should be able to recreate the workshop machine exactly (the workshops are actually running on Docker).
Sean Davis (14:07:46): > https://github.com/Bioconductor/BiocWorkshops2019/blob/master/README.md#running-workshop-materials-locally
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FelixErnst (15:40:29) (in thread): > Thanks for the example. So this function does not exist does it? > > Sorry for not using the appropriate channel. The functionrescalefrom thescalespackage was not on my radar. The vocabulary for the inputs is also more appropriate then, what I came up with initially.
Hervé Pagès (15:46:24) (in thread): > Nope the function does not exist in IRanges. It feels very specialized to me. Maybe we could addzoom(). Oncezoom()is available,rescaleis just a matter of doingshift->zoom->shift. Not sure it’s worth adding a dedicated function for that. I don’t know the functionrescalefrom thescalespackage – the name clash is accidental.
FelixErnst (16:06:33) (in thread): > Thezoomfunction would be a nice addition, since it would allow the conversion of range information to a fixed range length. This would make a nice accessor for a metagene analysis. > > That was the initial thought, which make me look for such function in the first place. I couldn’t find anything like it, so the question was, whether it doesn’t exist or I have overlooked it.
FelixErnst (16:07:58) (in thread): > I also realize, that it is quite a dangerous function, since the inverse operation does not necessarily result in the original object due to rounding errors
Hervé Pagès (19:08:30) (in thread): > Right. Only ifzis a positive integerzoom(zoom(x, z), 1/z)is guaranteed to return the original object.zoom()should also support a 2nd argument to specify the center of the zooming. Something like: > > zoom <- function(x, z=1, center=0) > { > if (!is(x, "IRanges")) > x <- as(x, "IRanges") > > stopifnot(is(x, "Ranges"), is.numeric(z)) > > if (length(z) > length(x) && length(z) != 1L) > stop("'z' is longer than 'x'") > if (anyNA(z) || min(z) <= -1L) > stop("'z' contains NAs and/or negative values") > > if (length(center) > length(x) && length(center) != 1L) > stop("'center' is longer than 'x'") > if (anyNA(center)) > stop("'center' contains NAs") > > new_start <- as.integer((start(x) - center) * z + center) > new_width <- as.integer(width(x) * z) > BiocGenerics:::replaceSlots(x, start=new_start, width=new_width) > } > > Then: > > > zoom("5-10", 3) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 15 32 18 > > zoom("5-10", 3, center=5) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 5 22 18 > > However, whencenteris on the end of the range, this looks wrong: > > > zoom("5-10", 3, center=10) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] -5 12 18 > > (by definition the center of the zooming should not move) so my current naive implementation is broken:pensive:
Jenny Drnevich (23:12:47): > After an amazing BioC2019 conference, I am left with one thing dragging on my conscious that I need to put out (I’m not on Twitter and thought here was broader than the bioc2019 channel). The attention drawn to the code of conduct and the availability of lactation rooms was FANTASTIC, especially after spending Sunday with my Aunt who finally told me horror stories of her getting a MS degree in 1962 with the rampant sexism at the time. Here is one area where the BioC community needs to be proactive on change: we should change “whitelist”/ blacklist” that is common terminology in single-cell RNA-Seq to “allowlist”/“denylist”. Why did I finally realize this? When I thought about having to explain these terms to the two undergraduate interns from a Historically Black College whom I am mentoring this summer. My eyes were opened, so I thought this post was the very least I could do.
Seth Falcon (23:41:50): > @Seth Falcon has joined the channel
2019-06-27
FelixErnst (03:01:09) (in thread): > I think the center has to be offset by1L, since the coordinate system is 1-based > > function(x, z = 1L, center = 0L) > { > browser() > if (!is(x, "IRanges")) > x <- as(x, "IRanges") > > stopifnot(is(x, "Ranges"), is.numeric(z)) > > if (length(z) > length(x) && length(z) != 1L) > stop("'z' is longer than 'x'") > if (anyNA(z) || min(z) <= -1L) > stop("'z' contains NAs and/or negative values") > > if (length(center) > length(x) && length(center) != 1L) > stop("'center' is longer than 'x'") > if (anyNA(center)) > stop("'center' contains NAs") > > center <- center + 1L > new_start <- as.integer((start(x) - center) * z + center) > new_width <- as.integer(width(x) * z) > BiocGenerics:::replaceSlots(x, start=new_start, width=new_width) > } > > The the result of your first exampled is also correct > > > zoom("5-10", 3) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 13 30 18 > > and the third example works as well > > > zoom("5-10", 3, center=10) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] -7 10 18 > > fourth is also correct > > > zoom("5-10", 3, center = 8L) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] -3 14 18 > > and the original example is also correct > > > zoom("5-10", 10, center = 0L) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 41 100 60 >
Hervé Pagès (08:21:45) (in thread): > but not this one (my 2nd example, withcenteron the start): > > > zoom("5-10", 3, center=5) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 4 21 18 >
Aedin Culhane (08:30:14): > we need to update wikipediahttps://en.wikipedia.org/wiki/Bioconductor. The “Package” section says “Most Bioconductor components are distributed as R packages, which are add-on modules for R. Initially most of the Bioconductor software packages focused on the analysis of single channel Affymetrix and two or more channel cDNA/Oligo microarrays. As the project has matured, the functional scope of the software packages broadened to include the analysis of all types of genomic data, such as SAGE, sequence, or SNP data.”
Aedin Culhane (08:31:11): > Need to update “package” section on wikipedia - File (PNG): Screen Shot 2019-06-27 at 8.30.22 AM.png
FelixErnst (09:09:50) (in thread): > hmm. for me the result is different: > > > zoom("5-10", 3, center=5) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 3 20 18 > > > > > zoom("1-10", 3, center=0) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 1 30 30 >
FelixErnst (09:11:05) (in thread): > And the reverse looks good as well > > > zoom(zoom("5-10", 3, center=5),1/3,5) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 5 10 6 >
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Hervé Pagès (15:01:25) (in thread): > The last result I showed was with a center correction of 0.5 (center <- center + 0.5) instead of 1, my bad. But still, the result you get forzoom("5-10", 3, center=5)is still not what one would expect. By definition the center is the fixed point of the zooming operation so when you set it on the start of the range, the start should not move.
FelixErnst (16:11:30) (in thread): > The problem is how to define whatcenteris. For me it describes the origin of the coordinate system, and not a position on a discrete scale with blocks ofwidth = 1L.centerdescribes the edge between two position (two blocks) and I think the example produces a valid result. > > Withcenter = 5, the default center 0 is moved 5 blocks up, which is the edge between the blocks 5 and 6. Therefore, the block 5 is “divided” into 3 blocks and the first block is reported as boundary for the new range, which is 3. > > For me it is more “important”, that the width fits the expectation. Also, the default value of center is 0, not 1. So if the default of center is 1 the result of putting center to the end of the range, results in the same “weird” result. > > zoom <- function(x, z = 1L, center = 1L) > { > if (!is(x, "IRanges")) > x <- as(x, "IRanges") > > stopifnot(is(x, "Ranges"), is.numeric(z)) > > if (length(z) > length(x) && length(z) != 1L) > stop("'z' is longer than 'x'") > if (anyNA(z) || min(z) <= -1L) > stop("'z' contains NAs and/or negative values") > > if (length(center) > length(x) && length(center) != 1L) > stop("'center' is longer than 'x'") > if (anyNA(center)) > stop("'center' contains NAs") > new_start <- as.integer((start(x) - center) * z + center) > new_width <- as.integer(width(x) * z) > BiocGenerics:::replaceSlots(x, start=new_start, width=new_width) > } > > > > > zoom("5-10", 3, center=10) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] -5 12 18 >
FelixErnst (16:17:54) (in thread): > I just realized, that whether the upstream or downstream edge is used as a origin, could be an additional argument. edit:middlecould also be a valid option
Hervé Pagès (16:20:02) (in thread): > Well, thewidthalways fits the expectation. The problem is that there doesn’t seem to be an easy way to conceptualize/implement the notion of arbitrary center for the zooming (with good properties).
Hervé Pagès (16:26:26) (in thread): > So I’m taking back my earlier proposal to add a 3rd argument tozoom()to control the center. Whatever I was trying to achieve with thecenterargument the user can achieve it (and with more control) with the right combination ofshiftandzoomoperations. These 2 operations provide basic range arithmetic (shiftis+andzoomis*). Sozoom()should just do that i.e. multiply the coordinates of the range by the supplied value.
FelixErnst (17:22:16) (in thread): > I agree. To produce the result as expected for all the examples above, theshiftandzoomoperation in therescalefunction need to be offset by-1/1. My current function look like this: > > .zoom_default <- function(x, z = 1L) > { > if (!is(x, "IRanges")) > x <- as(x, "IRanges") > .zoom_IRanges(x, z) > } > > .zoom_IRanges <- function(x, z = 1L) > { > stopifnot(is(x, "Ranges"), is.numeric(z)) > > if (length(z) > length(x) && length(z) != 1L) > stop("'z' is longer than 'x'") > if (anyNA(z) || min(z) <= -1L) > stop("'z' contains NAs and/or negative values") > > new_start <- as.integer((start(x) - 1L) * z + 1L) > new_width <- as.integer(width(x) * z) > BiocGenerics:::replaceSlots(x, start=new_start, width=new_width) > } > > .normarg_scale <- function(scale) > { > if (is(scale, "IRanges")) > return(scale) > if (is.numeric(scale)) > return(IRanges(1L, scale)) > as(scale, "IRanges") > } > > ## 'from' and 'to': integer vectors or IRanges > ## objects recycled to the length of 'x'. > .rescale_default <- function(x, to = 1L, from = 1L) > { > if (!is(x, "IRanges")){ > x <- as(x, "IRanges") > } > .rescale_IRanges(x, to, from) > } > > .rescale_IRanges <- function(x, to = 1L, from = 1L, ...){ > from_scale <- .normarg_scale(from) > to_scale <- .normarg_scale(to) > z <- width(to_scale) / width(from_scale) > ans <- shift(x, -start(from_scale) + 1L) > ans <- zoom(ans, width(to_scale) / width(from_scale)) > shift(ans, start(to_scale) - 1L) > } > > setGeneric("zoom", signature="x", > function(x, z = 1L) > standardGeneric("zoom")) > setMethod("zoom", > signature = c(x = "ANY"), > function(x, z = 1L){ > .zoom_default(x, z) > }) > setMethod("zoom", > signature = c(x = "IRanges"), > function(x, z = 1L){ > .zoom_IRanges(x, z) > }) > > setGeneric("rescale", > function(x, to = 1L, from = 1L, ...) > standardGeneric("rescale"), > useAsDefault=scales::rescale, > signature="x") > setMethod("rescale", > signature = c(x = "ANY"), > function(x, to = 1L, from = 1L, ...){ > .rescale_default(x, to, from, ...) > }) > setMethod("rescale", > signature = c(x = "IRanges"), > function(x, to = 1L, from = 1L, ...){ > .rescale_IRanges(x, to, from, ...) > }) > # Examples > x <- IRanges("5-10") > rescale(x, 100, 10) > zoom(x, 10) > rescale("505-510", 100, "501-510") > rescale("505-510", "101-200", "501-510") > zoom("5-10", 3) > zoom("5-10", 10) > rescale(x, "31-60", "5-14") > > I think these result are valid, aren’t they?
2019-06-28
Hervé Pagès (00:08:40) (in thread): > As far asrescale()is concerned it doesn’t seem to matter whether you use a 0-centeredzoom()(let’s call itzoom0) or a 1-centeredzoom()(let’s call itzoom1). With the former,rescale()needs to do: > > ans <- shift(x, -start(oldscale)) > ans <- zoom0(ans, width(newscale) / width(oldscale)) > shift(ans, start(newscale)) > > And with the latter, it needs to do: > > ans <- shift(x, -start(from_scale) + 1L) > ans <- zoom1(ans, width(to_scale) / width(from_scale)) > shift(ans, start(to_scale) - 1L) > > You end up with 2 versions ofrescale()that are equivalent but thezoom1-based version introduces additional+ 1Land- 1Ladjustements (two inrescale()and two inzoom1()). So it feels that a 1-centeredzoom()would be slightly more complicated to use than a 0-centeredzoom(), at least in therescale()use case. > > Having other use cases forzoom()would help choose the right behavior (i.e. 0- or 1-centered) but I can’t think of any besides therescale()use case. > > So another solution would be to addrescale()to IRanges and forget aboutzoom()?
FelixErnst (01:49:50) (in thread): > Yep, I agree with that. If zoom is exported, I would prefer the zoom1 version, since the results are otherwise quite confusing to me. > > > zoom1("5-10", 10) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 41 100 60 > > zoom0("5-10", 10) > IRanges object with 1 range and 0 metadata columns: > start end width > <integer> <integer> <integer> > [1] 50 109 60 > > But that is probably personal preference. Without is fine as well, since the rescale function was, what I was looking for.
Fotis E. Psomopoulos (03:19:33): > @Fotis E. Psomopoulos has joined the channel
Kevin Blighe (03:23:53): > @Kevin Blighe has joined the channel
Juan Monroy-Nieto (13:26:03) (in thread): > What exactly do you think it is missing? I’m a novice so I fail to notice what is wrong with that description.
Jason Vander Heiden (13:42:14): > @Jason Vander Heiden has joined the channel
2019-06-30
Sean Davis (10:36:43): > I’m teaching a course and want to be able to quickly make plots of “regions” in a GRanges object. It is simple example data and I want the students to be able to visualize what happens to ranges when doingflank,disjoin, etc. Any suggestions about functions to do this easily in an interactive session?
Charlotte Soneson (10:55:01): > @Sean DavisWould > > grt <- Gviz::GeneRegionTrack(gr) > Gviz::plotTracks(grt) > > work? Addingmcols(gr)$transcript <- ...to connect multiple exons into a transcript if needed.
Kevin Rue-Albrecht (11:42:42): > A little while back I saved a few helpers for Gviz, perhaps they can be helpful:https://github.com/kevinrue/Bioinformatics/tree/master/Bioconductor/Gviz
Kevin Rue-Albrecht (12:16:24): > Ps: I’ve made significant progress thanks to#bioc2019(scientifically too!) - File (JPEG): Image from iOS
Sridhar N (12:17:29): > yea you need the new 16” macbook pro
Kevin Rue-Albrecht (12:20:38): > Anyone hiring? I already got the touchbar 13” mackbook pro from my PI last year:grimacing:
Sridhar N (12:21:58): > no one in academia can afford the 16” try industry
Sridhar N (12:22:00): > :stuck_out_tongue:
Aaron Lun (18:16:25): > ’fraid industry only hands out 13’s as well.
Shian Su (18:47:40): > That is a bit silly given it’s like $1-2k extra over 4-5 years. You’d think letting someone you’re paying tens of thousands be more productive is good value.
Shian Su (18:48:43): > *sticker count may or may not have a causal effect on productivity.
Aaron Lun (19:33:24): > “tens of thousands”? Ho ho ho. I wouldn’t even get out of bed for that much.
Shian Su (19:34:56): > Elevens of thousands then.
Aaron Lun (19:37:36): > I might brush my teeth for that.
Aaron Lun (19:38:21): > I mean, anything less than 40K after tax is not survivable.
Aaron Lun (19:39:05): > Literally. I’d have to move.
Davide Risso (19:40:03): > Yeah but not everyone lives/works in the bay area
Davide Risso (19:40:44): > But I do agree… less than 50k in the us is hard
Aaron Lun (19:44:12): > So much for my bathtub of money.
Aaron Lun (19:44:24): > I guess I’ll have to settle for $1 bills.
Aaron Lun (19:44:36): > I was thinking I could do $10, maybe even $20.
Aaron Lun (19:45:13): > Oh well.
Davide Risso (20:19:55): > I’d go for coins… like scrooge mcduck… quarters should work
Aaron Lun (20:41:01): > Dunno, might chafe a bit.
Aaron Lun (20:41:39): > Sort of thinking like American Beauty-style
Aaron Lun (20:41:47): > Look forward to my Christmas cards!
Aaron Lun (20:44:23): > Oh,@Davide Risso, while you’re here, keep an eye on the scRNAseq repo.
Aaron Lun (20:45:21): > I’m dumping one dataset into it per day - see if there’s any datasets you know of (or that you know other people are using) that you want to put in there.
Aaron Lun (20:45:55): > It’s getting pretty epic - I think we’ll hit 100,000 cells total across all datasets in the next round.
Shian Su (20:51:35): > Is there going to be a metadata normalisation effort?
Aaron Lun (21:03:08): > We could, if enough domain experts are willing to contribute.
Aaron Lun (21:03:44): > I am happy to do the gene-level munging (convert everything to Ensembl). But the column metadata is much more context dependent.
Aaron Lun (21:04:17): > Sometimes there’s donors. Sometimes there’s plates. Sometimes there’s other stuff.
Aaron Lun (21:04:37): > I mean, even a better description of the existing metadata fields would already be value adding.
Shian Su (21:08:59): > That’s alright, I’m sure once the package had enough data people will throw ML at it and have the computer annotate it all.
Aaron Lun (21:11:24): > Yes, that’s the plan.
2019-07-01
Lambda Moses (00:09:13): > I want to add some datasets to scRNAseq with one assay for spliced transcripts and another for unspliced, which can be used for RNA velocity.
Aaron Lun (00:25:58): > Where are these from? If they’re from public count matrices, then we’re game.
Lambda Moses (00:26:22): > Yes public, from GEO
Aaron Lun (00:27:13): > Have a look at the existing Rmd scripts ininst/scriptsto see the layout that we’re using.
Aaron Lun (00:27:31): > I would recommend looking atmake-zeisel-brain-data.Rmd, which is a tour-de-force of demangling.
Lluís Revilla (11:19:47): > What are the news of the latest Technical Advisory Board that was on 1st of June?
Lluís Revilla (11:20:11): > I couldn’t find any report on the website:https://bioconductor.org/about/technical-advisory-board/
Martin Morgan (16:33:53): > The june meeting notes need to be approved by the board…at the July meeting, which was originally scheduled for July 4, but will be delayed until next week…
2019-07-02
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2019-07-03
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2019-07-04
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2019-07-05
Juan Monroy-Nieto (15:09:00): > Hello, has anyone here attended the genomics with R and Bioconductor course from physalia in Germany? or taken any courses with Ludwig Geistlinger? I am considering attending the course and would like to hear other people’s experiences.
Ludwig Geistlinger (15:50:03): > I wouldn’t go - this guy has no idea what he is talking about.:slightly_smiling_face:But if this helps, I can put you in touch with participants of our (together with Levi Waldron) recent Introduction to Bioconductor course at Columbia University > (https://tinyurl.com/y3zsuhxp ) > and/or participants of my Bioc2017-2019 gene set analysis workshop (https://tinyurl.com/y5tvgr76 ). - Attachment (bioconductor.github.io): The Bioconductor 2018 Workshop Compilation > This book contains all the workshops presented at the Bioconductor 2018 Conference
Marko Zecevic (15:57:17) (in thread): > I was at this bioc 2017 workshop, would recommend :)
Sridhar N (16:08:20): > lol
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2019-07-08
Juan Monroy-Nieto (09:04:03) (in thread): > @Ludwig GeistlingerThanks for answering. My main goal is to get the differentiation points from other materials in bioconductor so that I can convince my boss:slightly_smiling_face:I am excited about the focus on background statistics for the analyses. I mainly wanted to hear from other participants how actionable they found the material on gene sets.
Sridhar N (21:02:29): > i am seeing more and more papers these days that use a cut off before deseq2 analysis, i wonder what is the rational and or how do they arrive at how many reads is right..for example from one of the papers > > DESeq2 was applied to genes having more than 20 reads in the half the number of samples >
Sridhar N (21:02:46): > ^ this study had n=8 4wt and 4ko
Sridhar N (21:03:39): > i could not comprehend how did they arrive at the number 20, even if they did what if the differences are genotype driven
Sridhar N (21:12:36): > more over deseq2 has independent filtering which takes care of low counts no?
2019-07-09
Aaron Lun (00:32:01): > Sounds like a question you should ask on the support site.
Vince Carey (10:23:52): > anyone thinking about vroom-backed GRanges?
Martin Morgan (10:29:10) (in thread): > ?vroom
Nicholas Knoblauch (10:36:29) (in thread): > I’m guessing this is referring tohttps://github.com/r-lib/vroom a package that takes advantage of ALTREP to read delimited data really quickly
Nicholas Knoblauch (10:38:16) (in thread): > Would the idea be that you would use something likevroomto read abedfile but return aGenomicRangeinstead of atibble?
Vince Carey (10:50:38) (in thread): > yes, in broad strokes,@Nicholas Knoblauch… i have only a vague idea of what the potentials are, and plyranges is surely relevant.
Nicholas Knoblauch (11:09:16) (in thread): > I imagine in many use cases there could be a substantial speedup (why parse strings you aren’t going to use?). Taking a peek at plyranges it looks like the approach is along the lines of “giveGRangesatibble-like interface”. I wonder in the case ofvroomwhether it would be easier to let atibblebe the “backend” for aGRange?
Martin Morgan (11:30:39) (in thread): > @Michael Lawrenceor@Michael Lawrenceor@Hervé Pagèswould have to provide details; my guess is actually you’d put the vroom-based vectors into GRanges slots directly – ALTREP present themselves as native vectors so can be used [in principle] where ever you’d use a standard vector – it could be quite interesting! Maybe@JiefeiWangcould tackle a prototype??:smile:
Martin Morgan (13:59:20) (in thread): > > ## BiocManager::install("vroom") > ## BiocManager::install("Jiefei-Wang/AltWrapper") > > library(vroom) > library(AltWrapper) # convenience function is.altrep() > > fl <- # a bed file > "~/b/git//GUIDEseq/inst/extdata/bowtie2.HEK293_site4_chr13.sort.bed" > > > Sys.setenv(VROOM_USE_ALTREP_NUMERICS="true") > > col_types <- c( > list(seqnames = "c", start = "i", end = "i") > ## rep(list(NULL), 4L) > ) > > vfl <- vroom( > fl, > delim = "\t", skip = 1, > col_names = names(col_types), > col_types = col_types > ) > > is.altrep(vfl$seqnames) # TRUE > is.altrep(vfl$start) # TRUE > is.altrep(vfl$end) # TRUE > > library(GenomicRanges) > gr <- GRanges(vfl$seqnames, IRanges(vfl$start, vfl$end)) > is.altrep(seqnames(gr)) # Nope, an Rle > is.altrep(end(gr)) # Nope, IRanges stores start + width > is.altrep(start(gr)) # Nope, not sure why > is.altrep(gr@ranges@start) # Nope, ... > > .A = setClass("A", representation( x= "integer")) > a = .A(x = vfl$start) > is.altrep(a@x) # Yep! >
Stuart Lee (17:40:58) (in thread): > I would be really keen to see this,@Michael Lawrenceand I had talked about making ops for reading + transforming genomic files lazy for plyranges but never quite got there
2019-07-10
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2019-07-11
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Sean Davis (10:26:47): > @Keegan Korthauer’s excellent teaching materials from CSHL Stats Genomics course:https://kkorthauer.org/fungeno2019/
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Martin Morgan (14:27:07): > <!channel>our ‘window’ of 10,000 messages stretches back only to May; I think we should decide to adopt a ‘paid’ plan and get complete slack history. My understanding is that this will ‘unlock’ old messages, not just retain messages since May. Please let me know your opinion::thumbsup:for persistence,:thumbsdown:to continue with the 10k rolling window. [Edit: please express your opinion without regard to monetary cost]
Vince Carey (14:28:04): > but around $8/user/month … is that right?
Aaron Lun (14:28:31): > woah, it’s per user?
Davide Risso (14:28:41): > Yeah the pricing is insane
Kevin Rue-Albrecht (14:28:45): > ouch
Aaron Lun (14:29:58): > I mean, do we need to remember what we said two months ago?
Aaron Lun (14:30:17): > Persistent discussions seem better somewhere else.
Kevin Rue-Albrecht (14:31:28): > I’m obviously not the one who’d be spending the money, but I remember that this same conversation happened the first time we crossed the 10k messages, and at the time no one seemed to mind losing track of old (unpinned, unstarred) messages. I personally don’t mind. It’s only in rare instances that I wish I could browse back to that one message, though I usually go back to the person for a fresh discussion.
James Taylor (14:31:58): > https://get.slack.help/hc/en-us/articles/204368833-Slack-for-Nonprofits - Attachment (Slack Help Center): Slack for Nonprofits > The Slack for Nonprofits program offers eligible organizations a free or discounted upgrade of one workspace to a paid plan. Here are the details: Standard Plan: We offer workspaces with 250 or f…
Davide Risso (14:32:03): > Is there a way of having only a subset of premium users ?
Davide Risso (14:32:22): > Oh nice!
Deepak Tanwar (14:33:38): > self hosting rocket.chat server?https://rocket.chat/install And, there is an option to import slack messages there:https://rocket.chat/docs/administrator-guides/import/slack/
Craig (14:49:32): > maybe also set something up likehttps://www.discourse.org/ instead for forum discussions
Juanes (15:01:31): > I would suggest: > - apply for non-profit as@James Taylorsaid. > - move the channel to discourse as@Craigsaid orhttps://gitter.im/ that are designed more for open communities, Slack is more for enterprise in my way of seeing it. - Attachment (gitter.im): Gitter > Where developers come to talk.
Artem Sokolov (15:06:36): > It’s peractive
Jon Bråte (15:26:28) (in thread): > I’ve heard some rumors that it’s possible to get the entire history, even on a free plan. But I haven’t tested it myself. There might be some info here:https://stackoverflow.com/questions/28818809/slack-retrieve-all-messages - Attachment (Stack Overflow): Slack: Retrieve all messages > I want to retrieve all the messages that were sent in my teams slack domain. Although, I’d prefer that the data be received in XML or JSON I am able to handle the data in just about any form. How…
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Martin Morgan (15:59:13): > don’t worry about cost; focus on whether you want a long-term or transient record
Davide Risso (16:53:01): > If costs are out of the equation, having permanent records is better. IMO it’s not always immediately obvious that a message is worth pinning and when you look back for the info is gone
Leo Lahti (17:16:54): > It would be quite a move to migrate to another platform yet it might be a good moment to consider which service provider would best deserve the support of the bioc community, through open source or other arguments.
Leo Lahti (17:18:14): > I have good limited experience with gitter and discourse. Slack is more developed however.
Martin Morgan (18:43:50) (in thread): > I know that gitter is ‘free’ to download, etc., but what are the license restrictions as a user? discourse seems slick but commercialized.
2019-07-12
Michael Lawrence (01:49:33) (in thread): > This would be really hard to achieve. All validation etc would need to be lazy. ALTREP is so low level that it is hard to provide speedups. For example, in principle you could do nchar() efficiently, but there is no way for an ALTREP to override nchar(). Nor is there any general framework for deferred evaluation, like DelayedArray. I’d be curious to hear actual use cases where this would help. Btw, Jim told me that it’s not the string parsing that is lazy (it scans over the entire file to get the delimiter offsets). It’s the string internalization, i.e., creating the CHARSXP. Perhaps we could improve the performance of that instead?
Stephanie Hicks (19:18:00): > @Martin MorganFor me it depends on what the goal is of Bioc Slack. If the goal is to provide support to users and developers, then I agree with@Davide Rissoon having a permanent record (however the Bioc Support pages also provides this). If the goal is to just have a space for communication, then I would say it’s less important to have a permanent record.
Aaron Lun (19:21:21) (in thread): > I was looking forward to talking shit and being secure in the knowledge that my nonsense would disappear after 10000 other messages.
Stephanie Hicks (19:29:25) (in thread): > Personally I agree with@Aaron Lunon that idea that I like how messages disappear after 10k messages. I’m in other Slack teams where this is the case. But again, it depends on what the goal is for Bioc slack.
Simina Boca (22:41:03) (in thread): > I also agree that in many ways it’s nice for things to disappear after 10,000 messages
Simina Boca (22:41:42) (in thread): > but even if we want a permanent record, I agree with the others that Slack may not be the best at this (probably harder to search than other options)
Martin Morgan (23:15:41) (in thread): > I think of the support site as the place where users get support. > > The challenge is I guess that ‘conversations’ end up becoming important projects, and then the record of those projects is lost. For instance there is no real record of our original HCA proposal development (which seemed like a really compelling scenario for a vehicle like this) and presumably of other activities like the development of iSEE and OSCA. Also as the channel becomes more popular the window of available messages becomes shorter – we currently have a couple of months worth of ‘memory’, and it’s easy to imagine wanting something more than that for the next slack-inspired project. > > Hmm…
Simina Boca (23:28:13) (in thread): > Yeah, I think more developed things need to get moved elsewhere - I’m not sure slack is good with that
2019-07-14
Stephanie Hicks (21:42:57) (in thread): > @Martin Morgani like your (maybe?) suggestion of (re-)imagining bioc slack as the place to record the history of projects (vs the support site as the history of questions asked by users). These are definitely different purposes. In that light, I much more supportive of keeping a history on slack.
2019-07-15
Martin Morgan (14:43:37): > <!channel>nominations for the Bioconductor technical advisory board are now open athttps://forms.gle/zTZLZJQrHL4ZGEGq9 Questions? join the#tech-advisory-boardchannel! - Attachment (Google Docs): Nomination Form: Bioconductor Technical Advisory Board (TAB) > Complete this form to nominate a candidate for a three-year appointment to the Bioconductor Technical Advisory Board (TAB). Self-nomination and nomination of others are acceptable; if nominating someone else please check with them first that they intend to accept the nomination. The composition of the TAB is determined through a nomination and selection process defined in the Bioconductor TAB governance document (https://bioconductor.org/about/technical-advisory-board/TAB-Governance.pdf ). The TAB should: - constitute a broad representation of the Bioconductor scientific community - include emerging and established researchers in biological, statistical, and computational domains - represent diversity of gender, race/ethnicity, geography, and other aspects of the Bioconductor community Participation in the TAB obligates the member to regular participation in a monthly TAB teleconference and to follow the Bioconductor Governance Document. The TAB helps determine the overall direction of the project, providing guidance to developers and investigators on new concepts in computational biology and genome research, and acts as an incubation group for the collaborative pursuit of funding for the project.
kipper fletez-brant (14:48:58): > @kipper fletez-brant has joined the channel
Martin Morgan (14:57:03) (in thread): > This is a close vote, much more so than the last time. I’d like to move forward with persistence, since it seems useful for the general purpose of the slack channel as a medium to enable collaboration. We’ll do this on a relaxed schedule as we explore costs and other issues…
Martin Morgan (15:04:43): > At the end of my useR2019 keynote (slides:https://docs.google.com/presentation/d/e/2PACX-1vQnSGdSu3iSrVTZadiuOEXXrnikX7qS_A4NBHDbNxVMojPy69zu_dLwWH5pjAb1chY4Jz5n74y72Q4z/pub?start=false&loop=false&delayms=3000 ; video:https://www.youtube.com/watch?v=YEQ5xFewbdA&feature=youtu.be&t=897 ) an anonymous individual posted “I learned recently that BioConductor was used in the research of targeted therapy for leukemia that saved my husband’s life” – it’s not often that the translational consequences of the Bioconductor community are recognized, and of course not clear what parts of Bioconductor played a role, but I wanted to share this with all of you, and to thank you for your transformative efforts. - Attachment (YouTube): useR! 2019 - Keynote : Martin Morgan
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Peter Hickey (23:10:00): > can anyone point me to info on how the Amazon-hosted RStudio instances are set up and configured for BioC workshops? > I’d like to replicate something similar for an upcoming (non-BioC) workshop I’m teaching.@Lori Shepherdgave me some pointers but I can’t find them now
Lori Shepherd (23:13:31): > We use the coursehelperhttps://github.com/Bioconductor
Lori Shepherd (23:14:53): > But it’s geared a lot towards our own setup. All of it was written before my time.
Peter Hickey (23:20:47) (in thread): > Thanks! that’s the repo I was looking for:slightly_smiling_face:I’ll see what I can learn from it
2019-07-16
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2019-07-17
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Vince Carey (10:02:53): > Didn’t we have a channel devoted to dimension reduction?https://github.com/beringresearch/ivis is recently published in sci reports doi 10.1038/s41598-019-45301-0 and has a tensorflow back end used in an R package!
Sean Davis (12:39:05) (in thread): > If you have 20-30 users, I typically start a single big machine (8-16 cores, 128-256G RAM) and create enough user accounts (based on babynames for username and password) for all the users (and some backups). I hand those accounts out to users. It saves a bunch of extra work and is usually enough power for everyone. Disk performance is the biggest issue limiting more users.
Peter Hickey (19:06:16) (in thread): > thanks, Sean. I’ve got ~40 users and have opted to spin up instances for each of them. Fortunately, I have email addresses for everyone who registered so I’ll email them all a unique IP prior to the workshop and cross my fingers that it all works
2019-07-18
Martin Morgan (05:40:11): > This poster at useR!2019https://github.com/chainsawriot/rstyle/blob/master/user2019_poster.pdf was pretty interesting, and the average style not so bad (though I’d say that was a mis-use ofifelse()and unnecessary use ofreturn(), and warnings and errors don’t need!to draw attention to them!)
Kasper D. Hansen (09:36:30): > Perhaps this already exists, but would it be worth it to describe the coding style for the core team + lintr settings?
Martin Morgan (09:49:20): > There is a style recommendation athttps://bioconductor.org/developers/how-to/coding-style/ ; it points to formatR but not with specific settings. This would be a good pull request (lintr or formatR or… if one is clearly better than another…) onhttps://github.com/Bioconductor/bioconductor.org/ under content/developers/how-to/coding-style.md
Lluís Revilla (10:08:48): > There are some efforts to create a lintr setting for Bioconductor packages:https://github.com/jimhester/lintr/issues/43 that could be used for this PR.
Aaron Lun (11:33:22): > Geez, obviously one would uselog1p.
Michael Lawrence (11:41:06): > Why is it a misuse ofifelse()?
Kevin Rue-Albrecht (11:45:07): > I’m surprised that@Aaron Lundidn’t jump yet on > > Don’t explicitly type integers (e.g.1L) > We’d have to update half of iSEE:stuck_out_tongue:
Michael Lawrence (11:46:56): > It’s just the average style, not a recommendation.
Martin Morgan (11:49:36) (in thread): > I guess I was readingvalueas singular, and wanting to fail [ok, be warned] if it were not. Soif (value > 0) { ... } else { ...}. But probably on reflectionvalueis not a scalar so I withdraw my complaint.
Martin Morgan (11:50:27): > And what’s that functionwarnings()anyway?:wink:It’s amazing how much information and subtlety are encoded in such a small chunk of code.
Michael Lawrence (11:51:50): > Anyway, that was by far my favorite poster of the conference.
Federico Marini (14:56:45): > and by the way the author gave an excellent lightning talk on using deep learning for guessing german names’ articles
Federico Marini (16:22:04): > Quick question for everyone, especially the ones of you versed also on the IT side: we were considering of getting a shiny server pro license, and after getting in touch with the sales team, I got to know little more of RStudio connect
Federico Marini (16:22:33): > So my question is: does any of you have direct experiences with either option and is happy to share it with me/us?
Federico Marini (16:25:40): > In the end in my understanding Connect is going to be the product they are pushingand actively developing
Michael Lawrence (16:25:41): > People on my team have a ton of experience with Shiny Pro. We haven’t moved to RStudio Connect yet, but we are exploring it for centralized hosting of plumbr web services.
Michael Lawrence (16:26:18): > Yes, I think Connect is the one moving forward.
Steve Lianoglou (16:27:10): > We haven’t opted to go with either (server pro or connect) just yet, and currently using shinyproxy to deploy shiny apps, however with Connect out there, I’m not sure why anyone would decide to go w/ Shiny Server Pro if they are just stepping into these waters for the first time now – which is to say, my money would be on connect.
Federico Marini (16:28:27): > That would be my guess as well. It offers the whole big pack of services which is probably an overkill once you don’t know all of them, but then might give you some neat extras once you get acquainted
Federico Marini (16:28:39): > (or even think of them as possible, say plumbr APIs)
Michael Lawrence (16:30:47): > One issue is that the Connect license is per-user, which was a problem for us until we made our big enterprise deal.
Michael Lawrence (16:31:07): > Server Pro is concurrent user, Connect is named user.
Federico Marini (16:32:26): > Connect has also the option of having anonymous users as well
Federico Marini (16:32:44): > if you have 100 named users, then hand in hand you’d get 100 anonymous
Michael Lawrence (16:33:23): > That might be a new development. We now have a special arrangement with RStudio where we basically have unlimited licenses.
Federico Marini (16:34:36): > We’Re not as big as Genentech
Federico Marini (16:34:40): > :stuck_out_tongue:
Michael Lawrence (16:35:12): > There are upsides and downsides to being big.
Federico Marini (16:35:16): > In my case it is more like we can start exploring the model of deployment
Federico Marini (16:35:24): > and see how well it gets received
Federico Marini (16:35:39): > > There are upsides and downsides to being big. > yup:slightly_smiling_face:
Michael Lawrence (16:36:09): > Aaron told me about your plan to publicly deploy iSEE. Ambitious.
Federico Marini (16:36:34): > That’d be it. At least worth a shot
Kevin Rue-Albrecht (16:36:41): > isee.humancellatlas.org :stuck_out_tongue:
Federico Marini (16:37:10): > It is not going to fight against others but rather provide the set of features to a broader audience
Kevin Rue-Albrecht (16:37:16): > a.k.a “isee.big”
Federico Marini (16:37:52): > I do likecellXgene, but for many of my purposes it is just not enough/not saving me so much time like our creature:smile:
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Matt Brauer (16:56:16) (in thread): > Do tell.
Federico Marini (17:00:58): > thanks to both@Michael Lawrenceand@Steve Lianogloufor sharing!
Steve Lianoglou (17:02:03): > sure thing – would be interested to learn how it goes for you with whatever decision you end up making.
Federico Marini (17:02:40): > happy to keep you in the loops
2019-07-20
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2019-07-22
Michael Love (06:52:43): > I have a feeling this new pkg of@Charlotte Sonesonwill be useful for Bioc users:relieved:https://twitter.com/csoneson/status/1153243772727287809?s=21 - Attachment (twitter): Attachment > Looking for an intuitive way of visualizing and interpreting your #rstats design matrices? Try our new R package ExploreModelMatrix: https://github.com/csoneson/ExploreModelMatrix (with @mikelove @FedeBioinfo
Michael Love (06:53:14): > Solving the big question, why are my design matrix columns linearly dependent??
Federico Marini (08:00:00): > Bioc-teachers will also have quite a benefit:grimacing:
Michael Love (08:08:43): > Yup!
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2019-07-23
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2019-07-24
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2019-07-25
Aaron Lun (00:42:50): > Did we have a guy from 10X genomics on this channel?
Shani Amarasinghe (01:14:34): > @Shani Amarasinghe has joined the channel
Michael Love (15:26:30) (in thread): > @Avi Srivastavahave any contacts that are on here, or could be persuaded to join?
Aaron Lun (15:28:36) (in thread): > I thought someone did join, but I can’t find their initial message on#general.
Michael Love (15:35:51) (in thread): > Avi interned there so maybe would know…
Aaron Lun (15:36:52) (in thread): > Sweet. I just wanted someone to talk to about the implementation differences for their version ofemptyDrops.
Avi Srivastava (15:45:15) (in thread): > Yep, I can check with some of the people from 10x btw@Aaron Lunmay I ask what’s the question ? Like are they using the old version of emptyDrops in the cellranger (on GitHub ) ?
Aaron Lun (15:48:36) (in thread): > The context is: a few people have asked me whether or not they need to runDropletUtils::emptyDrops()on the unfiltered count matrix produced by CellRanger v3. My advice has been that this is not necessary because CellRanger v3 has its own implementation, with the only difference being in the choice of theretainparameter. I just want to be sure that this advice is correct.
Avi Srivastava (15:52:38) (in thread): > Gotcha, yes now I remember you were talking about that in one of the github issues online. I’ll see if I can request someone to join or at least get the answer to this specific question.
Aaron Lun (15:52:57) (in thread): > I was a bit concerned because someone mentioned thatemptyDropswas calling a lot more cells than CellRanger v3. Usually it should be the other way around. It would be nice to be able to show that the implementations are more-or-less consistent when theretainparameter is set to the same value.
Aaron Lun (15:54:35) (in thread): > :+1:
Avi Srivastava (16:00:32) (in thread): > Any idea which dataset it was ? One reason could be that if they are talking about open 10x data then internally 10x might be using different version of emptyDrops when the output online was uploaded than the one on GitHub .
Aaron Lun (16:01:36) (in thread): > oh, no, it was just an in-house dataset generated by someone at U Cambridge.
Aaron Lun (16:02:16) (in thread): > I will have to ask my guy to do some more digging on his end.
Aaron Lun (16:02:53) (in thread): > But it would be nice to know if there were any surprises that aren’t listed in the “algorithms” overview for CellRanger.
Avi Srivastava (16:03:02) (in thread): > Yea because I think this can be easily checked from the 10x open data as they have uploaded their output online. Either way I’ll confirm with them too
Avi Srivastava (16:03:14) (in thread): > Yep I agree.
2019-07-26
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2019-07-29
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Shraddha Pai (15:37:06): > Hi BioC developers, had a package devel question. Sorry for cross-posting with the bioc-devel mailing list. I’m looking to contribute a software package with a large Java jar file dependency (11Mb). Package guidelines forbid files of >=5Mb. > 1. Should I create a separate annotation/experiment data package for this jar file and list that as a dependency for the software package? The jar file is actually code that’s used by my R package. > EDIT: I already have a companion BioC data package for example data, and could just add the Java jar in that package. > > 2. Or is it better to have the jar file hosted on e.g. a lab FTP site and add instructions in a prominently-titled vignette ? This would require all vignettes to download the file if it doesn’t exist in a pre-specified location. > > Option 2 seems like a hack. But I don’t know if the jar file is suitable content for BioC annotation/experimental data package type. > > Thanks! > Shraddha
Michael Lawrence (16:10:18): > I usually have the package download the file on first use and cache it, typically in the XDG spec data directory.
Shraddha Pai (16:14:58) (in thread): > Thanks, Michael. Is this different from installing the data package as a dependency? I’ve never used the “XDG spec data directory”, don’t know what that is. Also quick Google searches for “BioC XDG” don’t turn up anything relevant.
Aaron Lun (16:15:22) (in thread): > I’d probably useBiocFileCache .
Michael Lawrence (16:19:10) (in thread): > XDG is afreedesktop.org standard. R will have built in support for it in the next release. The CRAN rappdirs package implements it already. Presumably BiocFileCache would come to use the same scheme by default. R packages are a bit awkward when it comes to distributing library dependencies. It might make sense to use them for shared dependencies.
Martin Morgan (16:23:39) (in thread): > yes use BiocFileCache, which uses rappdirs
Shraddha Pai (17:14:54) (in thread): > Thanks all for the suggestions. I will read through the BiocFileCache documentation to see if I can understand where in the package setup/build/install process this jar file would be downloaded and cached. Will write back if there are more questions. > Thank you!
2019-07-30
Vince Carey (06:39:40): > https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1763-7 - Attachment (Genome Biology): Challenges in funding and developing genomic software: roots and remedies > The computer software used for genomic analysis has become a crucial component of the infrastructure for life sciences. However, genomic software is still typically developed in an ad hoc manner, with inadequate funding, and by academic researchers not trained in software development, at substantial costs to the research community. I examine the roots of the incongruity between the importance of and the degree of investment in genomic software, and I suggest several potential remedies for current problems. As genomics continues to grow, new strategies for funding and developing the software that powers the field will become increasingly essential.
Martin Morgan (08:00:33) (in thread): > wanted to mention that you need to make sure that you have the license to redistribute the jar file, and the license your package is under is consistent with that.
Shraddha Pai (10:17:22) (in thread): > Hi Martin, thanks for that. Yes we have the license to redistribute the jar file. Does the license of the jar file need to be indicated somewhere in my R pkg description?
Martin Morgan (10:46:58) (in thread): > ProbablyLicense: fileas described inhttps://cran.r-project.org/doc/manuals/r-release/R-exts.html#Licensing - Attachment (cran.r-project.org): Writing R Extensions > Writing R Extensions
Friederike Dündar (15:30:48): > If one wanted to specify in the DESCRIPTION file of a self-made package that the BioC dependencies should always be installed from the devel branch – how would that be done? I know how to specify a min. version, is there a way to co-opt that to set it to the devel branch?
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2019-07-31
Lluís Revilla (04:45:29) (in thread): > You need to use the Bioc-devel version check it withBiocManager::version(). If you useBiocManager::install(version = "devel")it should install the packages from the devel branch (if you use the associated R version)
Friederike Dündar (08:37:31) (in thread): > that would be the solution from the user-endpoint (which works fine); I was just wondering whether there was a way to enforce it from the developer’s perspective
Martin Morgan (09:09:42) (in thread): > A hack would be to Depend: orImport: BiocVersion (>= 3.10), but the version would need to be bumped for each version of Bioconductor. And one would need the ‘user’ (including developer) to install version 3.10, which leads back to Lluis’ answer…
Friederike Dündar (09:54:45) (in thread): > thanks!
Hervé Pagès (13:03:12) (in thread): > Or we could make an exception and allow the Java jar file to be part of the software package. My impression is that neither the developer nor the end user actually wins anything with the delayed installation approach or do they?
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Julian Flesch (19:00:24): > Hi developers, > > I am currently writing vignettes for a package and am stuck trying to fix a BiocCheck Note. It says that a line in the vignette is too long. The line contains only a markdown-formatted url and all attempts to shorten it have caused the link to break. > Is there a clever way to deal with >80 character urls in .Rmd code? > > Thank you! > Julian
Davide Risso (19:14:52): > I think that’s just a NOTE and you can safely ignore it?:man-shrugging:
Davide Risso (19:16:02): > Or you could try to get one of those short url liketinyurl.com ?
Aaron Lun (19:17:15): > A code line? Or a text line? Why would BiocCheck care about the latter?
Julian Flesch (19:18:07) (in thread): > Don‘t tiny URLs expire?
Davide Risso (19:19:40) (in thread): > It never expires according to them… unless they go out of business I guess:grimacing:
Julian Flesch (19:20:55) (in thread): > You are right. It also says so in this stackoverflow post:https://stackoverflow.com/questions/736792/is-there-an-expiry-on-bit-ly-or-tinyurl-urls/736794 - Attachment (Stack Overflow): Is there an expiry on bit.ly or tinyurl URLs? > Is there an expiry on bit.ly or tinyurl shortened URLs? I’m asking because I’m thinking of persisting these shortened urls into the db for a client’s twitter service. UPDATE: if you keep sending …
Julian Flesch (19:21:22) (in thread): > Thank you, Davide!:blush:
Julian Flesch (19:24:50) (in thread): > It is a text line like this: something > The url being more than 80 characters long.
Julian Flesch (19:26:25) (in thread): > I fixed it now with a tiny url. I didn‘t know they don’t expire.
2019-08-01
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Vince Carey (05:02:45) (in thread): > Another solution would be to assign the offending string constant to a variable (or serialize to something accessible via data()) in your package and retrieve and use the value in your vignette.
Martin Morgan (07:52:45) (in thread): > These are notes, please don’t take them overly seriously. The line length suggestion is for readability and version control, e.g., in github looking at a markdown document lines do not wrap, and in git when you edit a long line the default diff shows the entire line change. If you think those are poor reasons for avoiding long lines then don’t avoid long lines.
Shraddha Pai (09:08:17): > Hi all, while running BiocCheck I get a DESCRIPTION/NAMESPACE consistency error: > > WARNING: Import stats, utils in DESCRIPTION as well as NAMESPACE. > > I am importing individual functions from each of these libraries: > > $ grep "importFrom stats" **.** > buildPredictor.R:#' @importFrom stats median na.omit coef > $ grep "importFrom utils" **.** > buildPredictor.R:#' @importFrom utils read.delim write.table > nWay_netSum.R:#' @importFrom utils write.table > RR_featureTally.R:#' @importFrom utils write.table > > But if I add “stats” and “utils” in either the Imports or Depends field of DESCRIPTION, I get a warning about function imports overwriting identically-named functions in a Bioc package (GenomicRanges or similar). > > How can I indicate that I’m importing these packages inDESCRIPTIONwithout loading the entire package? Thanks!
Hervé Pagès (11:44:08): > Putting packages in Depends or Imports actually does not import anything. So having both importFromdirectives in the NAMESPACE file to selectively import the symbols you need should not produce any warning.
Shraddha Pai (11:47:37) (in thread): > Hi Hervé, OK let me try again. I have just been running R CMD check, then build, then BiocCheck , so one of these three (probably either check or build) generated the namespace clash error. But let me try.
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Jared Andrews (12:05:29) (in thread): > I was the hack who originally asked this in a different slack channel: I got around it by usingRemotes: bioc::3.10/packageName.
Shraddha Pai (12:24:43) (in thread): > Hello again, OK I added the packages under “imports”. Then got a set of error messages related to not calling importFrom in every R file that included functions from the stats/utils package. Updated that and now everything clears. > Not sure why I was getting that error message before. > > All resolved now, thanks Hervé.
2019-08-02
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2019-08-03
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2019-08-04
Aaron Lun (03:13:16): > BiocParallel ’s overhead seems to be getting worse and worse. > > Q <- list( > matrix(rnorm(3e6), 100000, 30), > matrix(rnorm(3e6), 100000, 30) > ) > system.time( > collected <- bpmapply(FUN = dim, x= Q, > BPPARAM = SerialParam(), SIMPLIFY = FALSE) > ) > ## user system elapsed > ## 0.001 0.000 0.002 > system.time( > collected <- bpmapply(FUN = dim, x= Q, > BPPARAM = MulticoreParam(), SIMPLIFY = FALSE) > ) > ## user system elapsed > ## 0.869 0.661 4.529 > > This is sending a 24 MB object to each worker, and it already induces a 4 second delay - and the delay increases with the size of the object. This is not good, as any job big enough to warrant parallelization is going to be throwing large objects to each worker. What makes this confusing to me is that MulticoreParam forks shouldn’t be explicitly copying pages, so why is there still a delay?
Aaron Lun (03:24:26): > I mean, even just saving the entire thing to file and reading it in again takes less time. I assume the extra time forBiocParallel is related to the cost of forking, but surely forking in memory should be cheaper than touching the file system. > > system.time({saveRDS(Q, "blah.rds"); readRDS("blah.rds")}) > ## user system elapsed > ## 2.015 0.028 2.146 >
Aaron Lun (03:30:26): > Bumping it up to a 200 MB object (not unusual in my neck of the woods) means that the MulticoreParam version takes 30 seconds to finish!
Davide Risso (03:49:31): > Are you on Mac or linux? I found that on Mac doParallel is much better than multicore
Davide Risso (03:50:27): > But yeah I also have the feeling things are getting worse judging by zinbwave ’s performance…
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Vince Carey (11:30:50): > @Aaron Lunmy understanding is that the fork copies the whole R process for the worker. If you want to be more selective as to what is transmitted to the worker you have to use a different approach. You could check this by shipping gc() to your workers – my reading is that each worker gets the whole workspace and thus all of Q.
Vince Carey (11:47:49): > If you are using forking to parallelize, you want to start with the lightest possible workspace, that you are willing to copy in toto to all workers. So a list of indices or filenames makes sense; then each worker should know how to use information shipped over (including its assigned task) to produce results for handing back.
Davide Risso (11:51:17): > This comment by@Martin Morganwas illuminating for me re: what is / is not passed to workers in bplapply(), pasting here in case it’s usefulhttps://github.com/YosefLab/scone/issues/57#issuecomment-260172915
Davide Risso (11:55:14): > But this may be snow specific, shouldn’t multicore use shared memory and not copy unless necessary?
Vince Carey (12:10:08): > From ?mcfork > > In a nutshell 'fork' spawns a copy (child) of the current process, > that can work in parallel to the master (parent) process. At the > point of forking both processes share exactly the same state > including the workspace, global options, loaded packages etc. > Forking is relatively cheap in modern operating systems and no > real copy of the used memory is created, instead both processes > share the same memory and only modified parts are copied. This > makes 'mcfork' an ideal tool for parallel processing since there > is no need to setup the parallel working environment, data and > code is shared automatically from the start. > > which tends to confirm your view. I have not looked at it critically but my working rule is that if I am forking a process, each child will consume as much RAM as the initiator … how to measure this, how to assess what is shared vs what is copied – I really don’t know and would love to learn.
Davide Risso (12:13:40): > Yes, I also would love to learn more about this, especially how to measure shared vs copied memory!
Vince Carey (12:33:48): > This is hardly definitive, but > > > system.time( > + collected <- bpmapply(FUN = dim, x= Q, > + BPPARAM = MulticoreParam(work .... [TRUNCATED] > user system elapsed > 0.103 0.115 1.099 > > > library(parallel) > 1/0 packages newly attached/loaded, see sessionInfo() for details. > > > options(mc.cores=2) > > > system.time( > + collected2 <- mclapply(Q, dim) > ) user system elapsed > 0.004 0.005 0.010 >
Vince Carey (12:35:50): > Comparing parallel to BiocParallel in various contexts seems worthwhile.
Aaron Lun (14:18:22): > @Davide RissoYes, DoparParam seems to do much better here.
Michael Lawrence (20:48:27): > See this issue:https://github.com/Bioconductor/BiocParallel/issues/85
Michael Lawrence (20:49:03): > There is a “LocalParam” branch mentioned there that might be worth trying:https://github.com/Bioconductor/BiocParallel/tree/LocalParam
Michael Lawrence (20:51:13): > But the basic problem is that the backend is not sharing memory, like DoparParam does.
2019-08-05
Davide Risso (06:30:30): > Would it be an option to change the default registered method to DoparParam?
Martin Morgan (09:44:20): > The *Param are meant to support workers that persist across calls, so for instance the cost of loading GenomicAlignments in the worker is paid only once > > fun = function(i) { library(GenomicAlignments); 1 } > bpstart() > bplapply(1:4, fun) # cost of loading GenomicAlignments > bplapply(5:8, fun) # reuse already loaded GenomicAlignments > bpstop() > > The idea that the workers are different from the manager is not radical. The design means that the ‘data’ has to be sent to the established worker, rather than relying on the forked process having access to the data – the started forked process does not know about 1:4 or 5:8, for instance. > > For this to be effective requires the discipline that the cost of distributing the work is small compared to the amount of work done, which would be the case if for instance one were distributing paths BAM files for calculation of coverage or GC content but not if one were distributing count matrices for colSums(). The idea that small data is communicated for large work is also not radical. > > I will update, this week,bplapply()etc., so that if one is using MulticoreParam and its life is within the loop, it behaves like a forked process. This will mean thatQis transferred quickly; the return value will still be serialized from the worker to the manager (this is also done with mclapply / foreach) so that there will still be a cost to returning large data.
Michael Lawrence (11:01:42): > Cool, thanks. It’s nice to have access to shared memory compute in addition to the distributed compute across persistent workers.
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Martin Morgan (16:05:06): > @Aaron Lun@Davide Risso@Vince Carey@Michael LawrenceWith > > BiocManager::install("Bioconductor/BiocParallel", ref="faster-multicore") > > things are much faster for large objects. > > > Q <- list( > + matrix(rnorm(3e8), 100000), > + matrix(rnorm(3e8), 100000) > + ) > > > system.time(res1 <- bplapply(Q, dim, BPPARAM = SerialParam())) > user system elapsed > 0.011 0.000 0.010 > > > system.time(res2 <- bplapply(Q, dim, BPPARAM = MulticoreParam())) > user system elapsed > 0.057 0.041 0.087 > > > identical(res1, res2) > [1] TRUE > > > system.time(res3 <- bplapply(Q, dim, BPPARAM = bpstart(MulticoreParam()))) > user system elapsed > 0.545 1.092 8.381 > > > identical(res1, res3) > [1] TRUE > > To me the speed (approximately constant with object size, about 1/10th of a second compared to 1/100th of a second for mclapply / bplapply with SerialParam())) is ‘good enough’? One still gets error recovery, progress bar, etc…
Aaron Lun (20:16:41): > Thanks@Martin Morgan, that seems to help a lot in my actual use case.
Aaron Lun (20:34:30): > Hm. Perhaps I spoke too soon.
Aaron Lun (20:35:38): > Watching thetopas my job ran, I saw that there were only two processes (out of 6) that were ever running at one time; they were only ever running at 50% each; and the two that were active would switch several times a second! Very bizarre.
Aaron Lun (20:39:30): > Oh wait, I suspect I know why that’s happening. It’s an algorithmic thing on my side.
Aaron Lun (21:01:12): > Hm. Well, I fixed one thing, but I’m still getting this weird effect where there is only one core out of 6 running at 100% (and the active core changes over the course of the function execution).
Martin Morgan (21:05:07) (in thread): > reproducible example?
2019-08-06
Aaron Lun (20:57:21) (in thread): > oops, knew I was forgetting something. Will do this tomorrow once I get back into work.
2019-08-07
Aaron Lun (01:40:58) (in thread): > Testing on my home computer indicates that this is not an issue on Unix.
Aaron Lun (01:44:38) (in thread): > Work computer is mac. Suspecting machine-specific behavior. Oh geez, it’s happening again.
Aaron Lun (12:51:25): > @Martin MorganGot it. Seems to be an issue withbpstart: > > > load("stuff.Rda") > > > > library(BiocParallel) > > BPPARAM <- MulticoreParam() > > system.time({ > + bp.out <- bpmapply(x = M, y = S, FUN = function(x, y, ...) { dim(x) * dim(y) }, MoreArgs=MoreArgs, > + BPPARAM = BPPARAM, SIMPLIFY = FALSE, USE.NAMES = FALSE) > + }) > user system elapsed > 0.036 0.036 0.028 > > > > > > bpstart(BPPARAM) > > > > system.time({ > + bp.out <- bpmapply(x = M, y = S, FUN = function(x, y, ...) { dim(x) * dim(y) }, MoreArgs=MoreArgs, > + BPPARAM = BPPARAM, SIMPLIFY = FALSE, USE.NAMES = FALSE) > + }) > user system elapsed > 2.748 1.699 15.630 > > stuff.Rdaprovided athttps://drive.google.com/open?id=1ZhG-xV7_MR9456DvlZhXll6aHIyaH0jc
Martin Morgan (13:54:13): > This is ‘by design’, where the explicit use ofbpstart()signals that you intend to re-use workers across calls to bplapply, so consequently data needs to be sent to the workers rather than obtained implicitly via the fork inside bplapply. But I’ll do some more work and make public another Param, currently TransientMulticoreParam (maybe it’ll become TransientParam() or a better name) that always assumes workers don’t persist.
Aaron Lun (14:30:17): > Right, and I’m fine with data being re-sent to workers. But I’m a bit bemused that this seems to be done one process at a time, so that only one process is every running at 100% (or at all) intop. Is sending the data a serial process? Seems to defeat the purpose if it is.
Martin Morgan (14:36:29): > There’s only one manager, so only one place for the data to be sent from. If communication time > (compute time / number of workers) then one gets serial execution taking as long as communication time.
Aaron Lun (14:49:33): > Hm. This is an awkward conundrum. So usingMulticoreParam()withoutbpstartdoes achieve the speed boost, but my function needsbpstartfor other situations where the worker set-up is expensive (e.g., batchtools, snow). Would yourTransientMulticoreParambe the solution here, wherebpstartdoes nothing and provides the advantage of usingMulticoreParam()withoutbpstart?
Michael Lawrence (16:25:15): > In theory it could use mclapply to send data to workers, but that would double the max number of workers.
2019-08-08
Aaron Lun (17:34:15): > Dunno if anyone has tested this, but if I were to write code using openMP, using all available threads; and I send a job onto a compute node on a cluster (say, SLURM or LSF); would it correctly throttle itself to only using the number of cores/threads that was requested from the scheduler?
Aaron Lun (17:35:00): > Or would it just go wild and see that there’s 32 threads on a compute node with 8 cores and just try to use all of them?
Nicholas Knoblauch (18:06:06): > on every cluster I’ve ever worked on you’re free to spawn more threads than you request. What ends up happening I think is that if you (or the person you’re sharing the node with at the time) spawns more than they request, you’ll get oversubscription
Nicholas Knoblauch (18:08:37): > some clusters might be clever and setOMP_NUM_THREADSfor you
Aaron Lun (18:08:57): > Right, I was thinking about what openMP believes to be the default number of threads in the context of a compute node. This post (https://stackoverflow.com/questions/24701397/how-are-openmp-threads-mapped-to-specific-cores-allocated-by-a-job-scheduler-ex ) seems to suggest that OpenMP’s choice of default would respect the requested resources, and I wonder if anyone has any experience with that. - Attachment (Stack Overflow): How are OpenMP threads mapped to specific cores allocated by a job scheduler (ex: LSF)? > When a program is run with a job scheduler, the scheduler allocates n processor cores (specified by the user) for the job. When a program using OpenMP runs, OpenMP will in general use OMP_NUM_THREADS
Aaron Lun (18:11:07): > Of course, you can always just force OpenMP to use way more threads than are available; I’m just wondering whether the default behavior is sensible.
Aaron Lun (19:16:14): > One cool thing would be if we could specifyOMP_NUM_THREADSviaBiocParallel , so that users wantingany BiocParallel objects to achieve it, rather than having a separate argument that needs to be passed down to all functions. Something like entry intobplapplysetsOMP_NUM_THREADSduring its lifetime such that any code running inside thebplapplywould pick up that setting and use the appropriate number of OpenMP cores.
2019-08-09
Michael Lawrence (03:53:38): > I wouldn’t be surprised if the batchtools backend supported something like that. I think it would just mean abstracting the request for the available number of cores.
Kasper D. Hansen (09:33:40): > Same issue but with multicore BLAS
Kasper D. Hansen (09:35:11): > I have not tested, but I would be surprised if it works as intended out of the box. Aaron’s suggestion is good, but perhaps batchtools and others deal with this already
Kasper D. Hansen (09:35:27): > From a sysadmin perspective this is something that would worry me
Martin Morgan (15:06:19): > Fromhttps://mllg.github.io/batchtools/reference/submitJobs batchtools can limit the number of cpus or omp threads, and this is available viaBatchtoolsParam(resource = list( ncpus = 4)). - Attachment (mllg.github.io): Submit Jobs to the Batch Systems — submitJobs > Submits defined jobs to the batch system. After submitting the jobs, you can use waitForJobs to wait for the termination of jobs or call reduceResultsList/reduceResults to collect partial results. The progress can be monitored with getStatus.
Casey Greene (16:05:02): > https://twitter.com/GreeneScientist/status/1159917176247246848?s=19 - Attachment (twitter): Attachment > The @CancerDataLab @wvauclain https://www.ccdatalab.org/blog/2019/8/9/pinning-transitive-r-dependencies-for-fun-and-reproducible-builds https://pbs.twimg.com/media/EBjahbBWsAQp0Fl.png
Casey Greene (16:05:28): > This is a thing we are doing. Looking forward to Cunningham’s law on this one :-)
Aaron Lun (19:50:45) (in thread): > Right - and if we could have something similar for execution on one machine… something likeOpenMPParam(nthreads=5)that does nothing but setOMP_NUM_THREADS. Don’t know whether this would fit into theBiocParallel framework, but it would instantly extend control to all OpenMP’d code… pretty cool if that could be done.
Aaron Lun (19:51:28) (in thread): > In brief, it would provide another channel for lightweight parallelization that doesn’t rely on the relatively coarse backends that are currently provided.
2019-08-10
Kasper D. Hansen (14:20:31): > After reflecting on this, isn’t this a bug in devtools. You’re using devtools to pin a specific version (while useful, this is not something that is easy to do using standard R tools). But then devtools doesn’t sort out the dependencies correctly, giving the pinning.
Casey Greene (14:32:37): > I don’t think we said it was a bug
Casey Greene (14:33:27): > It was a workaround we use to be able to run a large number of samples through the same container(s), even if those are built at different times
2019-08-11
Vince Carey (08:07:30): > This addresses an interesting predicament, and I can’t at the moment formulate a clear statement of the big picture. Keeping large durable workflows from failing in obscure ways is surely valuable. But having a workflow fail because a component is eventually found to be bugged and updated in its source repository is also valuable in some sense, and this approach of pinning may overinsulate against this sort of situation. It may be worthwhile to note that BiocPkgTools gives access to the current dependency graph for all Bioconductor packages as an igraph. Additionally this set of concepts has been worked on by Gabe Becker, whose take would likely be of interest. I don’t see Gabe’s handle in this slack…
Kasper D. Hansen (08:17:54): > I sayI think it is a bug in devtools
Kasper D. Hansen (08:19:43): > One way of doing the “keep pipeline locked down” is to use custom repositories. Gabe has been working on this I think, but there is alsodratfrom Dirk Edelbuettel
Vince Carey (08:33:32): > What part of devtools is bugged? The problem seems to stem from attempting to use a mosaic of package-defined environments in a collection of containers. Inconsistencies can arise depending on what versions are available in the repositories in use, depending on how you approach dependency resolution/repository usage. These seem to me to be pretty big topics related to policies of component selection/evolution. I would agree that controlling the repository content is a key element. drat (https://github.com/eddelbuettel/drat ) looks very germane indeed.
Peter Hickey (19:28:43): > i’ve been keeping half an eye onhttps://rstudio.github.io/renv/ - Attachment (rstudio.github.io): Project Environments for R > A dependency management toolkit for R. Using ‘renv’, you can create and manage project-local R libraries, save the state of these libraries to a lockfile, and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.
Kasper D. Hansen (22:45:00): > The reason why I said devtools is bugged - and upon further reflection I am not sure I think this anymore - is that the user says “install 0.3.1 of rlang” and this does not work. The reason it does not work is that rlang depends on vctrs and the newest version of vctrs does not work with version 0.3.1 of rlang. So basically the installation routine in devtools is not able to resolve the “real” dependency chain.
Kasper D. Hansen (22:46:30): > The reason why I am not sure devtools is bugged, is that it is impossible by looking at the DESCRIPTION files to figure this out. Basically rlang gets updated to 0.3.1 (and it works with the then-current version of vctrs). When vctrs gets updated (and rland 0.3.1) no longer works, it is impossible to note this in DESCRIPTION because the vctrs update happens after rlang.
Kasper D. Hansen (22:46:58): > Not sure how this can be handled automatically, at install time
Kasper D. Hansen (22:47:44): > The right thing for people who want reproducibility is to record all packages and their versions and install those, perhaps by using a custom repos or by some other means, which I am not sure I am up to date on
Kasper D. Hansen (22:48:35): > But basically, this shows, that when you install “old” versions of packages using devtools, it will not necessarily work.
2019-08-12
Federico Marini (03:53:48) (in thread): > If I am not mistaken, this is the evolved version ofpackrat
Casey Greene (11:28:49): > This is the cranlock approach:https://community-bioc.slack.com/archives/C35G93GJH/p1565578064153300 - Attachment: Attachment > The right thing for people who want reproducibility is to record all packages and their versions and install those, perhaps by using a custom repos or by some other means, which I am not sure I am up to date on
Kasper D. Hansen (11:33:21): > Kind of. You’re not actually storing the packages but depending on devtools to resolve them. A user also needs to execute this specific set of dependencies. With a repos, everyone could just use “install everything from the repos and we guarantee to make it all match”. That might be easier for a bigger organization who can then populate the repos with their “official” packages. Of course, as the repos changes over time, you just get the ability to install the latest set of packages
Kasper D. Hansen (11:34:21): > But clearly cranlock is one seemingly decent approach to this.
Michael Lawrence (11:44:58): > The switchr package supports many such approaches.
Kasper D. Hansen (11:47:57): > Ah that’s Gabe’s stuff. Yes, I am complete not up to date on this.
2019-08-13
Malte Thodberg (04:19:42): > Quick question: Is there a date for the next version of Bioconductor and/or last day for updates to the current devel branch?
Kevin Rue-Albrecht (05:10:02): > I suppose you’ve found the general information: > -https://bioconductor.org > Developers > Release Schedule (https://bioconductor.org/developers/release-schedule/ ) > - Though obviously, the link above still describes the latest past release. > - Releases happens every 6 months (April, October) > The core team generally sends a series of announcements (mailing list, Slack) and update the page above 5-6 weeks before the release.
2019-08-15
Eric Fournier (09:38:47): > @Eric Fournier has joined the channel
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brejnev muhire (12:48:51): > @brejnev muhire has joined the channel
Nitesh Turaga (12:59:28): > @Stephanie Hicks
Nitesh Turaga (12:59:46): - File (PNG): software_starting_letter_bias.png
Nitesh Turaga (13:00:15): > Choose packages with a different starting “letter” maybe? Haha. We have underrepresented letters.
Stephanie Hicks (13:01:40): > haha! Not sure how to make this one start with a j, q, u:z, but I’ll keep this in mind for future packages:joy:
Federico Marini (14:49:09): > Surprised to see j so underrepresented
Martin Morgan (17:08:10): > here’s a kind of null, I guess > > > rank(table(tolower(substr(readLines("/usr/share/dict/words"), 1, 1)))) > a b c d e f g h i j k l m n o p q r s t u v w x y z > 23 19 24 18 14 11 12 16 15 5 6 9 20 10 13 25 4 17 26 21 22 7 8 1 2 3 >
Kevin Rue-Albrecht (17:09:19): > Could the larger sample size of CRAN set a baseline?
Boris Hejblum (18:44:08): > @Boris Hejblum has joined the channel
Casey Greene (18:44:18) (in thread): > Quantro2, 3…
Casey Greene (18:45:02) (in thread): > It’s not different versions. It’s entirely different packages that do different things.:thinking_face::stuck_out_tongue_winking_eye:
Kevin Wang (19:10:03): > I hope this helps. BioC-Software packages are quite similar to CRAN in terms of distribution. Bioc-Anno likes “h”, “m” a bit more probably because of “human” and “mouse”? > (Rmd report is here:https://kevinwang09.github.io/tidytuesday/BiocPkgTools/start_letter.html ) - File (PNG): first_letter.png
Aaron Lun (19:10:58): > As we know, every single-cell software package is expected to start with “sc”.
Stephanie Hicks (19:13:58) (in thread): > Haha! Do you have a method in mind? I always was interested in extending quantro to continuous covariates
Stephanie Hicks (19:14:16) (in thread): > Or if the biological covariate was unknown
Casey Greene (19:14:24) (in thread): > Haha - no idea but just thought it’d get you a lot of q names:joy:
Aaron Lun (19:15:38): > Packages likeDropletUtils andbatchelor are heretics and should burn.
Kevin Wang (19:16:25): > What aboutSingleCellExperiment?:rolling_on_the_floor_laughing:
Aaron Lun (19:16:41): > Don’t get me started on that one.
Aaron Lun (19:16:56): > I mean, having to press Shift, and then s. I mean, geez.
Aaron Lun (19:17:07): > Can’t even autocomplete anymore now that SingleR is in the same directory.
Kevin Wang (19:18:42): > No autocomplete?! What ascary time we live in.:scream:
Martin Morgan (19:44:20): > There’s a thread on R-devel about allowing (or not)_in package names, e.g.,https://stat.ethz.ch/pipermail/r-devel/2019-August/078296.html ; it’s kind of interesting to compare package naming styles, for instance many more Bioc software packages adopt CamelCase package names. For SingleCellExperiment / SummarizedExperiment / GenomicRanges, it makes a lot of sense to name packages after the class (hierarchies) they provide, and to me it makes sense to name data classes (at least) in CamelCase, on the view that data representations play the role of ‘noun’ and methods play the role of ‘verb’, and proper nouns are capitalized. I was going to also say that I didn’t think typing skill limits output of software developers, but actually thinking of the many painful demos / debugging sessions I’ve watched / delivered I’m not so sure about that…
Dario Strbenac (19:55:11): > I think a lot more Bioconductor developers are familiar with object-oriented programming languages such as Java and C++ than CRAN developers which are typically simpler packages, so they would use camel case names.
Friederike Dündar (21:25:15) (in thread): > maybe we should think of names first and then try to find functions that may fit the names…:wink:so many great possibilities with poor, underrepresented Q: QualityAnalysis, QuiveR, QuackeR, quadrature, quantify, quickR, quaffeR, quiRky, quixote, …
2019-08-19
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2019-08-20
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2019-08-23
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2019-08-24
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2019-08-25
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2019-08-26
Christian P. Larsen (17:39:48): > I would like to get help in optimize aws platform for bioc processing of flowcytometry data. > > Our data consists of longitudinal tracking of PBMCs from clinical cohorts. 400 files of 18 color t cell panels with MHC tetramers (rare cell pops) ~200Mb/file. > We have preprocessing pipeline using openCyto, followed by flowSOM to export small (30-70Mb) clean CD4, CD8 fcs files for downstream analysis. In a separate ec2 we perform secondary ML approaches eg flowSOM and cytofWorkflow > . > > During the dev phase we just created very resource intensive and expensive ec2s (egr5 12x large) with large boot drives. This helped us build our pipelines and do a first wave of analysis but > now we need to get our resource allocation more reasonable and optimize our ec2. I would like to know what instance parameters make a performance difference this the workflows I have described? cpu, ram, storage type? I have listed some ranges and options below. I would appreciate the wisdom of the community. > > 1) instance type - general purpose (t), compute optimized (c) or memory optimized (r) > vCPUs? 8-98 > 2) RAM 32-384 > 3) instance storage - EBS or SSD? use d type? what boot vs other storage. > (we now pull data from s3 and send back processed files so we only need the large drive for the preprocessing ec2)
2019-08-27
Christian P. Larsen (08:44:48): > thanks. I’ll try biostars
Martin Morgan (08:54:50): > Actually,@Christian P. Larsenmaybe@Greg Finakor@Mike Jiangmight be able to provide insight into the flow package workflow requirements. From R’s perspective, usually it does not exploit low-level parallelism that would benefit from many cores, and is not particularly memory efficient. So probably the best machine has modest CPUs (e.g., 8 ) (not:sunglasses:as the emoji would have it) with ample (at least 4, maybe 8 or even 16 GB ram per core). Since R is in-memory, I would have guessed that the cost of slow disk would be paid once, so no particular value in SSD.
Martin Morgan (08:56:42): > It would be interesting to have a report back on where you end up with this…
Federico Marini (09:54:30): > Hi everyone, is some of you into the GitHub Actions CI?
Federico Marini (09:55:17): > If I recall correctly, it is in limited beta (?) so maybe some power users of you might have got access already
Jared Andrews (10:08:00): > Pretty sure anyone can sign up for it, though I’ve yet to try it.
Federico Marini (10:09:26): > I just noticed I can see the corresponding tab from today, so I was just curious to see if others had earl(ier) access
Christian P. Larsen (10:30:41): > @Kevin Blighe@Martin Morganthanks. I will try 16 cpu + large RAM approach and see is greg and mike have thoughts
Aedin Culhane (13:36:24): > https://www.statnews.com/2019-stat-wunderkinds/ - Attachment (STAT): STAT Wunderkinds: Celebrating young scientists in biomedicine/biopharma > We’re collecting nominations from across North America for early career scientists who are doing groundbreaking work. The deadline to enter is September 3.
2019-08-28
Aditya Bhagwat (10:05:14): > @Aditya Bhagwat has joined the channel
2019-08-29
Aditya Bhagwat (04:14:06): > Good morning:slightly_smiling_face:. New to this group (thanks Martin, for bringing me here). Trying to figure out what to post where: BioC support site, Bioc-devel mailing list, this BioC slack, and then off course the BioC git repos themselves.
Aditya Bhagwat (04:23:29): > For instance this question:slightly_smiling_face:. I use assertive to check range validity [1, chrlength] after a GRanges operation, since I couldn’t find an intrinsic range validity checker. Am I right or am I I overlooking (and so, double-coding) existing functionality?
Kevin Rue-Albrecht (04:32:51): > This question sounds similar to those posted on the BioC support site (https://support.bioconductor.org ). A chance to collect some more “reputation points” for those taking the time to answer
Kevin Rue-Albrecht (04:34:36): > Also, I suggest including a minimal working example (MWE) to illustrate what you’ve described. To be honest, I’ve read your message 3 times and still can’t precisely picture what code you’re running to do what you describe. Most of the time a MWE will help you get a faster and more accurate reply.
Aditya Bhagwat (07:07:18): > Thanks Kevin. The question itself (for which I now added a BioC support Q & A) was more of an example on figuring out what goes where…
Aditya Bhagwat (07:07:37): > ( BioC Q&Ahttps://support.bioconductor.org/p/124250 )
Mike Smith (07:09:51): > If anyone is interested in knowing how many downloads their packages get via bioconda, I’ve compiled the data provided by Anaconda in to tables like on the BioC site. They’re available athttps://github.com/grimbough/anaconda-download-stats We certainly get a non-negligible number of users choosing to install via conda - File (PNG): image.png
Mike Smith (07:53:06): > Similarly, I don’t think the downloads from any of the Bioconductor mirrors are included either (but I might be wrong).
Martin Morgan (08:00:29): > just the downloads frombioconductor.org (mirrors play a much less important role in Bioconductor than in R; we use Amazon cloud front to get pretty good global distribution).
2019-08-30
K Teijgeler (04:06:12): > @K Teijgeler has joined the channel
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Aaron Lun (20:04:49): > Gee,traceback’s tendecy to deparse the entire S4 object at times is pretty annoying
Aaron Lun (20:05:22): > especially when I see I have an error and I’m just waiting for R to finish creating the error message.
Martin Morgan (21:02:58) (in thread): > Is that thishttps://bugs.r-project.org/bugzilla/show_bug.cgi?id=17580 and is there something productive you can contribute to that discussion?
Aaron Lun (22:13:50) (in thread): > Yes, that does seem to be the issue, and there’s not much more that I can add - it gets pretty hardcore in there.
2019-09-09
Al J Abadi (02:50:19) (in thread): > Have had the same problem many times! Sooptions(deparse.max.lines= a_small_integer)should do the trick?
2019-09-11
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2019-09-16
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2019-09-17
Aaron Lun (02:36:31): > @Martin Morganit would be very nice if BiocNeighbors and BiocSingular could piggyback offBiocParallel::registerto set global defaults. Maybe if it got turned into a generic? Or even better, expose some of the registry internals so I can use the same machinery in those two packages?
Martin Morgan (04:34:19): > I don’t know enough about BiocN / BiocS to know how you’d useregister(), can you provide an illustrative use case, perhaps as an issue onhttps://github.com/Bioconductor/BiocParallel ?
2019-09-18
Lauren Hsu (11:11:27): > @Lauren Hsu has joined the channel
David JM (13:44:30): > @David JM has joined the channel
Aedin Culhane (14:05:57): > Dear Bioconductor Community, > > The organizing committee for BioC2020, to be held in Boston on July 29-31, needs organizers to help in planning the event. > > Participation involves attending approximately monthly remote meetings plus taking on responsibilities in one or more of the areas of: > > * Outreach (developing materials, promotion) > * Website > * Workshop technical organization > * Program development > * Sponsorship and funding > * Code of Conduct training and enforcement > * Local organization in Boston > > Please register your interest to participate on the Bioc2020 organizing committee athttps://forms.gle/Zs1gn2T9RtQ7Xysv5 Thanks > Aedin Culhane, Levi Waldron - Attachment (Google Docs): Bio2020 Committee Application > The organizing committee for BioC2020, to be held in Boston on July 29-31, needs organizers to help in planning the event. Participation involves attending approximately monthly remote meetings plus taking on responsibilities in one or more of the areas listed below.
Aaron Lun (14:43:44) (in thread): > Done.
Qian Liu (15:01:49): > @Aedin CulhaneJust applied!:smile:
Federico Marini (15:42:00): > @Aedin Culhane*there’s a C missing in the doc title:wink:
Aedin Culhane (15:56:26): > Thanks I’ll fix
Aedin Culhane (15:58:22): > Thanks for spotting this. I fixed the typo.
Aedin Culhane (15:58:39): > Do you know if it should be BioC2020 or bioc2020?
Aedin Culhane (15:59:16): > We also have a slack channel#bioc2020
Kevin Rue-Albrecht (15:59:21): - File (PNG): image.png
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2019-09-19
Princy Parsana (08:47:16): > @Princy Parsana has joined the channel
Aaron Lun (22:40:39) (in thread): > Was there any progress on the TransientParam?
Aaron Lun (22:52:08): > Tagging@Martin Morgan. Guess he’s asleep.
2019-09-20
Martin Morgan (01:26:29) (in thread): > apparently not.
Dario Strbenac (01:45:34): > rtracklayer’sreadGFFdoesn’t seem to fully import some gene IDs recently appearing in GENCODE Genes. For example, ENSG00000002586.20_PAR_Y is imported as ENSG00000002586.20 which introduces NA during ID matching. It seems that even some people who work at EMBL are surprised by ithttps://www.biostars.org/p/398174/ so I’m not sure if these IDs will disappear in a future version or if rtracklayer should handle them.
Michael Lawrence (08:04:55): > Please file an issue.
Helen (18:15:19): > @Helen has joined the channel
2019-09-22
Martin Morgan (16:31:06) (in thread): > @Aaron Lun…actually > > commit 85516c916cc2b0a7bc53527c096068128a3ce205 (faster-multicore) > Author: Martin Morgan <martin.morgan@roswellpark.org> > Date: Mon Aug 5 14:58:06 2019 -0400 > > mcparallel() / mccollect() impl of faster MulticoreParam >
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2019-09-23
Dan Bunis (15:57:31): > Hey, sorry to spam everyone but I don’t know of a specific channel that might be better for this technical issue: > > I’m running into an error with testthat where setup code (either within the test-file or in mysetup.R) seems to either not be run, or to be completely ignored by all test_that(…) calls, when I run R CMD Check. Has anyone else ever run into this issue before? And if so, what was your fix?
2019-09-24
Vince Carey (06:02:26): > do you have a call to “test_check([pkgname])” in tests/testthat.R? is there a repo to be examined? i am not familiar with setup.R, is there a documented convention on this?
Kevin Rue-Albrecht (06:05:34): > @Dan BunisHave you tried “setup-something.R” or “setup_something.R”? > - This works:https://github.com/csoneson/iSEE/tree/master/tests/testthat - Here are release notes (dated 2017 though):https://www.tidyverse.org/articles/2017/12/testthat-2-0-0/ which suggest “tests/testthat/setup-xyz.R”
Kevin Rue-Albrecht (06:10:39): > Actually, it looks like “setup.r” and “setup.R” should be picked up too:https://github.com/r-lib/testthat/blob/9d6ae665cfa4d70b8a152bf131d9cc89f04d6ef6/R/source.R#L64 So I guess Vince’s suggestion about checking your broader testing setup is the way to go.
Dan Bunis (13:48:20) (in thread): > I do have the test_check(“dittoSeq”) call. > > repo here:https://github.com/dtm2451/DittoSeq/tree/Development-v0.3.0-withtests
Dan Bunis (13:53:56) (in thread): > @Kevin Rue-Albrecht, addressing both of you here to keep the discussion together… > > I don’t think the issue is even with thesetup.Rcode not running… I currently have all the code in that copied into the top of all mytest-*.Rfiles, and that still doesn’t get noticed by the tests.
Kevin Rue-Albrecht (13:59:51) (in thread): > Isn’t it a just capitalization issue? > Your package repository is called DittoSeqhttps://github.com/dtm2451/DittoSeq/blob/118e2af3e3a4da20847dae1f9e88b92884b55981/tests/testthat.R#L2
Dan Bunis (14:00:53) (in thread): > Yea… recently decided to change the name of the package for camelCase. BUT: I’ve tried changing the directory name on my local machine and it didn’t help either.
Kevin Rue-Albrecht (14:01:12) (in thread): > Eventually test_check calls test_dir. So it probably doesn’t find the folder at all
Dan Bunis (14:02:32) (in thread): > Here is part of the testing output of R CMD Check: > > ── Test failures ───────────────────────────────────────────────── testthat ──── > > > library(testthat) > > test_check("dittoSeq") > Loading required package: dittoSeq > Loading required package: ggplot2 > ── 1. Error: dittoDimPlot can plot continuous or discrete data & raw or normalized ex > object 'pbmc' not found > 1: expect_s3_class(dittoDimPlot(disc, pbmc), "ggplot") at testthat/test-DimPlot.R:17 > 2: quasi_label(enquo(object), arg = "object") > 3: eval_bare(get_expr(quo), get_env(quo)) > ... >
Dan Bunis (14:07:25) (in thread): > (Same exact error with the directory name changed to dittoSeq. Just double checked.)
Kevin Rue-Albrecht (14:09:09) (in thread): > I would probably library(Seurat) in your setup.R
Kevin Rue-Albrecht (14:10:06) (in thread): > https://github.com/dtm2451/DittoSeq/blob/118e2af3e3a4da20847dae1f9e88b92884b55981/tests/testthat/setup.R#L2
Kevin Rue-Albrecht (14:11:30) (in thread): > Double colon might not be enough to make the data available.
Dan Bunis (14:15:09) (in thread): > Still gives the same result =/
Kevin Rue-Albrecht (14:20:04) (in thread): > Well I don’t use Seurat data in my tests. That said I do have a feeling that the double colon is not making the data available for the tests. Especially given that you said those lines are not more helpful in the individual test scripts. > Try data from scRNAseq instead?
Dan Bunis (14:20:42) (in thread): > :+1:
Dan Bunis (14:21:12) (in thread): > Need work on some other things now, but I’ll try that this evening and let you know how it goes.
Dan Bunis (14:21:30) (in thread): > Thanks for your help!
Dan Bunis (19:39:33) (in thread): > :man-facepalming:Turns out the issue was actually a non-standard method that my functions were consistently using. > > Out of legacy, my functions stored their target’s name as a String and looked to the workspace for the properly named object when grabbing data. Now that I have corrected them to use the object itself, the tests run fine works. > > My test-suite now runs and passes:smiley:
2019-09-25
Thomas Schwarzl (02:17:53): > Hello everyone. > brief question: Inhttps://bioconductor.org/spb_reports/DEWSeq_buildreport_20190924130728.html#malbec1_check_anchor we get an error because the maintainer is not in the bioc dev mailing list, but actually we are (biohentze@embl.de )
Thomas Schwarzl (02:18:35): > any hints how to solve that?
Mike Smith (03:21:34): > This isn’t an error that I have seen crop up a lot, suggesting this check generally works fine. Perhaps try sending a message to the devel mailing list from that email address? This will both alert the appropriate members of the core team (though they’ll probably see this too) and it’ll double check your membership as you’ll get a ‘you must be registered’ email bounce if you for some reason you’re not on that list.
Koen Van den Berge (03:51:32): > We recently bumped into this error too, which was due to an accent on the name of the maintainer. This was fixed upon removing the accent, i.e. changing ‘é’ to ‘e’. Maybe that helps?
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Thomas Schwarzl (05:16:47): > Thanks, we have bumped the version and triggered a rebuild, now it works without changing anything. We have recently subscribed to the email list, maybe there was a lag in updating or something. Thanks for the comments
Steve Hargreaves (05:43:01): > @Steve Hargreaves has joined the channel
2019-09-27
Laurent Gatto (07:13:50): > Flashlight and poster abstract submission are now open for the European Bioconductor meeting 9 - 10 December 2019 in Brussels - more details athttp://eurobioc2019.bioconductor.org/ - Attachment (eurobioc2019.bioconductor.org): EuroBioc2019 > European Bioconductor Conference 9-10 December 2019, Brussels, Belgium
2019-10-01
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2019-10-02
Shijie C. Zheng (14:52:00): > @Shijie C. Zheng has joined the channel
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Peter Hickey (20:54:31): > i’m seeing ‘you’ve hit the 10,000 msg limit’ in some of the channels which means we can’t see the chat history past August 8th. i remember a discussion a while back about this and i think it was decided to keep slack as a place for ephemeral chats, but it’s hit one of the conference organising channels which seems a problem
Peter Hickey (20:54:43): > is this worth re-thinking?
2019-10-03
Martin Morgan (06:27:17): > Yes we’ll update this in the near future…; there was discussion here (I think…) earlier; sorry for letting this slide
Peter Hickey (07:48:48): > Thanks Martin!
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Jared Andrews (15:27:01): > Has the bioconductor SSL cert expired?
Martin Morgan (15:27:36): > Yep; we’re working on addressing that…
Lori Shepherd (19:56:41): > The SSL cert should now be updated - please be advised sometimes clearing a web browsers cache is necessary to pick up the change
2019-10-06
Matt Ritchie (21:03:31): > On behalf of Bioconductor’s Technical Advisory Board, the first community survey has been launched to collect feedback on the project and help guide future activities. > > Please take a few minutes to complete the survey, which is available fromhttps://forms.gle/wweDz79cPxQpxuKB7 . > > Thanks in advance for your feedback! - Attachment (Google Docs): Bioconductor 2019 Community Survey > Welcome to the Bioconductor community survey! This anonymous survey aims to collect data from the Bioconductor user community (from users through to developers) to help guide future activities. Data collected in this survey will be made available to the community for re-analysis. The survey will take 5 to 10 minutes to complete. All questions are optional. Thank you for participating!
2019-10-07
Hervé Pagès (13:50:21): > Thx Matt. Maybe it should be “Bioconductor git repository” instead of “Bioconductor GitHub repository” in the survey?
Nicholas Knoblauch (13:59:04) (in thread): > The “tidyverse vs base R” question implies that it’s possible to use the tidyverse more frequently than base R, what would that look like?
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2019-10-10
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2019-10-11
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Sridhar N (17:18:28): > I have multiple seqeunces in fasta format (len=50nt) and for each of them i have predicted a polypyrimidine track (contiguous U and C) is there a R pacakge that i could use to highlight them?
Sridhar N (17:18:54): > for example in this sequenceTTTTTTTTGGCTCTTTTCCTCCTAAGAGCthis is the trackCTCTTTTCCTC
Shraddha Pai (17:39:35) (in thread): > How long is each sequence in your set? (the FASTA line is 50nt but each sequence can be arbitrarily long) > Is your goal to tell at a glance if each line has a pyrimidine tract? > > I don’t know of any packages that do exactly that but one solution could be: > 1) to use a BioConductor package like BioStrings to first convert the sequence of letters into one of integers (purines = 0, pyrimidines = 1) > 2) store in a binary matrix (of 50 columns) > 3) colour-code and viz the matrix (plotrix package) so you can see runs of 1’s.
Sridhar N (17:40:51) (in thread): > each of my fasta in 50nt
Sridhar N (17:41:04) (in thread): > and the the track could be wither 9 or 5 bases
Shraddha Pai (17:42:48) (in thread): > See if someone else offers a more canned solution, but I would convert to a binary matrix (rows are sequences, columns are pos 1-50) and viz the resulting matrix as mentioned above.
Sridhar N (17:44:20) (in thread): > i saw this somewhere online and came across this idea
Sridhar N (17:44:51) (in thread): - File (PNG): Screen Shot 2019-10-11 at 4.43.47 PM.png
Sridhar N (17:45:15) (in thread): > each row with be my seq and i could use either color or red box to highlight
Sridhar N (17:53:43) (in thread): > thanks for the thought
2019-10-12
SOHEILA ZAREI (00:46:37): > @SOHEILA ZAREI has joined the channel
Vince Carey (09:58:27) (in thread): > see page 10 ofhttps://bioconductor.org/packages/release/bioc/vignettes/CrispRVariants/inst/doc/user_guide.pdf … I don’t know how they did it but it seems germane and indicates that relevant infrastructure may not be too far off.
Vince Carey (09:58:48) (in thread): > @Sridhar N^
Sridhar N (10:30:58) (in thread): > thanks@Vince Careywill look at the source code
Martin Morgan (13:31:54): > <!channel>We will upgrade our slack subscription on Tuesday, October 15 to a plan that preserves (and reveals!) all previous posts.
Aaron Lun (13:32:03): > :+1:
Federico Marini (14:57:33): > May I ask what they will charge us? (a.k.a., did we get the nice non-profit discount mentioned by@James Taylor- if I recall correctly)
Federico Marini (14:57:55): > > if I recall correctly > Funny enough, soon we can double check who said that:slightly_smiling_face:
James Taylor (17:27:36): > Sounds like something that guy would say.
Federico Marini (17:36:27): > :dealwithit-parrot:
Martin Morgan (19:38:34) (in thread): > yes, we (‘Bioconductor Foundation of NA’) qualifies as a non-profit. This means that slack costs about $1 (instead of $8) per ‘active’ user per month. Slack says there are 96 active members (something about login frequency). There are different costs depending on whether bills are paid annually or monthly, so our bill is about $115 / month or $1150 / year.
2019-10-13
Federico Marini (04:44:11) (in thread): > Thanks Martin. Glad we did qualify for that, and glad we opted in:slightly_smiling_face:
wangmcas (20:31:44): > @wangmcas has joined the channel
Sridhar N (20:56:53) (in thread): > @Vince Carey@Shraddha Paiend product
Sridhar N (20:57:07) (in thread): - File (PNG): Screen Shot 2019-10-13 at 7.56.05 PM.png
Sridhar N (20:57:34) (in thread): > thanks both
2019-10-14
Ricardo de Matos Simoes (15:42:40): > @Ricardo de Matos Simoes has joined the channel
frederick boehm (15:50:44): > @frederick boehm has joined the channel
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2019-10-17
Stephanie Hicks (08:49:48): > @Martin Morgan— quick question. You mentioned older slack messages would be revealed on Oct 15. I’m still unable to see older messages. I’ve restarted Slack to see if it needed to be refreshed. Do you happen to know if that date is when we would expect to see older message? Thank you!
Federico Marini (10:39:12): > I think now it should work
Federico Marini (10:39:17): > > Slackbot [4:38 PM] > Your workspace was upgraded to Slack’s Standard Plan!
Martin Morgan (10:52:27): > Sorry for the delay@Stephanie Hicksas@Federico Marinimentions this should now be available, with a restart of the slack app…
Ludwig Geistlinger (15:29:44): > Hi@Lori ShepherdI’m wondering how the number in thedependenciesbadge on a package’s landing page is calculated. Does it take into accountDepends,Imports,and Suggests? Or onlyDependsandImports? Thanks!
Lori Shepherd (15:37:26): > @Ludwig GeistlingerI’ll dig around into the code shortly to find out and responds by tomorrow morning
Michael Lawrence (16:04:44): > Keep in mind that anything in Depends but not Imports is almost certainly a bug.
Marcel Ramos Pérez (16:10:04): > I’m not sure I follow. According to the manual,Packages declared in the 'Depends' field should not also be in the 'Imports' field.https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies
Michael Lawrence (16:13:27): > Good point, ignore my previous comment. I forgot about that change.
2019-10-18
Hervé Pagès (00:42:43): > @Ludwig GeistlingerDepends,Imports, andLinkingToonly. NotSuggests. This should normally be more or less the number of packages that get loaded when you load the package. The code is here:https://github.com/Bioconductor/biocViews/blob/43f2ad680a6a5e474123a57a502c241692c1af41/R/repository.R#L675-L684 (based ontools::package_dependencies(), which doesDepends,Imports, andLinkingToby default).
Lori Shepherd (07:31:39): > Thanks for looking it up for me@Hervé Pagès
Federico Marini (09:12:29): > Out of curiosity@Hervé Pagès: is there a slim way to check this info out for packages still under development - say, github only?
Federico Marini (09:16:20): > My workaround would involve copypasting the vector of theDESCRIPTIONand pass that topackage_dependencies
Federico Marini (09:16:35): > (and then unlist, unique, and see how long the vector would be)
Martin Morgan (10:13:54): > > db = available.packages(repos=BiocManager::repositories()) > deps = tools::package_dependencies( > c("BiocGenerics", "ShortRead"), db, recursive = TRUE > ) > length(deps[["BiocGenerics"]]) # 5 > length(deps[["ShortRead"]]) # 39 > > but oops, I see@Federico Mariniwants to do this for github-only; I guess I’d scrape with > > url = "[https://raw.githubusercontent.com/Bioconductor/ShortRead/master/DESCRIPTION](https://raw.githubusercontent.com/Bioconductor/ShortRead/master/DESCRIPTION)" > dcf = read.dcf(url(url), c("Depends", "Imports", "Suggests")) > pkgs = sub(" .*", "", trimws(unlist(strsplit(unlist(dcf), ",")))) >
Federico Marini (10:41:12): > Ok, “by hand” would also be the way to go for you then, thanks@Martin Morgan
Ludwig Geistlinger (11:17:15) (in thread): > Thanks a lot@Hervé Pagès!
2019-10-21
Sridhar N (14:24:19): > hello all trying to DL BS genome and keep seeing this error
Sridhar N (14:24:43): - File (Plain Text): Untitled
Sridhar N (14:24:57): > does any one know why?
Shraddha Pai (14:31:37) (in thread): > Did you end up using any particular package to achieve this?
Sridhar N (14:36:45) (in thread): > ggplot2
Sridhar N (14:37:10) (in thread): > logic extracted from crisprvariants package that@Vince Careysuggested
Vince Carey (15:33:11): > I am sure there is a better answer – but if you want to get around this, restart R and reinstall the BSGenome.Mmus…. The ‘unable to access’ warnings can be ignored. Basically you already have the package loaded and the installation you report is failing because of some conflicts in the interaction between newly installed and already loaded resources.
Hervé Pagès (16:03:03): > Also the “write error during file append” message makes me think that you might have a disk space problem so make sure you have enough disk space before you try to install a big BSgenome package like BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz
Hervé Pagès (17:10:59): > One more thing: any reason you’re still using Bioconductor 3.4? This is 3-year old and is no longer supported. The current version is 3.9 and it will soon be replaced with 3.10 (BioC 3.10 will be released next week).
Sridhar N (17:58:56): > legacy issues
Sridhar N (17:59:07): > i know i am using an older version
2019-10-22
Tokuwa Kanno (16:36:20): > @Tokuwa Kanno has joined the channel
2019-10-23
Shraddha Pai (11:15:49): > Good morning! I’m trying to remove all slot references from my package before BioC submission. > > Does anyone know what the accessor method for ROCR’s performance objects are? In particular the x.values and y.values? > > No luck in my search through the ROCR reference manual. Thanks!
FelixErnst (11:24:57): > I think ROCR’s performance class does not have accessor functions defined in the ROCR package itself. At least they are not used in the plot function and are not defined next to the class definition. Best bet: you have to directly access the slots
Shraddha Pai (11:26:55) (in thread): > Thanks Felix. Just trying to remove all direct slot references, but if there isn’t an accessor method, so much for that.
Martin Morgan (11:31:01) (in thread): > yeah, thanks for being conscientious about this, but as you say if the author hasn’t followed good practice then there’s not a lot you can do….
FelixErnst (11:35:13) (in thread): > Yep. I don’t know, what Martin thinks about this, but you could define accessors yourself and just don’t export the generic and method. If they change the slot layout ofperformance, you only have to change your code at one point. So it might be worth the effort in the long run. > > ROCR in itself very well designed (at least from skipping through the code), but it didn’t go through the BioC contribution process
Shraddha Pai (11:36:09) (in thread): > Okay, thank you for the input!
Hervé Pagès (12:39:20) (in thread): > As@FelixErnstpointed out, if you decide to define accesors for your own internal use, you shouldn’t export them. Also you don’t have to use generic+method for that.
Hervé Pagès (12:40:46) (in thread): > But I guess the best thing to do would be to bring this to the attention of the ROCR folks, maybe by contributing a patch.
Shraddha Pai (12:45:59) (in thread): > OK - thanks Hervé!
Ritche Long (13:18:53): > @Ritche Long has joined the channel
2019-10-24
Thomas Schwarzl (08:19:11): > Hi there. Unfortunately, some images are missing in the bioc build of our vignette (which are not missing in the local build).http://bioconductor.org/packages/devel/bioc/vignettes/DEWSeq/inst/doc/DEWSeq.html - any ideas?
Martin Morgan (08:28:13): > I see images in the vignette; can you be more specific, e.g., a particular section and after a particular sentence?
Thomas Schwarzl (08:30:48): > Figure 2, 4, 5, 6, 7, 9 cannot be displayed. Figure 10 is very small. Tested this on 2 different machines and 3 different browsers.
Thomas Schwarzl (08:32:00): > image is missing - File (PNG): image.png
Martin Morgan (09:28:52): > When I try and build your package on my own current, up-to-date bioc-devel, I get > > $ git -C DEWSeq status > On branch master > Your branch is up to date with 'origin/master'. > > nothing to commit, working tree clean > $ bioc-devel CMD build DEWSeq > * checking for file 'DEWSeq/DESCRIPTION' ... OK > * preparing 'DEWSeq': > ... > Quitting from lines 577-589 (DEWSeq.Rmd) > Error: processing vignette 'DEWSeq.Rmd' failed with diagnostics: > object 'ihw' not found > --- failed re-building 'DEWSeq.Rmd' > > SUMMARY: processing the following file failed: > 'DEWSeq.Rmd' > > Error: Vignette re-building failed. > Execution halted > > any hints?
Thomas Schwarzl (10:13:40): > Thanks Martin. That’s strange, the builds have been successful so far. Initially we had it in Suggests but BiocCheck was complaining because it was not in the code, just in the vignette. > We’ll update and push a new version. Cheers
Sudeep Sahadevan (10:37:40): > @Sudeep Sahadevan has joined the channel
2019-10-25
Martin Morgan (11:08:19): > #containers#generalWe’d like to hold a discussion about Bioconductor Docker containers on Tuesday November 5 at 11am eastern. The call will be athttps://bluejeans.com/434715813 Please mark your calendars!
Steve Lianoglou (13:58:19): > can anyone dial into those calls, or? would like to maybe be a fly on the wall on that one … also, is that eastern time?
Martin Morgan (14:34:12): > @Steve Lianoglouyep anyone can join the call. I wasn’t too clear on the agenda; I’ll provide more details on the#containerschannel…
2019-10-26
Nitesh Turaga (09:08:08) (in thread): > Yes, 11am EST on November 5th.
2019-10-30
Shian Su (21:06:24): > Anyone got ideas forhttps://support.bioconductor.org/p/125973/ ?
Shian Su (21:07:37): > I am half way through writing my own code to do this, would it make sense to push that into Biostrings or GenomicAlignments?
Stuart Lee (22:07:22): > Does anything in cigar utils help page in GenomicAlignments provide what you’re after > > ?GenomicAlignments::`cigar-utils` >
Ambrose Carr (22:08:18): > @Ambrose Carr has joined the channel
Shian Su (22:45:45) (in thread): > Based on a brief look,queryLoc2refLoclooks close to what I want, except I think I need the reverse.
2019-10-31
Kasper D. Hansen (09:35:46): > We do need utilities for this, for sure
Kasper D. Hansen (09:36:01): > No idea on how to do it, but a strong support for the idea that this should be easy
Lauren Fitch (10:10:11): > did you already look atmapToAlignments?
Lauren Fitch (10:11:27): > “Map range coordinates between reads (local) and genome (reference) space using the CIGAR in a GAlignments object.”
Lauren Fitch (10:12:29): > it’s in theGenomicAlignmentspackage
Shian Su (20:58:21): > Thanks Lauren, that’s perfect! Now I just need to work out how I want to deal with the nightmare that is VCF files.
2019-11-01
Shian Su (00:49:48): > Can someone tell me how to do block processing of BAM files by n reads at a time?
Shian Su (00:52:31): > The example in the documentation shows how to do it by blocking on coordinates, is it possible to do it with a number of reads?
Shian Su (01:12:19): > From what I can tell, I need to use BamFile() and scanBam(). But scanBam isn’t advancing the yield and always only gives the first chunk.
Shian Su (01:13:14): - File (Plain Text): Untitled
Aaron Lun (01:18:29): > readGAlignments was able to do this, I think.
Shian Su (01:26:55): > Unfortunately I need the sequence/qual, fortunately I found out you just need toopen()the bamFile first.
Lauren Fitch (10:34:02): > you can get seq/qual withreadGAlignments. you need to doparam <- ScanBamParam(what=c("seq", "qual"))and thenreadGAlignments(bamfile, param = param)
Martin Morgan (10:48:50): > @Shian Suit’s confusing to have this conversation here and on the support sitehttps://support.bioconductor.org/p/125973/#126027 , and leads to duplicate effort – in the future, please choose your poison:wink:
Kasper D. Hansen (14:34:43): > HTML vignettes with BiocStyle is not good with my iPhone. Almost 50% of the precious screen estate is whitespace.
Vince Carey (17:18:36): > @Kasper D. Hansen, I had a look at the GenomicRanges vignette 1, in landscape mode on iphone, and it looked more like 25% whitespace. One item that might be interesting to address in vignette rendering is the number of digits with which floating point numbers are rendered. This is often excessive, eats horizontal space, and forces awkward linebreaks. I have no idea if this can be solved in a satisfactory way except by author setting of options.
2019-11-02
Kasper D. Hansen (15:37:01): > Landscape is prob better. I think it’s because margins are fixed with kills phone on portrait.
Kasper D. Hansen (15:37:15): > But I use phone in portrait…. :(
2019-11-04
Izaskun Mallona (07:55:15): > @Izaskun Mallona has joined the channel
2019-11-05
Michael Love (09:13:20) (in thread): > agree. the standard rmarkdown templates “just work” across monitor, tablet, phone. i often need to look up vignette sections on phone
Kasper D. Hansen (13:19:07): > UsingBiocManagerto installaffyunder R-devel with Bioconductor 3.11 yields … nothing… > > Bioconductor version 3.11 (BiocManager 1.30.9), ?BiocManager::install for help > Bioconductor version 3.11 (BiocManager 1.30.9), R Under development (unstable) > (2019-11-04 r77365) > Installing package(s) 'affy' > Warning message: > package 'affy' is not available (for R Under development) >
Kasper D. Hansen (13:19:19): > I’m confused. There is a tarball on the website
Kasper D. Hansen (13:19:29): > https://www.bioconductor.org/packages/devel/bioc/html/affy.html - Attachment (Bioconductor): affy (development version) > The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. ‘affy’ is fully functional without it.
Lori Shepherd (13:25:01): > Affy hasnt built yet on 3.11 if you look at the build report its failing
Lori Shepherd (13:25:40): > There wont be a download if it has never built
Lori Shepherd (13:27:29): > when I go to the devel page you listed at the bottom there is no tarball if you look down at the source archives -
Lori Shepherd (13:28:37): > The information is filled in from the description and that the tarball was created and successfully built but the tar never gets propogated because it fails check -
Kasper D. Hansen (15:04:38): > oh yes, the link at the bottom is missing
Kasper D. Hansen (15:04:57): > Ok, at least its consistent. That’s the thing that was bothering me
Diana Firkins (15:37:34): > @Diana Firkins has joined the channel
Martin Morgan (16:03:10): > but then it’s a sad day when affy isn’t available…:cry:… wonder what the problem is…?
Hervé Pagès (16:13:10): > https://bioconductor.org/checkResults/3.11/bioc-LATEST/affy/malbec2-checksrc.html Could it be a change in R?
hcorrada (16:57:45): > Someone should alert the maintainer:slightly_smiling_face:
Martin Morgan (17:12:10): > I’ll take a look; I think this specific problem is because there’s a plot.ProbeSet S3 method that is defined but not registered in the NAMESPACE file…
Kasper D. Hansen (20:28:13): > His email might bounce though
2019-11-06
Federico Marini (12:03:49): > Hi, general post-release question
Federico Marini (12:04:02): > Are the data packages not autobumped like the software ones?
Federico Marini (12:05:26): > Sorry, forget the message above. I did not fetch –all with the one I was checking out
Federico Marini (12:06:15): > h/t to@Nitesh Turagaand@Hervé Pagèsfor this:wink:
Federico Marini (12:10:43): > But piggybacking on the affy bad news
Federico Marini (12:10:56): > I noticed alsotopGOdid not build yet for release
Federico Marini (12:12:08): > I do not recall whether Adrian Alexa is still currently active in maintaining - a couple of years ago someone else I guess had to switch fromcattomessagewhen the functions were logging the progress
Lluís Revilla (12:14:14): > He did some updates 2 years ago
Lluís Revilla (12:14:20): > He has a fork onhttps://github.com/adrianalexa/topGO/
Federico Marini (12:15:03): > Same forIHW(andlpsymphony), now that I check more in detail
Lluís Revilla (12:15:35): > It might not be related but I can’t see the download stats of topGO for this year or for SingleR or BiocSet
Federico Marini (12:18:05): > I am almost sure Lori’s automail system will catch these already
Lori Shepherd (12:20:38): > topGO and BiocSet dont have stats I’m assuming becausse they havne’t built yet - SingleR is different an access forbidden @Hervé Pagès
Lori Shepherd (12:24:45): > and yes@Federico MariniI will start sending emails about broken packages again probably next week and should catch these - but they should already be getting the BBS failure notification emails too
Federico Marini (12:25:36): > I knowideal’s affected as well - that’s how I spot out topGO and IHW. I will keep it under watch:wink:
Hervé Pagès (12:34:43): > No stats for BiocSet because it has 0 downloads. The script that generates the download stats only looks at the Amazon CloudFront log files, it doesn’t know anything about our manifest files. This is why we see download stats for packages that have been removed from Bioconductor many years ago or even for packages that never seem to have existed. Need to investigate for topGO (no downloads reported for 2019, can’t be true) and for SingleR (Access Forbidden).
Hervé Pagès (13:28:17): > Should be fixed now. The fix won’t be effective before next Friday though…
Hervé Pagès (20:27:50): > Please check again on Friday. The issue I addressed was affecting many packages, not just topGO or SingleR.
2019-11-07
Mike Smith (09:01:45) (in thread): > I got this working fairly well inmsmbstyle BiocStyle
Kasper D. Hansen (09:56:18) (in thread): > That would be good. If it is . possible to detect phone / tablet vs computer, I think also disabling TOC on phone/tablet is a good idea
Mike Smith (10:00:16) (in thread): > It’s possible to detect the resolution of the screen area and conditionally deploy CSS according to that e.g. this site should restructure the layout & navigation based on your screen sizehttps://www.huber.embl.de/users/msmith/msmbstyle/bootstrap/ - Attachment (huber.embl.de): MSMB HTML Book Style > MSMB HTML Book Style
Kasper D. Hansen (10:02:37) (in thread): > how do they deal with the very high DPI (high resolution) but low physical size of “retina” iPhones?
Kasper D. Hansen (10:02:49) (in thread): > You’re probably on top of this already though
Kasper D. Hansen (10:03:48) (in thread): > that link looks good on my phone though
Mike Smith (10:13:51) (in thread): > It’s a good question, I’m not sure if the phone itself does some scaling and reports a lower resolution that in actuality. A lot of the work on that site is actually done by using Twitters Bootstrap layout which is designed to be reactive from the get go, so I don’t have to worry too much. Hopefully we can steal some tricks without having to totally overhaul BiocStyle, because I agree the current phone rendering is terrible.
Shraddha Pai (10:18:21): > Hi all, I’m starting to work more in Rstudio and have activated vim keybindings. > Is there a way to activate multi-line cutting? (e.g. ” ,d” where and are line numbers). > Thanks!
Marcel Ramos Pérez (10:26:47): > Hi Shradda, RStudio has a lightweight version ofvimas provided by the ACE editor. I don’t expect the full functionality of vim to be available. There are more details here:https://blog.rstudio.com/2015/02/23/rstudio-0-99-preview-vim-mode-improvements/ To answer your question, you can check theTools>Global Options>Code>Editing>Modify Keyboard Shortcutsto see if that functionality is available. Otherwise, it’s not supported (yet?).
Shraddha Pai (11:02:46) (in thread): > Thanks@Marcel Ramos Pérez. Handy cheat sheet to see what functionality is available. Also it’s nice to have a “filter” option in the keyboard shortcuts menu. > > Doesn’t look like the functionality is supported (yet). I’ll just copy paste the GUI way (select) and switch to vi for editing if it’s too distracting. > > Thanks again.
Aedin Culhane (11:18:58): > Hi Everyone. We set up a#jobschannel. There are many postings of PhD studentship, postdoc and other positions on the channel.
2019-11-08
Lluís Revilla (05:04:13): > A new technical advisory board note has been posted:https://bioconductor.org/about/technical-advisory-board/
Alan O’C (08:16:02): > @Alan O’C has joined the channel
Hervé Pagès (12:05:37): > Just a heads-up that it’s unlikely that the download stats issues will go away today. Might actually get worse:worried:For some reason, the scripts generating the stats are running much slower than usual and these delays are causing all sorts of problems. Investigating now…
Hervé Pagès (12:16:48): > The scripts were running so slow, it was hopeless. I rebooted the machine. Next update of the download stats will be next Tuesday (hopefully:crossed_fingers:)
Hervé Pagès (12:25:54): > The size of the download stats is growing insane: > > biocadmin@ip-172-30-0-230:~/download_dbs$ ls -lh > total 34G > -rw-r--r-- 1 biocadmin biocadmin 1.1G Mar 8 2018 download_db_2009.sqlite > -rw-r--r-- 1 biocadmin biocadmin 1.2G Mar 8 2018 download_db_2010.sqlite > -rw-r--r-- 1 biocadmin biocadmin 1.1G Mar 8 2018 download_db_2011.sqlite > -rw-r--r-- 1 biocadmin biocadmin 1.4G Mar 5 2018 download_db_2012.sqlite > -rw-r--r-- 1 biocadmin biocadmin 2.5G Mar 5 2018 download_db_2013.sqlite > -rw-r--r-- 1 biocadmin biocadmin 2.8G Mar 5 2018 download_db_2014.sqlite > -rw-r--r-- 1 biocadmin biocadmin 3.3G Mar 1 2018 download_db_2015.sqlite > -rw-r--r-- 1 biocadmin biocadmin 4.1G Mar 2 2018 download_db_2016.sqlite > -rw-r--r-- 1 biocadmin biocadmin 4.8G Mar 2 2018 download_db_2017.sqlite > -rw-r--r-- 1 biocadmin biocadmin 5.4G Jan 3 2019 download_db_2018.sqlite > -rw-r--r-- 1 biocadmin biocadmin 5.9G Nov 7 12:02 download_db_2019.sqlite > > :face_with_head_bandage:
Aaron Lun (12:28:15): > Is it storing each individual IP address? Seems kind of unnecessary.
Hervé Pagès (12:29:43): > Just a big table with one entry per download. The IP address is needed to count the number of distinct IPs.
Aaron Lun (12:31:04): > Hm, I guess. Well, I don’t know that the IP addresses from 2009 are all that interesting, seems like you could just aggregate them into summary statistics at the end of every year.
Aaron Lun (12:31:22): > On the flip side, you could do some really cool analytics if you also had the version bump dates.
Aaron Lun (12:32:00): > See how many/quickly people propagate version bumps, which would be pretty interesting from a developer perspective.
Aaron Lun (12:33:47): > And in the big scheme of things, ~10GB every year is nothing, really. Especially if you can put them mostly in cold storage.
Hervé Pagès (12:35:19): > Yes, the download stats that we provide are an aggregation of that. The SQLite dbs are just a curated version of the Amazon CloudFront log files which are way bigger. Just an intermediate representation that makes it convenient to do all kinds of queries. Package versions are stored so yes you could do all kinds of analytics. That’s why we keep all the SQLite dbs, even old ones, just in case.
Aaron Lun (12:44:47): > ha
Alejandro Reyes (12:45:35) (in thread): > Are these files public?
Hervé Pagès (12:45:52): > Nope
Sean Davis (13:23:25) (in thread): > Not sure where the bottleneck is, but that amount of data will be trivial for an elasticsearch node. Have you considered adding that into the tech stack?
Hervé Pagès (13:27:32) (in thread): > No
2019-11-09
Debbie (04:09:10): > @Debbie has joined the channel
Kasper D. Hansen (23:02:29): > I am trying to install a package with a autoconf generated configure script.
Kasper D. Hansen (23:03:15): > I want to get hold ofconfig.log. How do I get that? The only way I know for sure works is runningR CMD checkbut in this case I cannot do it sure to circular dependencies
2019-11-11
Kasper D. Hansen (10:02:44): > After runningR CMD checkI can find it inPKGNAME.Rcheck/00_pkg_src/PKGNAME
Kasper D. Hansen (10:03:42): > But there must be a way that I can get this out ofR CMD INSTALL? The issue withcheckis that I need allSuggestspackages operational.
Alan O’C (10:09:02): > Why not just runautoconfand then./configure?
Kasper D. Hansen (10:47:07): > there is a potential difference between runningconfigurestand alone and running it as part of R’s installation process. Or at least there is the possibility of inheriting environmental variables and query the master R process.
Kasper D. Hansen (10:47:31): > (you should never as a user have to runautoconf- that is only for the package author to run)
Kasper D. Hansen (10:48:33): > (andautoconfis used during the build process. You useautoconfto processconfigure.in /configure.ac (the same) to generatedconfigurewhich is then distributed.
Martin Morgan (12:33:56): > R CMD ./confgureI think set the environment variables…
Mike Smith (13:13:30): > Is this on a tarball? If I runR CMD INSTALL pkg_diron the unpackedpkg_dirthenconfig.logappears in that directory and seems to remain after the install process finished.
Mike Smith (13:23:43) (in thread): > I’ve submitted a pull request with some initial attempts at improving the mobile style (https://github.com/Bioconductor/BiocStyle/pull/67 ). Probably a work in progress, but feel free to give it a try and provide feedback if you have time.
Michael Love (16:45:12) (in thread): > cool, thanks Mike
Michael Love (16:45:15) (in thread): > appreciate the work
Chengyang Ji (22:42:50): > @Chengyang Ji has joined the channel
hzongyao (23:51:16): > @hzongyao has joined the channel
2019-11-12
Renan (11:30:48): > @Renan has joined the channel
Hervé Pagès (13:25:21): > Download stats are back and BiocSet got its first~3~5 downloads:https://bioconductor.org/packages/stats/bioc/BiocSet :rocket:(note that there is a lag of 2 or 3 days between a download and its inclusion in the stats). Let me know if you still see problems.
Hervé Pagès (13:28:47): > Am I the only one to see a big fat sea lion trying to climb a rock instead of a “party parrot”?
Federico Marini (13:43:17): > Now you should see that same sea lion using some adequate eye protection:slightly_smiling_face:
Martin Morgan (13:56:37): > Pro / curmudgeon tip: click on community-bioc then Preferences then Accessibility then disable “Allow animated images and emoji”:thumbsup:
Hervé Pagès (14:01:15): > Good to know. These super colorful animated emoji make the curmudgeon inside me dizzy:dizzy_face:
Kevin Wang (18:59:53): > Oh, this is awesome! I always wonder when will BioC and tidyverse get better integration, a dream came true!
2019-11-13
Vince Carey (09:44:24): > New PLoS paper lauds cqn and EDAseq for addressing sample-specific length-associated bias in RNA-seq, with particular attention to GSEA.https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000481 - Attachment (journals.plos.org): Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias > Analysis of numerous RNA-seq datasets reveals a recurrent sample-specific length bias that causes frequent false positive calls by gene-set enrichment analyses, leading to functional misinterpretation of the data. Its removal requires methods that allow the integration of gene length as sample-specific covariate.
Rob Patro (10:08:13): > I liked@Michael Love’s take on this.
Rob Patro (10:09:50): > Those types of biases are something that can and likely should be modeled at the quantification step, and relevant offsets can be passed off to downstream tools.
Kasper D. Hansen (10:11:07): > dude that’s what we did in CQN
Rob Patro (10:17:32): > I haven’t read the above paper thoroughly yet. Can someone tell me the main difference in result from the 2010 Oshlack paper?
Rob Patro (10:18:03): > Also, i did see they used TopHat2 + featureCounts …. so a length bias there doesnt suprise me at all.
Rob Patro (10:22:58): > @Kasper D. Hansenahh, i see@Michael Lovemade that point on Twitter and you basically answered the question I asked above!
Rob Patro (10:23:11): > Too many social media outlets to keep up!
Kasper D. Hansen (10:23:11): > So there is a differeence
Kasper D. Hansen (10:23:57): > I would say the PLOS Biology paper is really two things > 1) a re-finding of the things we found in CQN / edaSEQ: that there is a sample specific relationship between gene length and expression level
Kasper D. Hansen (10:24:47): > However, the claim in the plos biology paper is that this bias is extremely common and basically exists in every dataset in a way that biases DE. That is surprising to me
Kasper D. Hansen (10:25:08): > They are not say its new. They are saying its everywhere and people really need to look at this.
Kasper D. Hansen (10:25:32): > 2) Because of this bias there will be a relationship between gene length and DE (and direction of fold change)
Kasper D. Hansen (10:25:40): > And this will bias enrichment analysis
Kasper D. Hansen (10:25:53): > This is a very similar, but slightly different, from goseq in my opinion
Rob Patro (10:26:06): > But isnt this immediately an artifact of using a counting based approach
Kasper D. Hansen (10:26:12): > No
Rob Patro (10:26:43): > You can’t properly control for the length when the underlying gene has no consistent well-defined “length”
Kasper D. Hansen (10:26:49): > Say look at figure 3a
Kasper D. Hansen (10:27:00): > That is not implied by any counting model
Kasper D. Hansen (10:27:39): > It would be different if the y-0axis in fig 3 was “probability of being DE”. Then we would see a relationship and that relationship would be because of counting
Kasper D. Hansen (10:28:06): > (ok, of course you can make a non-standard counting model that implies this)
Kasper D. Hansen (10:28:36): > the counting model implies a fixed relationship between gene length and expression level
Kasper D. Hansen (10:28:50): > the cqn observation is that this relationship is sample specific
Kasper D. Hansen (10:29:59): > When you go this route > > You can’t properly control for the length when the underlying gene has no consistent well-defined “length” > you also have to say that gene level differential expression is nonsense
Michael Lawrence (10:30:09): > you guys need to make a thread for this discussion
Rob Patro (10:32:59): > @Kasper D. Hansen— I probably would never go so far as to claim it’s “nonsense”
Rob Patro (10:33:13): > but I would say it’s necessarily incomplete
Rob Patro (10:33:38): > i.e. the effect is sample-specific because gene-length is also sample specific
Kasper D. Hansen (10:34:04): > Ill finish my comment first: The impact of both of these biases on functional enrichment could be fixed by the approach in goseq, except that in goseq they impose a monotone relationship and I don’t think that the sample specific bias implies a monotone relationship between gene length and detection, it just implies a relationship. Should be easy to modify goseq to include any type of relationship. But this is based on my refreshing my reading of goseq in the last 10m so take this with hefty grain of salt
Rob Patro (10:34:32) (in thread): > or, at least, a consistent notion of gene length (e.g. the average expressed transcript lengths of isoforms of this gene in each sample) … moving to thread
Rob Patro (10:34:49) (in thread): > I see what you are saying though, and appreciate the difference
Kasper D. Hansen (10:35:02) (in thread): > I see what you’re saying but there is no way this is the cause of the sample specific bias
Kasper D. Hansen (10:35:58) (in thread): > If you look at figure 1 in our cqn paper you’ll see two biological replicates. One where - genomewide - rpkm (and the “k” matters here) increases with gene length and one where it decreases
Kasper D. Hansen (10:36:35) (in thread): > thats … not likely to be changes in isoform abundances. I could be wrong of course. I am saying likely
Rob Patro (10:36:55) (in thread): > So I think that hypothesis wouldn’t be too difficult to test
Rob Patro (10:37:14) (in thread): > e.g. look at these plots only over single-isoform genes (and genes that have no close paralog)
Rob Patro (10:37:50) (in thread): > or, you know, remake some of the plots in the new PLoS paper but doing transcript quantification to determine the sample-specific lengths of each gene
Rob Patro (10:38:05) (in thread): > if there were more hours in the day:slightly_smiling_face:
Kasper D. Hansen (10:38:23) (in thread): > but you see this between replicates as well
Rob Patro (10:39:04) (in thread): > biological or technical?
Rob Patro (10:39:11) (in thread): > (I’m guessing biological)
Kasper D. Hansen (10:39:21) (in thread): > I have only looked at biological
Rob Patro (10:39:35) (in thread): > it’s very interesting … do you have a hypothesis as to the mechanistic cause of this?
Kasper D. Hansen (10:39:50) (in thread): > No.
Kasper D. Hansen (10:40:09) (in thread): > My impression after the cqn paper was that it is dwarfed by sample speicifc GC content bias
Kasper D. Hansen (10:41:00) (in thread): > Its really hard to track down the origin of such things, because even if you do it for one special dataset, its not clear it generalizes
Rob Patro (10:41:56) (in thread): > I’ll add this to my list of yet one more thing we don’t really understand about RNA-seq (and, also, something else that simulators don’t properly recapitulate)
Kasper D. Hansen (10:53:29): > anyway, just to be clear: this paper should absolutely have mentioned and discussed goseq.
Federico Marini (11:16:42): > This is a major miss TBH
Federico Marini (11:16:52): - File (PNG): image.png
Federico Marini (11:16:58): > Neither Oshlack nor Young et al.
Michael Love (11:55:53) (in thread): > Difference in fragmentation & degradation
Michael Love (11:56:02) (in thread): > The mechanism
Stephanie Hicks (12:11:02): > hi everyone — I’m looking to coordinate some CZI open source applications in the#diversebiocchannel (https://community-bioc.slack.com/archives/CL21357E2/p1573611239006700 ). If you’re interested in getting involved in one (or suggesting another), could you fill out our poll? Thanks ! - Attachment: Attachment > hi #diversebioc — I’m looking to move forward with one of the CZI proposal ideas that I tossed out last month (https://community-bioc.slack.com/archives/CL21357E2/p1569947438001100 ). I see there were 9 :thumbsup: from people who are interested in at least one of these ideas. Could we revive that conversation? I’m going to open up a poll on Slack to help us figure if there are groups of people who want to work on different project proposals. From there, we can decide how to move forward with the december deadline? > https://community-bioc.slack.com/archives/CL21357E2/p1569947438001100
Rob Patro (14:18:41) (in thread): > yea — difference in degradation is not something that a model-based approach to transcript quantification would immediately pick up on, unless that was explicitly being modeled (e.g. per-transcript positional bias)
Dario Strbenac (15:00:13) (in thread): > Seemingly, changes at the RNA level often don’t convert into changes at the protein level, so everyone should be doing proteomics research instead:smirk:Extensive Post-transcriptional Buffering of Gene Expression in the Response to Severe Oxidative Stress in Baker’s Yeast,Scientific Reports , 2019https://www.nature.com/articles/s41598-019-47424-w
Evgeny Vlasov (15:33:32): > @Evgeny Vlasov has joined the channel
Michael Love (15:39:22) (in thread): > interesting, that paper seems to be missing the key figure: LFC of RNA vs LFC of protein
Michael Love (15:39:40) (in thread): > maybe it’s in supplement
Ludwig Geistlinger (17:47:25) (in thread): > Catching up a week later: it seems as iftopGOis still not building on both release and devel?
Federico Marini (17:49:27): > It is not
Federico Marini (17:50:41): > There is an issue in the vignette, namely at > > sel.go <- names(pValue.classic)[pValue.elim < pValue.classic] > cbind(termStat(sampleGOdata, sel.go), > elim = pValue.elim[sel.go], > classic = pValue.classic[sel.go]) > > basically it it because elim isnow never less conservative than classic
Federico Marini (17:51:35): > Somehow that condition is not verified anymore, and my guess is that the text itself in the vignette should be adjusted or commented out. Lori has been already made aware of this
Federico Marini (17:52:07): > Depending on how quickly Adrian might react, the timeline can vary:stuck_out_tongue:
Ludwig Geistlinger (17:53:06) (in thread): > Alright. Thanks for the update!
Federico Marini (17:53:29): > You are also on the suffering side of having some packages also not built as a chain reaction?
Federico Marini (17:53:36) (in thread): > :thumbsup:
Ludwig Geistlinger (17:54:27) (in thread): > Yes, also among the (not few) packages depending on it …:wink:
Federico Marini (17:56:01) (in thread): > The vignette could also receive some refreshment (alone Rmd would be great, I forgot how many potential pains are brought in by Rnw “nowadays”)
Federico Marini (17:58:11) (in thread): > That said: it would be interesting to track down what actually triggered the condition to be not verified anymore
Federico Marini (17:58:43) (in thread): > For sure theorgDbpackages have an evolving history of GO annotations as well
Noor Pratap Singh (18:40:23): > @Noor Pratap Singh has joined the channel
Stevie Pederson (20:49:28): > Related question to the above discussion, but I can’t find a package with transcript-level GC content pre-calculated. To include this in any standard workflow, it seems like it could be included inEnsDb(orTxDb) objects as a standard field to me. Am I missing an obvious package or does this need to be recalculated every time you want it (unless saved locally of course)?
Ludwig Geistlinger (21:57:48) (in thread): > I thinkEDASeq::getGeneLengthAndGCContentor accessingbiomaRtare among your options here
Stevie Pederson (22:02:48) (in thread): > Thanks Ludwig. I knew about those, but figured it was so common & useful that it might be easy to just include in those objects whilst building them. We’ve just built them locally as a set of objects so will host a database of common organisms on github in the meantime. I’ll post once it’s up if it’s useful.
2019-11-14
Ping Luo (08:31:59): > @Ping Luo has joined the channel
Shraddha Pai (09:28:03): > Hi all, I’m trying to delete a 17M pack file in my git repo (getting BiocCheck warning). > I’ve tried running BFG Repo-Cleaner as in this linkhttps://bioconductor.org/developers/how-to/git/remove-large-data/ but the pack file is still not being deleted. I’m wondering what I’m doing wrong?
Martin Morgan (09:39:44): > tagging@Nitesh Turagaon the above ^^^
Liz Ing-Simmons (10:17:54): > @Liz Ing-Simmons has joined the channel
Alan O’C (10:30:58) (in thread): > What commands did you run exactly? What operating system are you running?
Alan O’C (10:31:19) (in thread): > If you link the repository I can have a look
Shraddha Pai (10:36:25) (in thread): > Hi@Alan O’C, I first ran this in the directory where my source package resides: > > $ java -jar ~/software/bfg-1.13.0.jar --strip-blobs-bigger-than 5M netDx/. > > Using repo : /Users/shraddhapai/Documents/Software/netDx/./.git > > > This repo has been processed by The BFG before! Will prune repo before proceeding - to avoid unnecessary cleaning work on unused objects... > Completed prune of old objects - will now proceed with the main job! > > Scanning packfile for large blobs: 29490 > Scanning packfile for large blobs completed in 210 ms. > Warning : no large blobs matching criteria found in packfiles - does the repo need to be packed? > Please specify tasks for The BFG : > bfg 1.13.0 > Usage: bfg [options] [<repo>] > > -b, --strip-blobs-bigger-than <size> > strip blobs bigger than X (eg '128K', '1M', etc) > -B, --strip-biggest-blobs NUM > strip the top NUM biggest blobs > -bi, --strip-blobs-with-ids <blob-ids-file> > strip blobs with the specified Git object ids > -D, --delete-files <glob> > delete files with the specified names (eg '**.class', '**.{txt,log}' - matches on file name, not path within repo) > --delete-folders <glob> delete folders with the specified names (eg '.svn', '*-tmp' - matches on folder name, not path within repo) > --convert-to-git-lfs <value> > extract files with the specified names (eg '**.zip' or '**.mp4') into Git LFS > -rt, --replace-text <expressions-file> > filter content of files, replacing matched text. Match expressions should be listed in the file, one expression per line - by default, each expression is treated as a literal, but 'regex:' & 'glob:' prefixes are supported, with '==>' to specify a replacement string other than the default of '******REMOVED******'. > -fi, --filter-content-including <glob> > do file-content filtering on files that match the specified expression (eg '*.{txt,properties}') > -fe, --filter-content-excluding <glob> > don't do file-content filtering on files that match the specified expression (eg '*.{xml,pdf}') > -fs, --filter-content-size-threshold <size> > only do file-content filtering on files smaller than <size> (default is 1048576 bytes) > -p, --protect-blobs-from <refs> > protect blobs that appear in the most recent versions of the specified refs (default is 'HEAD') > --no-blob-protection allow the BFG to modify even your **latest** commit. Not recommended: you should have already ensured your latest commit is clean. > --private treat this repo-rewrite as removing private data (for example: omit old commit ids from commit messages) > --massive-non-file-objects-sized-up-to <size> > increase memory usage to handle over-size Commits, Tags, and Trees that are up to X in size (eg '10M') > <repo> file path for Git repository to clean >
Shraddha Pai (10:37:57) (in thread): > Then this: > > $ cd netDx > $ git reflog expire --expire=now --all && git gc --prune=now --aggressive > Counting objects: 14745, done. > Delta compression using up to 4 threads. > Compressing objects: 100% (13946/13946), done. > Writing objects: 100% (14745/14745), done. > Total 14745 (delta 9112), reused 5606 (delta 0) > $ cd .git/objects/pack/ > $ ls -lht > total 35184 > -r--r--r-- 1 shraddhapai staff 404K 14 Nov 10:37 pack-611472e3c885db0fa7210dc9dc6d88e0be72f9ba.idx > -r--r--r-- 1 shraddhapai staff 17M 14 Nov 10:37 pack-611472e3c885db0fa7210dc9dc6d88e0be72f9ba.pack >
Shraddha Pai (10:38:41) (in thread): > I’m running a Mac 10.13.6. > Repo is here:https://github.com/BaderLab/netDx
Shraddha Pai (10:38:56) (in thread): > Could it be because I’m not on the main branch? I’m doing dev on a branch calledbioc.
Alan O’C (10:39:18) (in thread): > bfg complains about the repo not being packed, and I thinkgit gcrepacks the repo
Alan O’C (10:39:25) (in thread): > See here:https://github.com/rtyley/bfg-repo-cleaner/issues/65
Shraddha Pai (10:39:42) (in thread): > I just tried runninggit gcafter noticing that message. Didn’t change anything.
Shraddha Pai (10:40:01) (in thread): > In fact the commands I posted above areafter git gc, just so you could see what commands I used.
Shraddha Pai (10:40:14) (in thread): > Let me trygit repack
Alan O’C (10:40:20) (in thread): > I suspected so, just checking!
Shraddha Pai (10:41:03) (in thread): > Typinggit repackin my package directory (insidenetDx/) returnsNothing new to pack.
Alan O’C (10:45:17) (in thread): > If I clone the repo from that link and runjava -jar bfg-1.13.0.jar --strip-blobs-bigger-than 5M .gitI see the following deleted files: > > Filename Git id > ---------------------------------------------------------------------------------- > BRCA_3data_input_170117.Rdata | e78d617b (36.0 MB) > GeneMANIA-3.2B7.jar | e9bdac69 (9.8 MB) > TCGA_BRCA.rda | e25d25e0 (25.1 MB) > buildPred_input.rda | 436c6386 (9.9 MB) > genemania-cytoscape-plugin-3.5.0.jar | 86b3a1a3 (11.0 MB), 067d33c0 (11.0 MB), ... > genemania-cytoscape-plugin-3.5.jar | 3ba655e9 (11.0 MB) > nestedCV_input.rda | 436c6386 (9.9 MB) > sample_predictor_KIRC_mut_data.Rdata | ba1ebc9c (9.8 MB) > sample_predictor_KIRC_mut_data.rda | ba1ebc9c (9.8 MB) >
Marcel Ramos Pérez (10:46:07) (in thread): > I go from 129 Mb to 21 Mb after using BFG. Perhaps there are no blobs bigger than 5Mb in the pack. If you have collaborators, make sure they are cloning and pushing with a fresh cleaned-up copy
Shraddha Pai (10:46:40) (in thread): > Thanks for trying that! So the first time I ran bfg it did delete some files. When I ran BiocCheck I still got a warning. The offending file is this one: > > PurpleMac:netDx shraddhapai$ cd .git/objects/pack/ > PurpleMac:pack shraddhapai$ ls -lht > total 35184 > -r--r--r-- 1 shraddhapai staff 404K 14 Nov 10:41 pack-9b526166645a3baea8e27a85e804503d60234180.idx > -r--r--r-- 1 shraddhapai staff 17M 14 Nov 10:41 pack-9b526166645a3baea8e27a85e804503d60234180.pack >
Shraddha Pai (10:46:47) (in thread): > It’s 17Mb
Shraddha Pai (10:47:03) (in thread): > Could it be because I’m running bfg on a branch?
Marcel Ramos Pérez (10:49:44) (in thread): > You could try making--strip-blobs-bigger-thansmaller
Alan O’C (10:50:01) (in thread): > It shouldn’t be, unless the large files were introduced in the current commit
Alan O’C (10:50:19) (in thread): > I wouldn’t do that - the current list of large files is reasonable: > > 291a2fa881e9 1014KiB examples/MB/WNT/query.txt-results.report.txt > 223421f09a19 1.1MiB examples/MB/SHH/query.txt-results.report.txt > f172065b9ffc 1.3MiB examples/MB/Group3/query.txt-results.report.txt > 7ef307350497 1.4MiB inst/extdata/example_output/rng2/predictionResults.txt > 89f1c5dfc222 1.4MiB inst/extdata/example_output/rng1/predictionResults.txt > 5ab0b6fcf93c 1.4MiB inst/extdata/example_output/rng3/predictionResults.txt > de55d5911e7f 1.4MiB inst/extdata/example_output/rng2/predictionResults.txt > 9b21dee821bc 1.5MiB examples/MB/Group4/query.txt-results.report.txt > ad1201cf9f1a 1.9MiB examples/other/KIRC_mut_rna_workbook.nb.html > 01a7dde8b1e6 3.1MiB netDx.examples/data/MBlastoma.rda > e9834822150d 4.5MiB netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/SURVIVEYES/SURVIVEYES_query-results.report.txt >
Alan O’C (10:50:42) (in thread): > Rungit rev-list --objects --all | git cat-file --batch-check='%(objecttype) %(objectname) %(objectsize) %(rest)' | sed -n 's/^blob //p' | sort --numeric-sort --key=2 | cut -c 1-12,41- | numfmt --field=2 --to=iec-i --suffix=B --padding=7 --round=nearestto check
Shraddha Pai (10:51:02) (in thread): > What is that command doing?
Shraddha Pai (10:51:14) (in thread): > Is that how you generated the list of large files?
Alan O’C (10:51:32) (in thread): > Yes it’s a git one-liner I snagged from stackoverflow at some point
Shraddha Pai (10:52:32) (in thread): > That list is showing data for all branches, it looks like.
Alan O’C (10:53:33) (in thread): > Yes, git blobs are branch independent. Branches are just pointers to a series of commits (the most recent being the HEAD), that in turn point to blobs and trees
Shraddha Pai (10:54:40) (in thread): > @Marcel Ramos Pérezyou mention getting collaborators to push a “cleaned-up” copy. You mean cleaned-up by bfg? > I don’t have collaborators per se but I do work on this package on different machines.
Shraddha Pai (10:55:35) (in thread): > I suppose I have to get rid of the pack object… because it still gets added to the final repo that BioC runs BiocCheck on? (ie it’s not a local blob that does not get committed).
Alan O’C (10:55:47) (in thread): > The problem is that anyone who pushes to the repository without first resetting to the cleaned version will add the large files back (along with large diffs usually)
Shraddha Pai (10:56:33) (in thread): > At present it’s just me on two workstations. So I just need to make sure the changes are synced and then clean both separately.
Alan O’C (10:58:38) (in thread): > That would work. You could also push branches from a cleaned version, and then reset the branches on the 2nd machine to the updated versions
Alan O’C (10:59:48) (in thread): > Have you tried adding.gitto a.Rbuildignorefile in the package root?
Marcel Ramos Pérez (10:59:49) (in thread): > i.e. do a fresh clone of the cleaned up version
Alan O’C (11:00:09) (in thread): > Yes that would be simplest, actually
Shraddha Pai (11:00:34) (in thread): > @Alan O’CI have not added .git to Rbuildignore. Is this what you refer to simplest? I’m all for simplest!
Shraddha Pai (11:01:14) (in thread): > OK, yes. I will set machine 1 to have the cleaned version. Make sure there is nothing on machine 2 I want to commit. And then do a fresh clone on machine 2 and work on that.
Alan O’C (11:01:25) (in thread): > I meant that Marcel’s solution (fresh clone on the 2nd machine) is simpler than cleaning the repo twice or resetting branches on the 2nd machine
Shraddha Pai (11:01:34) (in thread): > But first I will add.gitto.Rbuildignorebecause it seems easy.:slightly_smiling_face:
Alan O’C (11:02:45) (in thread): > Unfortunately it doesn’t seem to remove the warning:disappointed:
Alan O’C (11:06:03) (in thread): > I think the issue is that BFG doesn’t remove all references to large objects. I usually usegit filter-branchso I hadn’t considered this. If you run the following commands, it should reduce the size of.gitfrom ~360MB to ~20MB
Alan O’C (11:06:29) (in thread): > > git update-ref -d refs/original/refs/remotes/origin/master > git for-each-ref --format='delete %(refname)' refs/original | git update-ref --stdin > git reflog expire --expire=now --all > git gc --aggressive --prune=now >
Alan O’C (11:07:01) (in thread): > git’s desire to remember everything can be hard to overcome:slightly_smiling_face:
Shraddha Pai (11:07:50) (in thread): > Wow, I had never heard ofgit-filter-branch. I think I need to understand something basic about how git stores and references objects across(?) branches to understand how to use it. > Let me check out yourupdate-refcommand.
Shraddha Pai (11:12:04) (in thread): > OK I ran the command. The.gitdir is still at 17Mb and runningbfgfound no new objects. Strange. Does thepackdir contain some kind of archive of all my data objects, which is why it adds up to 17M? Of course it would be great if it weren’t recognized as an additional object to add to the package.
Shraddha Pai (11:12:29) (in thread): > Maybe I should runBiocCheckon the package tarball instead of the source package?
Marcel Ramos Pérez (11:13:01) (in thread): > @Alan O’CI don’t see the warning
Alan O’C (11:13:11) (in thread): > The pack contains everything ever committed, including all versions of all files, so 17MB is not bad (considering there are quite a few files > 1MB in the git history)
Alan O’C (11:13:33) (in thread): > Unless one of the individual pack files is still very large, you should be fine as-is
Shraddha Pai (11:14:07) (in thread): > Well, that is the issue. The problem pack file is 17Mb. I’m now building the package and will run bioccheck on the tarball. Maybe I won’t see a warning?
Alan O’C (11:15:05) (in thread): > The pack dir is large but it’s split over multiple files. BiocCheck only cares about individual files
Shraddha Pai (11:16:12) (in thread): > I have a particular file that is 17M and for which BiocCheck gave me a warning.
Alan O’C (11:25:36) (in thread): > git repack -a --max-pack-size=5m
Alan O’C (11:25:47) (in thread): > That’ll ensure nothing over 5mb
Hervé Pagès (11:51:04) (in thread): > But why would BiocCheck care about the size of.gitin the first place?
Alan O’C (11:52:33) (in thread): > Fromhttps://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html : > > Checking individual file sizes The current size limit for all individual files is 5 MB. (WARNING)
Hervé Pagès (11:54:11) (in thread): > But aren’t we talking about stuff that is inside.githere i.e. stuff that should not be BiocCheck business?
Alan O’C (11:55:11) (in thread): > Normative claims aside, that is currently not the case and BiocCheck will complain
Hervé Pagès (11:58:45) (in thread): > I understand that it will complain but maybe it shouldn’t.@Shraddha PaiYou could always open an issue herehttps://github.com/Bioconductor/BiocCheck/issues
Shraddha Pai (12:01:18) (in thread): > @Alan O’CI tried thegit replace -a --max-pack-size=5mcommand, but it didn’t help. Maybe because I’m simultaneously developing the test suite and the pack size is changing?
Marcel Ramos Pérez (12:01:19) (in thread): > it shouldn’t complain if it’s included in the.Rbuildignore
Alan O’C (12:01:52) (in thread): > git repack -a --max-pack-size=5mnotgit replace [...]. Weird
Shraddha Pai (12:02:12) (in thread): > Whoops, sorry that was a typo in my slack message, I didn’t copy-paste from command line.
Alan O’C (12:02:41) (in thread): > git shouldn’t repack unless you run git gc or similar again
Hervé Pagès (12:02:52) (in thread): > @Marcel Ramos PérezAFAIK.git/is always ignored byR CMD build. There should be no need to include it in.Rbuildignore.
Shraddha Pai (12:03:34) (in thread): > For the.Rbuildignoresolution to work, I would need to > 1. add to.Rbuildignore2. RunR CMD build3. When I callR CMD BiocCheckI will run it on the tarball and not source package. > And see if this helps.
Shraddha Pai (12:04:02) (in thread): > @Hervé PagèsOK will create an issue for it at the BiocCheck link.
Nitesh Turaga (13:01:13) (in thread): > Hi
Nitesh Turaga (13:01:19) (in thread): > Sorry, I just saw this.
Nitesh Turaga (13:01:23) (in thread): > Do you still need help?
Shraddha Pai (13:48:21) (in thread): > Hi all, OK! So: > - RunningBiocCheck('netDx_0.99.2.tar.gz')works – no warnings > - RunningBiocCheck('netDx')gives a warning about the pack files. > > So I need to just run it on the tarball in the future. I can still create an issue on BiocCheck so that when it’s provided with a package it doesn’t look for large objects in.git. > > Thanks for all your time and help!:star:@Nitesh Turaga@Marcel Ramos Pérez@Hervé Pagès@Alan O’C
Shraddha Pai (14:25:19) (in thread): > H’m. Looks like this issue of.gitnot ignoring large file sizes has already been addressed:https://github.com/Bioconductor/BiocCheck/issues/39
Hervé Pagès (15:00:50) (in thread): > You mean has NOT been addressed because it looks like this is intended behavior. Oh well…
Shraddha Pai (15:38:51) (in thread): > Well, “explained” is what I meant. But yes. Oh well.
Federico Marini (18:15:05): > Congrats@Vince Carey!
Federico Marini (18:15:05): > https://chanzuckerberg.com/eoss/proposals/bioconductor-build-system-continuous-integration-and-developer-feedback/ - Attachment (Chan Zuckerberg Initiative): Bioconductor Build System: Continuous Integration and Developer Feedback - Chan Zuckerberg Initiative
Federico Marini (18:15:49): > … and the same for the team of@Gordon Smyth! ->https://chanzuckerberg.com/eoss/proposals/enabling-differential-analyses-of-genomic-data-with-limma-edger-and-glimma/ - Attachment (Chan Zuckerberg Initiative): Enabling Differential Analyses of Genomic Data with limma, edgeR and Glimma - Chan Zuckerberg Initiative
Aaron Lun (18:18:40): > either I’m getting older, or those undergrads in the photo are getting younger and younger every day.
Federico Marini (18:19:21): > the latter
Federico Marini (18:19:35): > :grimacing:
Ludwig Geistlinger (18:21:05) (in thread): > well these days these kids even publishhttps://www.nature.com/articles/d41586-019-03371-0 - Attachment (Nature): More South Korean academics caught naming kids as co-authors > The practice was probably used to improve the children’s chances of securing a university place.
Aaron Lun (18:21:41) (in thread): > oh that’s smart.
Aaron Lun (18:21:48) (in thread): > gotta remember that trick.
Aaron Lun (18:22:13) (in thread): > 50 author nature paper, who’s gonna know?
Ludwig Geistlinger (18:22:38) (in thread): > Exactly
2019-11-15
Davide Risso (03:46:50) (in thread): > How would that even work? Reviewing college applications: “So I see that you published a paper 10 years ago…”
Kasper D. Hansen (07:05:35) (in thread): > You seem to have peaked with your Nature paper 10 years ago and since the its been a steady decline
Allison (08:42:00): > @Allison has joined the channel
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2019-11-16
Dario Strbenac (19:00:13): > Is gene length bias for gene set enrichment a novel discovery in 2019? > > Recurrent Functional Misinterpretation of RNA-seq Data Caused by Sample-Specific Gene Length Biashttps://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000481 > > Importantly, the way RPKM normalization handles the length effect is based on the assumption that this effect is the same for all samples. > But it’s possible to simply get the gene length of each sample from RSEM and use that as the denominator instead of using the gene length from a gene database.
Rob Patro (19:13:42): > @Dario Strbenacthat was my take as well ( see e.g.https://twitter.com/mikelove/status/1194375671948165125?s=19 ). However,@Kasper D. Hansenhas some reasons to hypothesize that the bias might not be accounted for by the transcript level probabilistic models. - Attachment (twitter): Attachment > @sandakano @EricTopol @TelAvivUni @mandelboum @PLOSBiology @AliciaOshlack
Dario Strbenac (19:25:10): > Oh, I overlooked the preceding discussion.
2019-11-18
Siyuan Ma (11:42:26): > @Siyuan Ma has joined the channel
Mohamed Gunady (12:48:00): > @Mohamed Gunady has joined the channel
Shraddha Pai (13:07:05): > Hi all, on Friday I reopened an issue for new package submission after a couple months (needed lots of changes). Do I need a trigger a package build by the BioC system before the issue gets reopened or is the order the other way around? Someone opens the ticket and then the build system looks for the repo to rebuild it? I have my webhooks set up from when I first opened the issue. Thanks!
Stephanie Hicks (13:11:21): > @Shraddha Pai— did you bump the version number?
Shraddha Pai (13:12:05): > I did, but yes, not in the recent update. Let me try that. Thanks,@Stephanie Hicks.
Lori Shepherd (14:35:38): > For reference: What you did was correct. We would ask that you tag the original reviewer to reopen the issue. The issue will be reopened and we will reactivate the build triggering process on our end (assuming you have kept the webhook intacted) . If all that looks good we will request you bump the version to trigger the new build. Cheers
2019-11-19
Shraddha Pai (08:26:18) (in thread): > Thanks Lori!
Shraddha Pai (08:28:41): > Hi everyone, is there a publicly-accessible Windows environment where I can debug the reason why my package build fails on Windows? I don’t have access to a Win machine. > Based on the error message from BioC build, I made an educated guess as to what the issue was (still think it’s related to file moving and copying) and switched those calls to usefile.copyand related, but I’m still getting the same build error. > Would be great to interactively debug. Thanks!
Federico Marini (08:45:30): > Would r-hub (https://builder.r-hub.io/ ) do the job? - Attachment (builder.r-hub.io): R-hub package builder > R package builder, by the R-hub project of the R Consortium, easing the R package development process.
Federico Marini (08:45:37): > There is also an r client for that
Shraddha Pai (08:47:30): > @Federico Mariniit sounds like it wouldn’t be interactive but presumably the turnaround time for R-hub is faster than with the bioc builder? or is the printout more descriptive?
Federico Marini (08:48:22): > Well the printout is some form of R CMD check (plus the Travis-like part)
Federico Marini (08:48:36): > If this is enough, then it could be a solution
Shraddha Pai (08:49:54): > Ooh, have never worked with Travis. Ok will check it out - thanks.!
Federico Marini (08:57:29): > :wink:
Martin Morgan (09:20:21): > @Shraddha Pailink to the build report that shows the problem and perhaps someone will be able to provide some insight
Shraddha Pai (09:24:40): > Hi@Martin Morgan, thanks. > Build report:http://bioconductor.org/spb_reports/netDx_buildreport_20191118221842.html My guess is, this is the offending function. It involves a lot of file manipulation.https://github.com/BaderLab/netDx/blob/master/R/compileFeatures.R The error mentions not finding a file calledcolours.txtwhich is being moved around by the R file linked to above.
Martin Morgan (09:41:08): > doescolours.txtexist before your java code tries to access it, or is java trying to create the file?
Shraddha Pai (09:46:18): > I put a breakpoint on unix to answer that question. The file exists before the java call. Infact, … a python script createscolours.txt. > I wonder if it’s the python call that isn’t working and the symptom is that the java can’t file the file when it needs it.
Martin Morgan (10:08:36): > sounds like you’ve got an incredibly complicated scenario going here, with R, python, java, and it’s not surprising they’re having problems across platforms… is this really necessary?
Madhuri Sudharshan Gota (11:01:18): > @Madhuri Sudharshan Gota has joined the channel
Hervé Pagès (12:02:50): > @Shraddha Paiwithout having looked at your code, one thing that comes to mind is the possibility of “unlucky timing” on Windows where the Java code tries to access the colours.txt file before the Python code is done writing to the file. This type of issue is particularly sensible on Windows where a process cannot access a file for reading if another process is still holding on the file (Linux/Unix systems have not problem with that). This type of problem is frequent on Windows and is hard to reproduce/debug because sometimes the timing is good and sometime it’s not (e.g. it could be that the process trying to read the file starts only a few milliseconds too soon, or, said otherwise, that the process writing to the file finishes only a few milliseconds too late).
Shraddha Pai (12:30:30) (in thread): > I agree that it’s complicated. Ideally we’d have the resources to have someone rewrite the python code in R because the python really is only being used for that one call. I haven’t personally done work in python (this bit of code wasn’t written by me) and given that everything else is working, I don’t want to open a can of worms to rewrite it and cause new bugs. The java needs to be there.
Shraddha Pai (12:32:11) (in thread): > I don’t know how reproducible the build failure is, to be honest. It’s just failed twice out of two times recently tested. My guess is there is some unix system-level call being made that doesn’t work on windows. It would be great to avoid having to descend into the python code.:cold_sweat:
Hervé Pagès (12:39:19) (in thread): > Wouldn’t you get the error each time if that was the case?
Shraddha Pai (12:40:40) (in thread): > Well, I’ve only tried it twice (via BioC build). And indeed, I got the error each time (2 out of 2). The error is only on Windows so I only realize that through the BioC build. I just got access to a Win machine so now I have to test there. I know, cross-platform compatibility, but ugh.
Hervé Pagès (12:45:51) (in thread): > Good luck. I couldn’t agree more with Martin’s advice to try to simplify the whole scenario though. Keeping things as simple as possible always pays off in the long run…
Shraddha Pai (12:47:07) (in thread): > Yes, I agree. Maybe I can find a python programmer who will rewrite this function for me for a nice lunch out. Thanks Hervé. Will let you know if I get to the bottom of this.
Russ Bainer (16:05:51): > @Russ Bainer has joined the channel
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Martin Morgan (19:48:38): > Just saying that I’m totally impressed byhttps://osca.bioconductor.org – that’s an amazing resource, bringing tremendous value to the community, and a real contribution to advancing science. One small example is the nuanced and intellectually informed discussion of normalization, and the explicit and unambiguous connection with software implementation. Also, I’m a pretty cynical person and fully aware of the rough edges of Bioconductor, but something like > > library(scRNAseq); library(scran) > sce.richard <- RichardTCellData() > sce.richard <- sce.richard[,sce.richard$`single cell quality`=="OK"] > sce.richard <- computeSpikeFactors(sce.richard, "ERCC") > > represents a really profound integration of many complicate software components developed by many independent groups. Amazing! - Attachment (osca.bioconductor.org): Orchestrating Single-Cell Analysis with Bioconductor > Online companion to ‘Orchestrating Single-Cell Analysis with Bioconductor’ manuscript by the Bioconductor team.
Peter Hickey (20:22:00): > Fully agree. It’s an incredible resource, bit of a bible for the people I”m working with
2019-11-20
Aaron Lun (00:42:12): > Should be alibrary(scran)call there, ascomputeSpikeFactorslives inscran rather thanscater .
2019-11-21
Zuguang Gu (06:46:37): > @Zuguang Gu has joined the channel
Stephany Orjuela (10:30:13): > @Stephany Orjuela has joined the channel
Steffen Neumann (11:10:21): > @Steffen Neumann has joined the channel
sonia barbieri (11:35:15): > @sonia barbieri has joined the channel
Sridhar N (17:54:25): > https://twitter.com/useR2020stl/status/1197245866618314752?s=20 - Attachment (twitter): Attachment > We are inviting professionals from all disciplinary fields to submit an abstract for talks and poster for #useR2020! Deadline February 3, 2020. Click below for submission process and requirements! > > https://user2020.r-project.org/news/2019/11/20/call-for-abstracts/ https://pbs.twimg.com/media/EJ14xOTXUAA-S-W.jpg
Aaron Lun (19:41:53): > Do we have any 10x Genomics folks here?
Aaron Lun (19:44:20): > Or people who can put me into contact with their CellRanger devs?
Sridhar N (19:55:58): > i can
Sridhar N (19:56:00): > wats up
Aaron Lun (19:57:11): > I’d like to know what thelibrary_idsandoriginal_gem_groupsare in the attributes of the matrix HDF5 file.
Aaron Lun (19:58:10): > Any docs would be good, the only reference I see is “The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes.”
Sridhar N (20:04:02): > i will shoot this to ian fiddes
Aaron Lun (20:04:16): > :+1:
Aaron Lun (20:05:01): > The motivation is thatDropletUtilshas awrite10xCounts()function that purports to create a HDF5 matrix in the CellRanger format.
Sridhar N (20:05:26): > dang
Sridhar N (20:05:30): > he left
Sridhar N (20:05:34): > 10x lol
Sridhar N (20:05:44): > 4 months back
Aaron Lun (20:06:07) (in thread): > Its real purpose is to geneerate some files for me to use for testingread10xCounts(), but ever since I’ve exposed it, people seem to have been using it and expecting that the files are ingestible bycellranger analyse. Which I guess is sort of reasonable to expect.
Sridhar N (20:07:15) (in thread): > Stephen Williams is still there i can ask him
Aaron Lun (20:09:44) (in thread): > :+1:
2019-11-22
Lluís Revilla (03:55:41): > Is there a way to undelete a post fromsupport.bioconductor.org and recover the answers/messages on that thread?
Lluís Revilla (03:56:19): > I deleted a postp/126575/and later I realized I got some messages that now I cannot read fully
Martin Morgan (05:06:17): > @Lluís Revillayes, a moderator can do that. I am a moderator. Do you want me to undelete your post?
Lluís Revilla (05:08:36): > Yes, thanks@Martin Morgan!
Martin Morgan (06:26:38): > Ok@Lluís Revillait’s been undeleted
Jared Andrews (09:52:08): > Is there a mechanism for contacting/leaning on devs of packages that have moderately serious bugs that are well-known, long-standing, and easily fixable that are not answering users (via the Bioconductor support forum or e-mail)?
Federico Marini (10:00:25): > Piggybacking on this: … or changing some behaviors that for example are not supposed to be in nowadays? Talking aboutDepends:overusage, or having to depend on these packages instead of importing them
Vince Carey (10:35:26): > @Jared Andrews@Federico Marinisend me an email with some examplesstvjc@channing.harvard.edu and maybe some options can be proposed after internal discussion
Federico Marini (10:35:48): > Will do Vince, thanks
Jared Andrews (10:35:54): > Thanks!
Leonardo Collado Torres (11:51:03): > Has anyone been able to use RStudio Cloudhttps://rstudio.cloud/ for some SC stuff? I just started playing around with it and it took me several “aborted sessions” to installSingleCellExperiment,iSEE,scRNAseqandscater. Now that they are all installed, I keep getting stuck in thelogNormCounts()step in the example ofiSEE::iSEE()
Leonardo Collado Torres (11:51:47): - File (PNG): Screen Shot 2019-11-22 at 11.51.27 AM.png
Leonardo Collado Torres (11:51:55): > my guess is that it needs more memory
Kevin Rue-Albrecht (11:52:53): > I’ve played with it for the RStudio Shiny competition quite a bit, and I kept running into crashes because of memory limitations. I ended up making a small SCE from a subset of Allen to get iSEE to run for our submission to the competition
Leonardo Collado Torres (11:53:14): > ohhh ok, thanks!
Kevin Rue-Albrecht (11:54:43): > Here is a Dropbox-hosted RDS file of the Allen subset that I used, if you want to try:https://www.dropbox.com/s/yps03y6ws8rtc1h/allen.subset.rds?dl=1 i.e.,curlit from your Cloud session toreadRDSit from there
Vince Carey (12:20:52) (in thread): > For those interested in this topic, we are confronting specific examples and will report back. The general policy for package end-of-life ishttp://bioconductor.org/developers/package-end-of-life/ and the “adoption” concept is relevant to what we are discussing.
Leonardo Collado Torres (12:36:03): > Thx!
Hervé Pagès (13:00:46) (in thread): > Next thing I would try after the Bioconductor support forum is to open an issue on GitHub (assuming their package is on GitHub of course).
Jared Andrews (13:01:44) (in thread): > It is not, unfortunately.
2019-11-25
Shraddha Pai (18:32:12) (in thread): > Hi@Hervé Pagèsand@Martin Morgan, wanted to loop back about this matter. I got hold of a Win machine and it turns out that Windows didn’t like the system call to python. > > SO, I bit the bullet and converted the python script to R. > Ended up taking about a day, but I also found some inefficiences that I tracked down. So now the package no longer depends on python (which is great). > > The change seems to have resolved the build issue in Windows. Now I just have warnings likeWARNING: Update R version dependency from 3.6 to 4.0.and one pertaining to the use ofresave-data. > > Thanks for your input!
Hervé Pagès (18:45:03) (in thread): > Was this an encoding issue or a bytes-versus-string issue? In my experience running Python 3 code on Windows often reveals this type of problems and these problems are typically not seen on other platforms (and not seen on Windows either when running the code with Python 2). This is almost always due to a dormant bug in the Python code though so is worth reporting to the authors/maintainers of the code. Anyway it’s great that you were able to get rid of the Python dependency and at the same time came up with a replacement that works and is faster!:+1:
Shraddha Pai (19:08:46) (in thread): > Yes, I’m glad to be rid of the weird dependency as well. > > It was a path issue of some sort, far as I can tell. The code made asystem2('python',...)call and Windows just ignored it. Which caused downstream operations to crash. Wasn’t worth it to get intoreticulateetc.,
2019-11-26
Stephanie Hicks (20:05:58): > I’m thinking of starting a #spatial channel for spatial analyses in bioc to form a “working group” of sorts to discuss what’s currently been done and how we can work towards developing data infrastructure and methods for spatial analyses in bioc. Would this be of interest to others? one question I have is it should be more specific for e.g. gene expression (#spatialexprs) or general enough to include other omics e.g. proteomics (e.g. #spatial) too?
Ambrose Carr (21:45:36) (in thread): > In my experience, spatial protein expression use cases are similar enough to merge (at least for now).
Kasper D. Hansen (22:32:56): > My guess is that a strong differentiator is going to be the resolution and type of spatial registration. Assuming we have single cell data (which is an assumption) we have a matrix of quantifications with cells x samples and then we have an object giving spatial information for each cell. At this level there seems to be little difference between proteomics and expression. This becomes more complicated - I think - for sub-cellular resolution.
2019-11-27
Justin Kiggins (00:42:16): > @Justin Kiggins has joined the channel
Kevin Rue-Albrecht (03:50:06) (in thread): > setGeneric channel first. You can setMethod-specific channels later as they arise:yum:
Casey Greene (05:08:39) (in thread): > Would it also work for the 10X platform data? I have a strong interest in having a good solution arrive for this by, say, Q2 of next year. If be interested in lurking
Stephanie Hicks (08:44:51) (in thread): > @Casey Greene— I think it would be nice to have one data infrastructure (i.e. theoretically should include 10X), but join#spatialand let’s find out!:slightly_smiling_face:
Stephanie Hicks (08:45:35): > Ok, anyone interested in spatial data infrastructure and analysis in bioc is welcome to the#spatialchannel to discuss morehttps://community-bioc.slack.com/archives/C35G93GJH/p1574816758301800 - Attachment: Attachment > I’m thinking of starting a #spatial channel for spatial analyses in bioc to form a “working group” of sorts to discuss what’s currently been done and how we can work towards developing data infrastructure and methods for spatial analyses in bioc. Would this be of interest to others? one question I have is it should be more specific for e.g. gene expression (#spatialexprs) or general enough to include other omics e.g. proteomics (e.g. #spatial) too?
Casey Greene (08:56:44) (in thread): > Ok! I have none of the necessary expertise to help build it but I am looking forward to robust solutions:joy:
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Dario Strbenac (19:00:12): > How can memory-efficient objects such asDelayedMatrixoperate with existing R functions? For example, > > TC = counts(tenx) > RF = randomForest(x = t(TC), y = sample(LETTERS[1:2], ncol(TC), replace = TRUE)) > Error in storage.mode(x) <- "double" : > no method for coercing this S4 class to a vector > > Is there any vignette that explains how to hack existing code?
Kasper D. Hansen (19:40:39): > Some code won’t work out of the box, although the intention is that data will get read into an in-memory matrix (bad idea)
Kasper D. Hansen (19:41:08): > To really take advantage of this you need code which accesses the data and does the computation in a piecewise fashion
Dario Strbenac (19:45:12): > Ah, so it would be hard to benchmark againste0171orrandomForestwithout first changing their implementations, for instance.
Kasper D. Hansen (20:00:57): > Most likely
Kasper D. Hansen (20:01:42): > In my experience, run naively, algorithsm on DA objects are much slower, because they are typically written in a fashion that makes sense for in-memory calculations
Kasper D. Hansen (20:02:50): > We are still learning, but my current impression is that you need a substantial amount of re-engineering to be performant.
Dario Strbenac (20:05:15): > Either that or RAM. > > %Cpu(s): 52.7 us, 1.0 sy, 22.0 ni, 24.3 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st > GiB Mem : 1007.883 total, 608.184 free, 63.360 used, 336.339 buff/cache >
Kasper D. Hansen (20:38:34): > So this is a side effect. If you take a DelayedArray object and pass it into a standard R function, chances arevery high that the standard function will try to do something that DelayedArray doesn’t understand.
Kasper D. Hansen (20:39:27): > When that happens, there is a function which takes your DelayedArray object on disk and converts it into an in-memory matrix. When that gets triggered, it will read everything into memory (and there is really no point in having it as DelayedArray anymore)
Dario Strbenac (20:40:30): > Good to know. But, I was just suggesting I could use an ordinary matrix with the amount of RAM which the server has. It’s not from an actual run usingDelayedMatrix
Kasper D. Hansen (20:43:22): > To avoid all of this, you want to construct your algorithm so it only ever accesses part of the data, for example with row-wise or column-wise calculations. Depending on algorithm this can be easy or hard.
Kasper D. Hansen (20:43:43): > If you have it on disk you may also want to minimize passes over data
Kasper D. Hansen (20:44:48): > By which I mean, I often code stuff which looks like this > > y = f1(x) > z = f2(y) >
Kasper D. Hansen (20:45:37): > You don’t really need y. So you might want to code it more like > > z = f2(f1(x)) >
Kasper D. Hansen (20:46:29): > There is some magic in DA which does some of this for you, but sometimes that magic doesn’t work (as you can see, I am 100% on top of the basic concepts here).
Kasper D. Hansen (20:46:49): > This is partly where the “Delayed” comes in.
Aaron Lun (22:05:53): > Well, backing up a second, why do you want to run a RandomForest on (presumably) the TenxBrainData?
Dario Strbenac (23:00:04): > I have an R package which wraps around common classifiers such as logistic regression and random forests to do performance evaluation (S4-centric and similar to caret). I was wondering how much development would be involved in making it work with a delayed container as simply as it works on adata.frameobject. I picked TENxBrainData for no particular reason other than it has aDelayedMatrixwith real data ready to try out. In reality, you would probably use something more specialised than those classifiers, but I’m exploring the software implementation rather than a particular analysis.
2019-11-28
Alan O’C (05:17:38): > Why re-re-invent the wheel given that caret and tidymodels exist?
Alan O’C (05:20:27) (in thread): > I might be mistaken but I’m fairly sure that R will assignf1(x)to a temporary variable, so these will be equivalent (except that y will stop garbage collection until out of scope)
Dario Strbenac (06:30:06) (in thread): > I wanted to have some different evaluation criteria than those packages offer and also work seamlessly with Bioconductor data types such asMultiAssayExperimentandDataFrame. Caret is plain R and doesn’t use classes to package results nicely or check input types like defining withsetMethoddoes.
Alan O’C (09:17:19) (in thread): > Fair enough. I would be more inclined to add the criteria to yardstick but I can see some value in having modelling packages that can interface with Bioc classes
Alan O’C (09:18:00) (in thread): > Although again I think you might get better value for time by working with the existing frameworks rather than re-implementing wrappers for hundreds of models
Vince Carey (10:52:38) (in thread): > Interfaces between ML and Bioc data structures are of value and were a concern of the early MLInterfaces package.@Dror Berelhas written a medium post on the topichttps://towardsdatascience.com/meta-machine-learning-packages-in-r-c3e869b53ed6 … perhaps we should start a channel on this topic? - Attachment (Medium): ‘Meta’ machine learning packages in R > Do you remember learning about linear regression in your Statistics class? Congratulations! You are now a fortunate member of a diverse…
Dario Strbenac (19:00:10) (in thread): > Oh, I won’t implement so many models myself. I have implemented about a dozen common wrappers and a couple for gene set / gene network based classification (which is more suited to bioinformatics than generic classification tasks) and have a specified set of rules for users to develop their own wrappers for other functions. Version 1 had support forExpressionSetandmatrixbut Version 2 supportsmatrix,DataFrameandMultiAssayExperiment. Apart from my ClassifyR (seehttps://bioconductor.org/packages/release/bioc/vignettes/ClassifyR/inst/doc/ClassifyR.html for a short overview) and the MLinterfaces packages developed by Vincent, there is MCRestimate and CMA which are two other Bioconductor packages with the same goals as ClassifyR and MLinterfaces. I could participate in a channel and have created machine-learning.
Dror Berel (19:12:37) (in thread): > Bioc2mlr is a small utility package that attempt to demonstrate how “flatten” bioconductor S4 assay objects could be bridged and used by meta machine learning unified aggregator packages (mlr is my favorite). It is basically going the other way instead of bring them all into S4. Basically its a simplified way to connect them, but have to “break” the knots of the S4. > I would argue that the best way to win both S4 assay objects with ML is to write recipes/CPO monads that implement common Bioconductor procedures, e.g. limma’s eBayes etc.https://drorberel.github.io/Bioc2mlr/ - Attachment (drorberel.github.io): What the Package Does (Title Case) > More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
2019-11-29
Alan O’C (08:23:28) (in thread): > I’d be interested in contributing to Bioc2mlr, though probably more on the caret/tidymodel side as I’ve never used mlr
Dror Berel (10:50:46) (in thread): > Hi Alan, > Bioc2mlr was developed over 1 years ago as a proof of concept, when tidymodels and mlr3 were still in early development. Today there are probabaly neater ways to refactor it on both bioconductor and mlr3/tidymodels side. I am excited this suggested approach finally get some attention.
Alan O’C (10:51:36) (in thread): > Probably for the best in the end - caret is being deprecated in favour of tidymodels, which afaik is still in development :)
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2019-12-03
Dario Strbenac (01:45:07): > Does anyone have experience with total RNA-seq data analysis? If I have some samples with 30% of reads mapping to GENCODE Genes’ exons and others with 75% in exons. That suggests some samples have more nuclear (unspliced) RNA sequenced and others have more cytoplasmic (introns were spliced) RNA. The samples were processed in the same batch. Counting in exons might mean trouble if comparing between samples. Any creative workarounds?
Federico Marini (03:04:29): > If the %s would be more similar, it would be interesting to do the intron level analysis. > Aside from the creativity: can you really consider them samples as “replicates”?
Dario Strbenac (06:30:08): > Probably not. They are all cancer samples of the same type of cancer, but I don’t think it’s likely that the large differences are biological (intron retention) but something else.
Stevie Pederson (06:57:01) (in thread): > I assumed rRNA has been looked at? Is there variability in that GC spike above the main peak which usually screams rRNA? They often show up in overrepresented sequences too. I usually work in non-human samples, but I find the rRNA removal kits to be very inconsistent in non-human samples.
Ludwig Geistlinger (10:39:56) (in thread): > Maybe it’s worth taking a look here:https://www.biorxiv.org/content/10.1101/352823v2
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Russ Bainer (13:56:27) (in thread): > I agree that the amount of variation you are talking about really sounds technical. rRNA is a possible culprit, but it could also be related to sample quality or contamination. > > More generally examining the mapping locations of the non-exonic reads would probably be a good place to start (e.g., verify that most of them map successfully to intronic sequences).
Hervé Pagès (14:00:55): > Package downloads passed the bar of 80k distinct IPs for the first time in November:https://bioconductor.org/packages/stats/bioc/index.html :sunglasses:
Dario Strbenac (14:30:03) (in thread): > I’ll check that it’s really intronic and not some weird unannotated intergenic location.
Jenny Drnevich (14:59:10) (in thread): > @Michael Love- as to your first thought above: I’m analyzing a data set that had lots of DE ribosomal proteins so I checked for the gene length bias ala Mandelboum et al. and it was present, even though I’m using Salmon (with the lengthScaledTPM instead of offsets). I also think it is unusual that most short genes end up down-regulated OR up-regulated instead of an even mix of both if they are random, sample-specific biases. I’ve been playing around with all 126 permutations of 10 individuals into two groups and 120 of them have significant Spearman correlations (71 pos and 49 neg) based on the threshold used in the paper (p < 10e-8). Thoughts? I’m off to try cqn…
Michael Love (15:02:21): > @Jenny Drnevichre: Salmon, if there was a sample specific bias wrt length, my opinion is that you’d need to use the positional bias flag to capture it (or use cqn or EDASeq to capture it post hoc). the only default bias which Salmon estimates that would help is the FLD (fragment length dist) but it’s not my opinion that this is the main culprit
Michael Love (15:03:12): > i recommend with my collabs to always use MultiQC and then you can pick what bias flags to use. i basically always use GC since it is so common, but don’t always use positional bias flag unless i see it in the QC plot
Michael Love (15:05:58): > e.g. here is the kind of QC plot you could get from RSEQC (which MultiQC can collate) - File (PNG): image.png
Jenny Drnevich (15:09:11): > @Michael Lovewe used –seqBias and –gcBias but not –posBias. Thanks for the example - you’d run –posBias on this because of the two different sets of distributions, or just whenever you see 3’ bias instead of even distribution?
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Michael Love (16:50:20): > I guess whenever I saw differential (across samples) or extreme coverage bias
2019-12-04
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Jenny Drnevich (10:36:42) (in thread): > Are you running RSeQC on bams from genome or transcriptome alignments?
Michael Love (13:57:58) (in thread): > genome – most of my collaborators perform genome alignment as well, and then Salmon separately either by projecting genome alignments or just in read mode
Jenny Drnevich (15:57:21): > @Kasper D. Hansen@Michael LoveAny thoughts on combining Salmon with cqn? Since cqn adjusts for both GC content and gene length, should I not run Salmon with –gcBias? I think I should still adjust for transcript length differences when summing to gene level with tximport, but then what to use for a single gene length for all samples - the median gene length? I am seeing a correlation between gene length and fold-change like in the Mandelboum et al. paper, and also a troubling trend for up-regulated genes having longer gene lengths and down-regulated genes having shorter gene lengths. cqn does seem to remove both of these effects, so I want to make sure I’m using it right.
Kasper D. Hansen (15:59:21): > cqn is a post alignment fix. I see no issues in using it together with Salmon
Dario Strbenac (16:00:01): > 10 years ago, when I analysed my first RNA-seq data set, I thought we would have full length transcriptome sequencing be commonplace in 10 years’ time. Interesting that it’s still mostly short Illumina reads!
Kasper D. Hansen (16:00:39): > “all” it does is fitting a restricted cubic spline as a function of gene length and then forming the residuals. I don’t see why that shouldn’t work and I don’t think the precise gene length is essential
Kasper D. Hansen (16:01:20): > I mean, all you’re doing is forming residuals. Of course, its probably true that the right gene length yields a better model, but it is really not doing anything fancy
Michael Love (16:18:16): > @Jenny Drnevichyou can just use cqn if you know it works and dont want to do the pos bias rerun (which may or may not work). For inputting to cqn id recommend counts-from-abundance to avoid double correcting for GC bias
Michael Love (16:19:07): > For further Qs lets switch to support site to make the thread searchable / findable to others
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2019-12-05
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Sean Davis (07:01:48): > I posted a new fellowship opportunity in#jobs.
Michael Love (08:51:47) (in thread): > i agree the precise gene length isn’t essential for the estimation of the curve, more for the per-gene offset
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Aedin Culhane (19:20:57): > Slides from our webinar describing the data challenges and abstract submission forMathematical Frameworks for Integrative Analysis of Emerging Biological Data Types meeting @Kim-Anh Lê Caohttps://vimeo.com/376936827 - Attachment (Vimeo): BIRS meeting webinar Dec 2nd 2019 > Information Webinar on Data Challenges for the meeting, Mathematical Frameworks for Integrative Analysis of Emerging Biological Data Types, to be held, June 14- 19, 2020 in Banff, Canada.
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2019-12-06
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Hervé Pagès (19:54:29): > New in devel: a DataFrame can now be transposed and the types of the variables preserved. Can be useful if one wants to store “horizontal” variables in theassaycomponent of a SummarizedExperiment derivative. See?TransposedDataFramein S4Vectors >= 0.25.6
Aaron Lun (19:55:10): > Woah:konata:
Aaron Lun (19:55:34): > That’s pretty freaky. What’s the use case?
Hervé Pagès (20:01:03): > Not really sure:nerd_face:Was kind of motivated by an devteam internal discussion we had about this submission:https://github.com/Bioconductor/Contributions/issues/1265#issuecomment-558379564 I’m not the reviewer but my understanding is that they’re trying to come up with some data structure analog to SE but where the layout is transposed. I don’t like it and I think we should stick to SE and allow people to transpose their DF if they want.
Hervé Pagès (20:02:11): > So this is an attempt to prevent some damage:wink:
Aaron Lun (20:03:37): > Sometimes people store mass cyt data with features in columns and cells in rows, so this might also see some use there to properly fit it in an SE. Yes, I know, they could just transpose the matrix, but they don’t want to.
Hervé Pagès (20:05:13): > Right, if they have a matrix there is no excuse for not transposing it. But if they have a DF with heterogeneous variables, they had no choice, until now.
Aaron Lun (20:05:50): > And now I can abuse the S4 system even more, but storing per-feature nested DF’s in each transposed row…
Aaron Lun (20:05:53): > Oh yeah.
Hervé Pagès (20:07:45): > DataFrames nested in TransposedDataFrames nested in DataFrames nested in … oh yeah! Largely untested and display might be ugly.
Aaron Lun (20:08:45): > I’ll go one better. I’ll use SingleCellExperiment’s transposed SE class; store that as a column in a DF; and then convert that DF to a TDF; so that each row of an SE is itself an SE.
Aaron Lun (20:08:48): > And repeat.
Hervé Pagès (20:09:34): > Not sure your users will like it. Let me know how it goes.
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2019-12-07
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2019-12-09
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Robert Castelo (12:16:03) (in thread): > Hi, sorry for the late reply, we did recently a total RNA-seq data analysis, which is part of this preprint (https://www.medrxiv.org/content/10.1101/19000109v2 ), and you probably want to produce a barplot such as the one i’m attaching (from Fig. 1 in the preprint). We also observed about 1/3 of exonic exons only. - File (PNG): SequencingDepth.png
Dario Strbenac (18:00:08) (in thread): > @Charity Law, it appears that exonic read proportion can be quite low.
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2019-12-10
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Avi Srivastava (11:12:15): > For peeps interested in spatial single cell data
Avi Srivastava (11:12:16): > https://satijalab.org/seurat/v3.1/spatial_vignette.html - Attachment (satijalab.org): Satija Lab > Lab Webpage —
Avi Srivastava (11:13:49) (in thread): > 10x has shared some great dataset as well for their visium protocolhttps://www.10xgenomics.com/solutions/spatial-gene-expression/ - Attachment (10x Genomics): Spatial Gene Expression - 10x Genomics > Spatial Gene Expression Visualize Gene Expression within Tissue Organization Contact Me Request Pricing Watch to learn about where researchers see the Visi
Davide Risso (11:14:39) (in thread): > Nice! I’ll forward to the#spatialchannel
Avi Srivastava (11:16:01) (in thread): > Oh sorry about that, I didn’t know about the channel.
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2019-12-11
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2019-12-12
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Shraddha Pai (19:22:37): > Hi everyone, I’m getting an error withR CMD CHECK, saying that it doesn’t know what the functionseqlevels(), used in an R function, is. I use it in the context of getting levels of aGRangesobject. I’ve tried@import GenomicRanges,@import GenomeInfoDband@importFrom GenomicRanges seqlevels. > None of these work. The?seqlevelscommand says that the function is from theGenomeInfoDbpackage. > How can I resolve this? > Thanks!
Aaron Lun (19:23:57): > I guess you should try@importFrom GenomeInfoDb seqlevels.
Shraddha Pai (19:26:36): > I think I did try that… (although I didn’t mention it above)… but let me try again.
Shraddha Pai (20:20:08): > @Aaron Lunif I add@importFrom GenomeInfoDb seqlevelsI get:Namespace dependency not required: 'GenomeInfoDb'
Aaron Lun (20:20:28): > Well, you would have to add it to yourImports:.
Shraddha Pai (20:38:01): > Ok, I added the@importFromtag in the R file (as mentioned above) and also addedGenomeInfoDbinImports:in theDESCRIPTIONfile. > The error is still the same as above.
Aaron Lun (20:38:52): > don’t know what to say here, that’s how csaw does it and it works fine.
Aaron Lun (20:38:53): > https://github.com/LTLA/csaw
Shraddha Pai (20:53:33): > Ah, the link to LTLA is helpful, thank you. Also just realized my build script was using an outdated version number (I just updated it for merge). Let me try again.
Shraddha Pai (22:57:16): > Hey@Aaron Lun, thanks for the LTLA link. After a few more similar errors (now resolved), the packages passescheckandBiocCheckwith no errors or warnings.:smile:Halleluiah. Thanks for your help.
2019-12-13
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2019-12-15
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2019-12-17
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2019-12-18
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Federico Marini (15:40:03): > Hi, I’d have a somewhat general question. > Input: a list of polyphosphate-binding proteins > Desired output: some fine grain expression level/detection in particular cell types (e.g. macrophages)
Federico Marini (15:42:25): > Starting more general, I was thinking of > * gtex > * HPA > * gxa (from EBI) > Plus, some more specific (yet tinier) databases, but these will not cover the spectrum of the cells
Federico Marini (15:42:57): > Any suggestion on this is highly appreciated:pray:
Jared Andrews (16:02:34): > Are you just looking for protein expression databases?
Federico Marini (16:03:21): > Also “classical” mRNA
Federico Marini (16:03:39): > (I’d add to my own list the good old immgen)
Jared Andrews (16:05:10): > Any particular cell types of interest or just need well-defined groups/tissues?
Federico Marini (16:08:04): > Blood cell types, mostly.
Federico Marini (16:08:53): > macrophages, platelets (at least these are two focal interests for the person that requested this)
Federico Marini (16:09:41): > ((another add:https://amp.pharm.mssm.edu/archs4/ ) ))
Aaron Lun (16:11:02): > Well, if you find another reference, I’m happy to throw it into SingleR. At some point we could probably cut this out into another data package, we already have 8 I think.
Federico Marini (16:11:36): > true, I could also check out that vignette
Jared Andrews (16:11:40) (in thread): > Lots of the databases where we grabbed the reference datasets for SingleR will be helpful for this. Blueprint and HCPA both have erythryocytes I think.
Federico Marini (16:12:07) (in thread): > Excellent, added to the list
Jared Andrews (16:12:07) (in thread): > Oh, and DMAP.
Jared Andrews (16:12:38) (in thread): > At least some of those have macrophages.
Federico Marini (16:15:11) (in thread): > Got a link (unambiguous) for DMAP? Or is the resource re: connectivity map
Jared Andrews (16:16:26) (in thread): > Sorry, used to be hosted by the Broad as DMAP, but they took it down apparently. Data is here:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24759 - Attachment (ncbi.nlm.nih.gov): GEO Accession viewer > NCBI’s Gene Expression Omnibus (GEO) is a public archive and resource for gene expression data.
Federico Marini (16:18:16) (in thread): > Uh, on that line:https://www.haemosphere.org/ - Attachment (haemosphere.org): Haemosphere > Gene Expression Analysis Tool
Federico Marini (16:18:42) (in thread): > that’s good for hematopoietic dev datasets
Jared Andrews (16:21:22) (in thread): > Yeah, I think I found this but creating the reference sets for SingleR was enough of a hassle that I didn’t feel like doing it for more immune/blood sets.
Vince Carey (16:21:23): > If you would be looking for RNA-seq studies in which a PP-binding protein varies you could use HumanTranscriptomeCompendium code shown in the EuroBioc 2019. Here is an example getting boxplots for one possibly relevant gene, over 2000 samples from the BigRNA project > > sym = "C4BPB" > par(mar=c(13,4,3,3), las=2) > nsamp = 2000 > library(SummarizedExperiment) > library(HumanTranscriptomeCompendium) > ht = htx_load() > ht = addRD(ht) # i forgot some annotation > onepp = which(rowData(ht)$gene_name==sym) > tag = paste0(ht$study_accession, ":", substr(ht$study_title,1,35)) > boxplot(split(as.numeric(log(assay(ht[onepp,1:nsamp])+1)), > tag[1:nsamp]), cex.axis=.35, ylab=sprintf("log %s + 1", sym)) > > What cell types are involved? You would have to look at the study annotations… OmicIDX
Federico Marini (16:22:45): > Excellent pointer Vince, thanks!
Vince Carey (16:23:31): - File (PNG): c4bpb.png
Federico Marini (16:24:20) (in thread): > A db-dump from their side could actually be feasibl
Federico Marini (16:24:22) (in thread): > e
Federico Marini (16:25:24): > I’ll pass all the info to my collaborator, but also store these bits - I’ll try to wrap up some kind of permanent record (at least more permanent than slack)
Jared Andrews (16:25:32) (in thread): > If somebody else wants to make one, I’m all for it. There was enough manual buffoonery in my initial pass to last me for a while though:upside_down_face:
Federico Marini (16:28:55) (in thread): > You should try to ping the developer team behind it
Federico Marini (16:29:13) (in thread): > at least, say, if you really want to have their extra ref
Federico Marini (16:30:50) (in thread): > > HCPA both have erythryocytes I think. > HCPA would be the HPA?
Jared Andrews (16:52:28) (in thread): > Human Primary Cell Atlas, not sure if that’s what you’re referring to.
Federico Marini (16:56:52) (in thread): > Ok, I was meaning human protein atlas
Federico Marini (16:56:57) (in thread): > so, one more to the list
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2019-12-19
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Shubham Gupta (20:28:55): > I face a WARNING on Bioconductor build. It says > > Checking R Version dependency... > * WARNING: Update R version dependency from 3.6 to 4.0. > > The latest version I see is 3.6.2 on the R project website. Does anyone know what is causing this warning?http://bioconductor.org/spb_reports/DIAlignR_buildreport_20191219202412.html
Shubham Gupta (20:29:41): > This warning is withR CMD BiocCheck
Shubham Gupta (20:33:20) (in thread): > When I build the packageR CMD buildIt adds it automatically to support some data/datalist
Shubham Gupta (20:33:39) (in thread): > Therefore, I decided to have it hardcoded
Dan Bunis (20:34:03) (in thread): > R-4.0 is under development, but it is obtainable && what the next release of Bioc will be built for.
Dan Bunis (20:34:51) (in thread): > I had the same issue myself until I upped the line toDepends: R (>= 4.0)
Shubham Gupta (20:34:53) (in thread): > Yeah I do see that in build_report it uses****RVersion****: 4.0
Shubham Gupta (20:35:43) (in thread): > Is there a way to tell bioconductor to test it on lesser version? Otherwise no one is going to be able to install the package.
Dan Bunis (20:37:10) (in thread): > Idk. You should post that outside this thread where others are likely to see who might know better.
Dan Bunis (20:38:20) (in thread): > But what I did for dittoSeq (https://github.com/dtm2451/dittoSeq ): > I have my submitted version in the master branch of my github, and a stable pre-submission version that still has the R 3.6.2 line in another branch. Then I direct users to install from the proper branch.
Shubham Gupta (20:40:30) (in thread): > This is a good workaround. Did you try to FLAG it to the reviewer?
2019-12-20
Dan Bunis (00:41:37) (in thread): > I did not. And I don’t see this as an issue worth bringing up to a reviewer. It makes sense to me for Bioconductor devel to operate off of the version of R that it will be released on.
Robert Ivánek (07:20:41): > Hi, I realised that the website of the EuroBioc2016 meeting is down. I still have all the materials/slides, would be possible to create a Biocnductor/EuroBioc2016 repository so I can upload the content there?
Martin Morgan (10:56:45): > I’ve created a repository and invited you as a collaborator; let me know if I can help in any way, we’ll try to update our links to the material once it’s there…
2019-12-22
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2019-12-23
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2019-12-24
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2019-12-25
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2019-12-30
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2019-12-31
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2020-01-03
Robert Ivánek (06:49:27) (in thread): > Dear Martin, I have just copied the content there, intodocsfolder. I did the setup according to the EuroBioc2019 meeting’s website. Thanks for linking it. And all the best for 2020!
2020-01-05
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2020-01-07
Andrew McDavid (23:20:07): > Is anyone (especially@Hervé Pagès) running R devel r77631 yet? I can’t get S4Vectors to create aDataFrame, it dies withDatFrm> df <- DataFrame(score) # single column****Error in is(listData[[1L]], getClass("Annotated")) : ******** trying to get slot "className" from an object of a basic class ("character") with no slots****, and i’m trying to figure out if it’s something about my machine or if this breaks in the newest R snapshot.
Andrew McDavid (23:23:41): > On a related note, if anyone is on a Mac and is struggling to compile R devel, I’ve got notes posted here:https://amcdavid.github.io/2019/12/Compiling-R-From-Source
Hervé Pagès (23:44:51): > Looks like you ran into this:https://github.com/Bioconductor/S4Vectors/issues/58
Andrew McDavid (23:54:53): > Ah yes. And I now see that build r77637 is available, which I just compiled, and indeed it does fix the issue:+1:
2020-01-08
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2020-01-10
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2020-01-11
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2020-01-12
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2020-01-13
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2020-01-14
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2020-01-15
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2020-01-16
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Aedin Culhane (11:03:28): > What do people this of Calendly? useful, trustworthy etc???
Jared Andrews (11:39:10) (in thread): > Don’t know, have only used Doodle polls, which always worked well for me.
Sean Davis (14:49:15) (in thread): > @Aedin Culhane, don’t know about trustworthy, but I have been using calendly lightly as one approach for contacts.https://seandavi.github.io/#contact see book an appointment. - Attachment (seandavi.github.io): seandavi(s12) > Senior Associate Scientist
2020-01-17
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Aedin Culhane (12:38:38) (in thread): > Thanks:wink:
Aedin Culhane (12:40:15) (in thread): > Sean for yourgithub.io page, did you play around with different githhub web templates ? Whats the easiest (quickest) to implement, maintain etc
Jared Andrews (12:46:18) (in thread): > Pretty much any of the Jekyll templates are super easy. There are some geared specifically towards academics that are quite good.
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Sean Davis (17:55:31) (in thread): > I use a very slightly customized Hugo Academic theme, create the website with blogdown (again a little customization), and push to github pages with ghp-import. The entire site is public on github.
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2020-01-19
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2020-01-20
Stuart Lee (00:21:02): > would anyone be able to help me with this package maintenance issue? i’m not sure what’s gone wrong… the vignette for my package is not building on all platforms in devel and release (http://bioconductor.org/checkResults/devel/bioc-LATEST/plyranges/ ). Should I just wait it out and see? Looks like a knitr issue.
Stuart Lee (00:21:44) (in thread): > oops I see@Hervé Pagèsis already on the casehttps://github.com/yihui/knitr/issues/1797
Federico Marini (02:14:36) (in thread): > Yep, quite some packages are affected
Stephanie Hicks (06:39:27) (in thread): > Oh thanks@Stuart Leefor asking! I saw the email about one of my packages failing but was ignoring it until back in the office today. Ok sounds like it’s being worked out.
2020-01-27
Teun van den Brand (12:05:46): > On the topic of data frames and S4-object columns, does anyone know why there is noformat()method for our favorite classes? A while ago I was struggling to understand why I wasn’t able to put aGRangesobject in a base R data.frame column, but I think (perhaps naively?) that writing a format method solved my issue. (related SO question here:https://stackoverflow.com/questions/59370461/granges-as-column-in-basedata-frame/59935327 ) - Attachment (Stack Overflow): GRanges as column in base::data.frame > I would like to store a GenomicRanges::GRanges object from Bioconductor as a single column in a base R data.frame. The reason I’d like to have it in a base R data.frame is because I’d like to write…
Hervé Pagès (12:32:00): > The columns of a data.frame cannot be S4 objects. That’s why we have DataFrames. Your workaround withformat()doesn’t solve the problem: it just stores the GRanges as acharacter vector , not as a GRanges object i.e. if you extract the column (withdf$x) you get a character vector.
Teun van den Brand (12:52:44): > Maybe I’m overlooking something here or have a weird version problem, because this seems to work:
Teun van den Brand (12:52:51): > > library(GenomicRanges) > > x <- GRanges(c("chr1:100-200", "chr1:200-300", "chr2:100-200")) > > df <- data.frame(y = 1:3) > df$x <- x > > format.GRanges <- function(x, ...) {showAsCell(x)} > # Subsetting to check class preservation > class(df[c(1,3), ]$x) >
Marina Nikolova (13:06:32): > @Marina Nikolova has joined the channel
Alan O’C (13:13:45): > That’s a GRanges object for me alright
Hervé Pagès (13:14:21): > Oh I see. Yes, that seems to work! mmmh… interesting… This is a huge revelation to me, with possibly some important consequences. I’ll need some time to process it… Thanks for your input!
Alan O’C (13:15:22): > I don’t think data.frames have any restrictions on what you put in them, there are just difficulties printing, and in some cases you need to wrap the assignment in (eg)I(). I know Hadley has been advocating storing models etc in dataframes for a while now
Hervé Pagès (13:19:04): > Thanks@Alan O’Cand@Teun van den BrandThe first immediate consequence of this is that we probably shouldn’t be using theshowAsCellgeneric and methods for our display needs. That’s whatformat()is for and that’s probably what we should use.
Michael Lawrence (13:25:47): > Note that they’re storing models in data.frames using lists; you can store anything that way. The data.frame implementation may make assumptions in certain places that columns are at least vectors (including lists). Over the years I’ve tried to generalize stuff so it relies on primitives and abstractions to support arbitrary column types. Then again, I was a total newb when I created DataFrame; there was probably a smarter way. The Vector framework has also come a long way since then.
Alan O’C (13:29:25): > Ah true, I mixed my concepts slightly. Storing a list ofhtestobjects is v different to storing a GRanges object that somewhat resembles a list/vector
Teun van den Brand (13:31:10): > Might have been this R 3.2.0 bug fix bulletpoint: “[<-and[[<-gain S4data.framemethods to avoid corruption of S4 class information by the S3 methods.” that caused the change
Hervé Pagès (13:32:47): > Thanks@Michael Lawrence. Even though the primary motivation for introducing DataFrame (support S4 columns) might seem a little bit less relevant today, we still have a lot of good reasons to use them:https://github.com/Bioconductor/S4Vectors/issues/56#issuecomment-566768077 So zero regrets here!
Hervé Pagès (13:34:08): > (I quickly added items 4-6 5 min ago to make my point stronger:wink:)
Nicholas Knoblauch (13:50:32): > @Hervé PagèsI don’t think all of those are true/useful > 1-2) you can puttibbles(or anything else for that matter) in the column of atibble, and you can set the attributes to be whatever you want: > > > (x <- tibble::tibble(a=list(data.frame(x=1:3),data.frame(z=runif(2))),b=c("row1","row2"))) > # A tibble: 2 x 2 > a b > <list> <chr> > 1 <df[,1] [3 × 1]> row1 > 2 <df[,1] [2 × 1]> row2 > > attr(x,"something") <- c("something","else") > > x > # A tibble: 2 x 2 > a b > <list> <chr> > 1 <df[,1] [3 × 1]> row1 > 2 <df[,1] [2 × 1]> row2 > > 4. If rownames contain duplicates, how are they row names? > 5. you can put all the metadata you want in tibbles via attributes > 6. I thinkDataFrameis “open” to bioconductor developers, but effectively closed to end users (as compared totibble/data.frame, which plays with the rest of the R ecosystem)
Michael Lawrence (13:50:37): > You could also add stuff like the abbreviated printing. Quality of life stuff.
Michael Lawrence (13:51:37): > Comparing tibble to DataFrame is a different story, since tibble did not exist 12 years ago.
Nicholas Knoblauch (13:52:16): > everything that is true of tibbles is also true of base R data.frames
Michael Lawrence (13:53:40): > Just focusing on data.frame then, by metadata, we mean not just arbitrary attributes (which is not the same anyway) but also a formal notion of metadata along the columns.
Hervé Pagès (13:56:04): > > If rownames contain duplicates, how are they row names? > For the same reason that the rownames of a matrix are still row names even when they contain duplicates. Or that the colnames of a data.frame are still column names even when they contain duplicates. Or that the names on a vector are still names even when they contain duplicates. And we all know that the automatic mangling of the rownames to preserve unicity is BAD (e.g. mangled gene names).
Michael Lawrence (13:58:01): > I’ve definitely considered the possibility of DataFrame extending data.frame, but it would expose/enforce implementation. For the same reason, a tibble is not a data.frame, only a tbl_df is. DataFrame implements the same API as data.frame so it should integrate easily into existing workflows.
Nicholas Knoblauch (14:10:59): > I think atibbleis adata.frame. (theclassattribute of atibbleis"tbl_df","tbl","data.frame") . I don’t want to start a flame war about S3 vs S4, but I would argue that the API fordata.frameincludes the API for lists, and isn’t justrownames,colnamesand[
Kasper D. Hansen (14:14:35): > a tibble is not a data.frame
Kasper D. Hansen (14:15:02): > Its the tibble creators making a mistake and they are only allowed to do that because S3 does not check this
Hervé Pagès (14:16:44): > > .. the API fordata.frameincludes the API for lists, and isn’t justrownames,colnamesand[ > Yes, it’s also$,[[,dim,nrow,ncol,dimnames, and many other things that are also supported by DataFrame objects. Not sure what’s your point.
Barbara Hilzinger (14:24:39): > @Barbara Hilzinger has joined the channel
Nicholas Knoblauch (14:27:29): > @Hervé Pagèsmy point (and I concede it is totally my S3-biased opinion) is that outside of the S4/bioconductor ecosystem, things that behave like base vectors and lists do so because theyare vectors and lists
Hervé Pagès (14:38:37): > I see. That’s a good thing but at the same time it also has its limitations. We have plenty of objects in Bioconductor that we want to behave like base vectors, lists, or matrices, and for which deriving from the base data types would be totally inefficient. E.g. implementing DNAStringSet objects on top ofcharacter vector , or GRangesList objects on top oflist , or SummarizedExperiment objects on top ofmatrix would NOT work. Using S4 frees us from being stuck with base data types and allows all kinds of internal tricks that make these objects performant and compact in memory. The tidyverse approach to data representation does NOT work for the kind of data we use in Bioconductor. It would be too inefficient!
Nicholas Knoblauch (15:21:46): > (DNAString, GRangesLists, DelayedArray etc) are all amazing but there is a trade-off. The R language doesn’t really allow for “internal” tricks. R objects aren’t designed to have public and private ways of getting and setting data (except maybe attributes). You can write a[method for your type, but once you try to make an object “behave” like one thing while being another thing you’re making it harder to play with the rest of the ecosystem
Hervé Pagès (15:35:13): > The trade-off is well known but do we have a choice? How could we have a DelayedArray object extendarray ? Or how could the sparseMatrix class extendmatrix ? Why do you think the authors of the Matrix package also felt the need to use S4? Other major players in the R ecosystem seem to think that the R language actually allows for “internal” tricks. Not just Bioconductor. This kind of freedom is actually one of R’s strengths.
Michael Lawrence (15:44:31): > It’s true that there is a tension: a language designed for data analysis is going to make compromises when it comes to writing software. Languages like Python have the opposite problem. Engineering is all about overcoming such challenges.
Michael Lawrence (15:46:10): > We’re building bridges, not roads.
Nicholas Knoblauch (15:50:32): > yeah I think you’re right about the data analysis aspect being at the root of this tension. In most programming languages you want to abstract away the representation of the data, in a data analysis context that isn’t always helpful
Michael Lawrence (15:55:01): > At least, the mechanisms for abstraction are unnatural and feel tacked on. No one cares about ALTREP abstractions, because they’re at a very low level. The rownames on a data.frame are often stored in a compressed format, but no one knows the difference. The methods package gets in the way more than it should.
Michael Lawrence (15:56:44): > And yet I still spend a lot of my free time maintaining it.
Nicholas Knoblauch (16:04:39): > It’s really too bad that it isn’t easier to work with ALTREP because I feel like it could solve a lot of these problems
2020-01-28
Alan O’C (06:12:43) (in thread): > What do you mean by this? data.frame is the parent class to catch any non-implemented methods (egdim). It’s normal inheritance unless I’m missing something
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2020-01-30
USLACKBOT (08:02:21): > This message was deleted.
Michael Love (11:48:52): > Lori pointed out to me DESeq2 had error in devel because ashr was removed from CRAN. I’ve just removed ashr from the vignette, example, and testing code. Do I also have to remove it as aSuggests?
Michael Love (11:50:00): > I have a DESeq2 function that optionally can call an ashr function after checking whether ashr is installed, and if not installed it prints a message about installing ashr
Michael Love (11:50:19): > (i imagine ashr will be fixed and re-posted to CRAN, but if not i’ll change the instructions to say install from github)
Ludwig Geistlinger (12:05:08) (in thread): > If you want to also inspect association with survival over a bunch of expression datasets, some inspiration can be drawn fromhttp://bioconductor.org/packages/release/data/experiment/vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf (Section 4, Association of CXCL12 expression with overall survival)
Hervé Pagès (12:09:47): > Yes you also need to remove it from Suggests otherwiseR CMD checkwill fail. Thanks!
Michael Love (12:16:17): > thanks. i’m going to remove it from Suggests, which will then give me a warning instead of an error
Michael Love (12:16:34): > and i’ll need to find out if ashr is going to be kept off of CRAN or if this is temporary
Hervé Pagès (12:47:57): > If you comment out the function that uses ashr then you shouldn’t get any warning. Inserting it in anif (FALSE) {}should work: > > if (FALSE) { # --- hide foo() for now --- > > foo <- function(...) { > ... > ... > } > > } # end of if (FALSE) >
Michael Love (13:26:48): > thanks. I’m going to contact Matthew Stephens and see what his immediate plan is, if he is abandoning CRAN then i need to rework my function altogether (e.g. you could pass in a function as an argument so i can avoid calling his function by name)
Nicholas Knoblauch (14:01:05): > @Michael Loveashrwas taken off CRAN due to a dependencymixsqpbeing removed.mixsqpis back on CRAN (as of a few hours ago) so I assumeashwill be back up fairly soon
Michael Love (14:58:13) (in thread): > Thanks for note— ill revert once its available
Michael Love (14:58:51) (in thread): > Interesting how package removal ripples through many communities
Kasper D. Hansen (15:32:09) (in thread): > This is why you should be careful about dependencies
2020-01-31
Michael Love (12:11:36) (in thread): > dependencies lead to hassles, while re-writing other’s well tested functions may lead to hidden bugs. definitely a tradeoff
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Vahid (17:46:29): > what is the recommended method to get when a given tool was added to bioconductor?
Vahid (17:47:50): > (an API call would be ideal; also, the more accurate (e.g., day/month/year) the date, the better it is)
Martin Morgan (17:52:52) (in thread): > Probably the easiest isBiocPkgTools::firstInBioc()
Vahid (18:11:26) (in thread): > still installing the package, will try when its done.
Vahid (18:11:53) (in thread): > (i.e.,install.packages("BiocManager"))
Martin Morgan (18:17:48) (in thread): > BiocManager is ‘just’ a CRAN package with no source compilation or other dependencies; it should not cause problems for installation, or no more problems than any other CRAN package. Are you running this in a new R session, without loading any other packages or .Rhistory, etc?
Vahid (18:20:36) (in thread): > running in R Studio, and its been a while it is still installing.
Vahid (18:37:49) (in thread): > reg syntax, should it be used as: > > x = BiocPkgTools::biocDownloadStats() > BiocPkgTools::firstInBioc(x) >
2020-02-01
Martin Morgan (04:24:36): > Nice comments from@Aaron Lunon package use of Bioconductor objectsGRanges/SummarizedExpermientetc, and on the release cycle / CRAN dependencies.
Aaron Lun (04:47:19): > My pleasure, as always. I was aiming for some soaring oratory but@Michael Lawrencemade a comment while I was half-done and stole my thunder.
Shian Su (05:01:52): > Where can these comments be found?
Aaron Lun (05:42:44): > https://github.com/Bioconductor/Contributions/issues/1355
Alan O’C (07:13:46): > > Now, I can’t possibly imagine Seurat changing their data structure between versions > Now that would be a really strange occurence for sure. > > Great comments. Unless R introduces decent package versioning somehow (I think it’s basically impossible) Bioconductor has to maintain a stable interoperable ecosystem
Sam Fisher (11:38:50): > @Sam Fisher has joined the channel
Aaron Lun (14:28:03): > The Python world provides an instructive example of what would happen if we had “proper” versioned dependencies; namely, if packages can specify anything other than>=in the versions of their dependencies. This is desirable for software developers who have full control over the subset of Python packages that they need for a particular project. However, it is not desirable for interactive data analysis where I might need tools A and B operating in the same Python session. If A and B require incompatible versions of the same dependency… well, that’s too bad. > > By comparison, aslaissez faire as the R package management system might be, it supports the implicit expectation that - at any given snapshot in time - all CRAN/BioC packages should be able to operate in the same session. This is precisely because other versioning types (like==,<=,>or<) are not supported; everyone is expected to play nice with the latest versions of everyone else.
Aaron Lun (14:38:23): > Or in short: in Python, the implicit decision is that package version incompatibilities are the user’s problem (which is only somewhat alleviated by things likeconda), while in R, they are the package developer’s problem. This reflects the cultural differences underpinning the two languages and ecosystems, as Python “users” are typically other developers who wouldn’t have any problem dealing with these issues, whereas R caters to a user base that has, on average, a much weaker computational background.
Martin Morgan (18:00:57) (in thread): > A different approach is inhttps://gist.github.com/mtmorgan/d41ada0a49584266d394471b4a0154cd which includes a csv file of packages (truncated at release 1.6, 2005), the code used to generate the list, file, and an example snippet for input and query
2020-02-02
Vahid (11:16:14) (in thread): > Thanks, I guess that answers my questions.
2020-02-03
Alan O’C (03:48:21): > People always assume I’m comparing to Python when I say that, actually ruby/bundler is the example I would go for (especially given how often I’ve experienced dependency hell in Conda). Though perhaps that’s a language where more attention is paid to stable interfaces
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2020-02-04
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2020-02-05
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Krithika Bhuvanesh (09:13:01): > I have a question related to Rwikipathways. Is there a better channel to ask pathway-annotation related questions ? We are trying to extract the nodes and edges from some Rwikipathways of interest. The help documentation says “GPML is short for Graphical Pathway Markup Language and it is a custom XML format”. I’ve tried to use XML and XML2 R packages to query and extract this information from the GPML data object, but the information is not getting extracted as expected. When I test the same code on another teset xml file, the code works fine. Is there a better way to do this ? Please advise
Martin Morgan (09:47:25) (in thread): > I don’t know about a better way, but my guess is your use of xml needs to use the ‘namespace’ concept. If you wanted to post a VERY SIMPLE chunk of code somewhere (e.g., a git gist) illustrating what you’re trying to do, and no one else comes up with a better solution, i could take a look.
Krithika Bhuvanesh (12:49:42) (in thread): > Thank you for the response. I created a Github gist that shows what all I tried and failed:https://gist.github.com/Krithika-Bhuvan/55c41870a66da5f89c52818626ed78f5
Martin Morgan (13:18:35) (in thread): > So the last line of > > library(xml2) > gpml <- rWikiPathways::getPathway('WP1589') > x2 <- xml2::read_xml(gpml[[1]]) > dataNode <- xml2::xml_find_all(x2, ".//DataNode") #not working > > can be made to work by noting thatDataNodeis part of thed1XML namespace, so > > > xml2::xml_find_all(x2, ".//d1:DataNode") #not working > {xml_nodeset (26)} > [1] <DataNode TextLabel="Nucleotide Synthesis" GraphId="a9be0" Type="Pathway ... > [2] <DataNode TextLabel="ALDH1A1" GraphId="ad1b0" Type="GeneProduct">\n <Gr ... > [3] <DataNode TextLabel="THF" GraphId="af2aa" Type="Metabolite">\n <Graphic ... > ... > > I got thed1from > > > xml2::xml_ns(x2) > d1 <->[http://pathvisio.org/GPML/2013a](http://pathvisio.org/GPML/2013a)bp <->[http://www.biopax.org/release/biopax-level3.owl#](http://www.biopax.org/release/biopax-level3.owl#)... > > and a lucky guess that the first namespace was the most relevant. > > The XML library approach is more-or-less similar. It says there’s a single namespace (maybe xml2 get namespaces recursively? > > > xml = xmlParse(gpml, asText = TRUE) > > xmlNamespaces(xml) > [[1]] > $id > [1] "" > > $uri > [1] "[http://pathvisio.org/GPML/2013a](http://pathvisio.org/GPML/2013a)" > > $local > [1] TRUE > > attr(,"class") > [1] "XMLNamespaceDefinition" > > attr(,"class") > [1] "XMLNamespaceDefinitions" > > It’s not named, so create a map and use it > > > nmspc = c(ns = "[http://pathvisio.org/GPML/2013a](http://pathvisio.org/GPML/2013a)") > > length(getNodeSet(xml, "//ns:DataNode", nmspc)) > [1] 26 >
Krithika Bhuvanesh (13:34:52) (in thread): > Thank you for this ! This is brilliant ! I didn’t know about this name space concept for XML. I will read up on this and use your code snippets to move forward with this. Many thanks !
Alexander Pico (14:22:44) (in thread): > Sorry for chiming in late. If you have any further issues with RWikiPathways, feel free to post here, DM me or post github issues.
Hassan DAKIK (23:26:47): > @Hassan DAKIK has joined the channel
2020-02-06
Alan O’C (05:13:59): > Does anyone use packrat with Bioc? It consistently 404’s me on Bioc pkgs when I try to restore from a .lock file
Charlotte Soneson (05:31:25): > Notpackrat, but we were playing a bit withrenv, which seemed to play nicely also with Bioc packages
Alan O’C (05:31:56): > Ah, have Rstudio abandoned packrat just as I started using it then
Charlotte Soneson (05:33:38): > To some extent, yes. This is from the RStudio:conf the other week:https://kevinushey-2020-rstudio-conf.netlify.com/slides.html#12
Alan O’C (05:34:30): > I’m not mad I promise
Alan O’C (05:34:35): > Thanks anyway
Peter Hickey (06:53:39): > i’ve been usingrenv
Peter Hickey (06:54:51): > workflow is roughly: runrenv::init(),renv::install("BiocManager")then userenv::install("bioc::pkg")syntax for BioC packages, e.g.,renv::install("bioc::limma")
Peter Hickey (06:55:20): > think there’s a way to migrate packrat to renv but not tried
Alan O’C (07:35:25): > Seems to work with justBiocManager::install("foo")unlike packrat
Federico Marini (09:55:30): > Following up on a discussion I opened back then on checking what one of my packages depends on, I figured out a way to inspect this in more detail. > Thought it could be useful to others as well. > Ingredients:itdepends(remotes::install_github("jimhester/itdepends")) + basic stuff
Federico Marini (09:57:10): > > library("magrittr") # just cause it is practical... > > remotes::install_github("jimhester/itdepends") > mydeps <- itdepends::dep_usage_pkg("GeneTonic") %>% dplyr::count(pkg,sort=TRUE) > View(mydeps) > > db <- available.packages(repos=BiocManager::repositories()) > depsnr <- tools::package_dependencies(mydeps$pkg, db,recursive = TRUE ) > depsnr > > length(unique(unlist(depsnr))) > sort(sapply(depsnr, length)) >
Federico Marini (09:59:10): > Then one can see what each package additionally brings on the “standard” core of dependencies, by changing thePACKAGESinlength(unique(unlist(tools::package_dependencies(PACKAGES, db,recursive = TRUE ))))
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2020-02-07
Kevin Rue-Albrecht (07:47:06): > https://www.biorxiv.org/content/10.1101/2020.01.24.918342v2 Am I missing why this review would focus on.h5adformat without considering more general HDF5 thatis supported bySummarizedExperiment(and therefore#isee) ? > Happy to move that to a channel, but I wanted to cast the net wide in case anyone has experience with the two file formats (I haven’t usedscanpythat much yet)
Sean Davis (08:21:15): > Perhaps@John Readey(from the HDF group) has some thoughts.
Kevin Rue-Albrecht (08:40:51): > Thanks. I’m also interested to know if there is any Bioc developer/user feedback about > > saveHDF5SummarizedExperiment(x, dir="my_h5_se", replace=FALSE, > chunkdim=NULL, level=NULL, verbose=FALSE) > loadHDF5SummarizedExperiment(dir="my_h5_se") > > that affects their adoption in Bioc workflows
Davide Risso (08:45:17): > Not sure what type of feedback you’re looking for but@Stephanie Hicksand I have been gaining some experience with that…
Davide Risso (08:46:00): > For instance how you set chunkdim is very important
Davide Risso (08:46:14): > And very application dependent
Kevin Rue-Albrecht (08:46:41): > Are they usability issues? Barrier to entry? How many datasets out there (e.g. ExperimentHub) are using HDF5-backed assays?
Kevin Rue-Albrecht (08:48:30): > I’ve just played with the toy?SingleCellExperimentexample, saved it withsaveHDF5SummarizedExperiment, read it back in usingloadHDF5SummarizedExperimentand the assay was then aDelayedMatrix. So (as an experienced Bioc user/developer) I don’t really see a problem to using it.
Davide Risso (08:49:25): > To me, it works like a charm…
Kevin Rue-Albrecht (08:49:35): > I’m just puzzled why their Table 1 would useh5adinstead ofhdf5as a criteria
Davide Risso (08:50:18): > The TENxBrainData and TENxPBMCData packages ship hdf5-backed SummarizedExperiments
Davide Risso (08:52:33): > Not sure if there is any effort to import h5ad into Bioconductor. There’s the LoomExperiment package for loom files, not sure if someone has a similar package for h5ad…
Davide Risso (08:53:25): > Independently, it looks like not mentioning iSEE in that biorxiv is a pretty big miss… (edit: they mention it my bad)
Kevin Rue-Albrecht (08:53:39) (in thread): > ?
Kevin Rue-Albrecht (08:53:43) (in thread): > they do mention iSEE
Davide Risso (08:53:54) (in thread): > Oh ok sorry
Davide Risso (08:54:16) (in thread): > I thought that’s what you were saying
Davide Risso (08:54:25) (in thread): > (Didn’t read it)
Kevin Rue-Albrecht (08:54:58) (in thread): > no no - my point here was just about clarifying (to me) the difference between h5ad and hdf5
Martin Morgan (08:55:19): > is there a specification for h5ad somewhere? superficially seurat -> h5ad -> Bioc/SCE would just be an awkward way of converting between Seurat & SCE
Kevin Rue-Albrecht (08:56:10): > this threadhttps://github.com/theislab/anndata/issues/180 gives a brief explanation and a link to the pythonh5pypackage
Davide Risso (08:56:52): > https://icb-anndata.readthedocs-hosted.com/en/stable/index.html
Davide Risso (08:57:24): > Seems similar enough to a SE..
Krithika Bhuvanesh (14:19:28) (in thread): > Hello@Alexander Pico. I do have a question related to the tag in the GPML file. I’m trying to figure out how to extract edges in the network from the tags. I’m using the example of WP1589.gpml. > > Issue#1: Many tags have two tags, which I understand to be starting point and ending point. But other tags have 3 , so not sure how to figure out the edges in this case.
Krithika Bhuvanesh (14:20:47) (in thread): > Example: > > <Interaction GraphId="id4462416a"> > <Graphics ZOrder="12288" LineThickness="1.0"> > <Point X="674.04063397511" Y="362.13571842239054" GraphRef="ad1b0" RelX="0.0" RelY="1.0" /> > <Point X="674.8406339751103" Y="381.13571842239054" GraphRef="ab5ca" RelX="0.0" RelY="0.0" ArrowHead="mim-catalysis" /> > </Graphics> > <Xref Database="" ID="" /> > </Interaction> > <Interaction GraphId="id509aebaa"> > <Graphics ConnectorType="Curved" ZOrder="12288" LineThickness="1.0"> > <Point X="487.36974789915985" Y="178.16806722689094" GraphRef="d3cdc" RelX="-1.0" RelY="0.0" ArrowHead="mim-conversion" /> > <Point X="454.1596638655463" Y="204.668067226891" /> > <Point X="475.36974789915985" Y="231.16806722689105" GraphRef="b9d15" RelX="-1.0" RelY="0.0" ArrowHead="Arrow" /> > <Anchor Position="0.6103164243999473" Shape="None" GraphId="eb61e" /> > </Graphics> > <Xref Database="" ID="" /> > </Interaction> >
Krithika Bhuvanesh (14:24:11) (in thread): > Another problem. Issue # 2: > Not all “GraphRefIDs” used in tags are defined in the nodes. Example “bf654” is not defined previously in “DataNodes” tag > > <Interaction GraphId="id1d27bcec"> > <Graphics ZOrder="12288" LineThickness="1.0"> > <Point X="530.0406339751084" Y="400.13571842239054" GraphRef="df139" RelX="0.0" RelY="-1.0" /> > <Point X="528.8984024554125" Y="380.70445998539964" GraphRef="bf654" RelX="0.0" RelY="0.0" ArrowHead="mim-catalysis" /> > </Graphics> > <Xref Database="" ID="" /> > </Interaction> >
Krithika Bhuvanesh (16:38:09) (in thread): > Adding a screenshot for issue # 1 in case its easier to understand: If you see [[9]] and [[10]] in the list, they each have 2 tags that could represent the “From” and “To” nodes of the edges. But see [[11]] in the list - it has 3 tags, and one tag. Not sure what this means, and which would be “From” node and “To” node in this case. - File (PNG): Screen Shot 2020-02-07 at 4.30.06 PM.png
Krithika Bhuvanesh (16:42:22) (in thread): > Explaining Issue # 2 more: Attached is a csv file of the nodes I extracted with the help of Martin’s code. > I found some GraphIDs (example “bf654”) which are in the section, but not defined previously in “DataNodes” tag. So don’t know if this is a gene, or metabolite or anything else - File (CSV): WP1589_nodes.csv
2020-02-08
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2020-02-09
Federico Marini (08:30:46): > Ehub could be the answer in such case I’d say
Aaron Lun (14:24:04): > EHub FTW
USLACKBOT (18:18:33): > This message was deleted.
2020-02-10
Lambda Moses (07:57:33): > I used to work in a lab that does GWAS on both humans and mice, and would like to visualize GWAS results of both species in one plot: Plot the Manhattan plot of both mouse and human results over synteny blocks. This helps to visualize similarities between the significant mouse loci and loci correlated to a related human disease (e.g. mouse liver triglyceride level and non-alcoholic fatty liver disease in humans). I sort of have some idea how to implement that in R, given JAX synteny annotations, but I don’t want to reinvent the wheel. Has anyone here heard of a tool to compare GWAS results for multiple species (doesn’t have to in R, can be web interface as I’m asking on behalf of a friend who doesn’t code)?
Shraddha Pai (10:19:13): > Good morning, Bioc folks. Is there a special process for submitting articles to the BioC gateway at F1000? > I see that@Sean Davishas issued invitations in 2018 and 2019. > We’re preparing a package-based workflow filled with vignettes for our patient classifier,netDxand are trying to decide where to publish it. > Thanks!
Sean Davis (12:16:58): > https://f1000research.com/gateways/bioconductor - Attachment (f1000research.com): Articles from gateway Bioconductor - F1000Research > Read the latest peer reviewed Bioconductor articles and more on F1000Research
Sean Davis (12:17:27): > Click on submit to this gateway. - File (PNG): image.png
Sean Davis (12:18:48): > We’ll be doing another call for submissions this year with “deadline” to coincide with Bioc2020. That said, the channel is open for submissions at any time.
Sean Davis (12:19:56): > Thanks for bring it up,@Shraddha Pai.
Mikhael Manurung (12:40:03): > Hello! Is there a way to automate literature searching of a gene function in R? I’ve seen bash or perl scripts in biostars but I my knowledge of those languages were nonexistent!
Nicholas Knoblauch (12:49:06): > https://github.com/ropensci/rentrez is worth a look
Aaron Lun (12:49:53): > https://bioconductor.org/packages/devel/bioc/html/PubScore.html looks kind of interesting. - Attachment (Bioconductor): PubScore (development version) > Calculates the importance score for a given gene. The importance score is the total counts of articles in the pubmed database that are a result for that gene AND each term of a list.
Sean Davis (13:23:53): > I’d encourage folks to also consider asking general questions on the Bioconductor support site, which gets a lot more exposure and answers become public and searchable. A note here that you have done so will alleviate double-answers.
Sean Davis (13:26:58): > https://support.bioconductor.org/
Shraddha Pai (13:33:15) (in thread): > Great, thank you for clarifying.
Dario Strbenac (14:00:04) (in thread): > Quite similar to Gene Valorizationhttp://www.bioguide-project.net/gv/index.php - Attachment (bioguide-project.net): Attachment > Provides a concise overview of the publications associated to a list of genes studied within a given context (described by filters).
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Mikhael Manurung (15:34:17) (in thread): > Thanks for the reminder! I’ll keep this in mind for sure.
Mikhael Manurung (15:36:42) (in thread): > Wow these are gold:first_place_medal:
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Leonardo Collado Torres (23:44:39) (in thread): > That is ExperimentHub, not EHub in case you were looking for the package
2020-02-11
Julien Roux (03:38:43): > @Julien Roux has joined the channel
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Stephanie Hicks (12:56:09): > welcome@Ariel Hippen!
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2020-02-13
Lauren Fitch (15:23:06): > I’m having trouble understanding some behavior inGenomicAlignments::mapFromAlignmentsand have posted a question here if anyone can help out
2020-02-14
Hervé Pagès (03:06:59) (in thread): > @Lauren FitchSee my answer. Sorry for making it so long, I was hoping there would be a simpler way.@Michael Lawrence?
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Lauren Fitch (09:26:43) (in thread): > Thanks a lot for the detailed explanation. I did end up using shift to adjust the results, I’ll reply to the thread with the code I used.
Hervé Pagès (11:29:12) (in thread): > I believemapFromAlignments()is actually broken when soft-clipping is involved: > > > mypos <- IRanges(1:5, width=1, names=rep("read1", 5)) > > mapFromAlignments(mypos, GAlignments("chr1", pos=1L, cigar="2S3M2D7M", strand("+"), names="read1")) > IRanges object with 5 ranges and 0 metadata columns: > start end width > <integer> <integer> <integer> > read1 1 1 1 > read1 2 2 1 > read1 3 3 1 > read1 4 4 1 > read1 5 5 1 > > The deletion is ignored! Don’t have time now but I’ll need to look more into this.
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Hervé Pagès (12:01:43) (in thread): > I just opened an issue for this:https://github.com/Bioconductor/GenomicAlignments/issues/12
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2020-02-15
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2020-02-16
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2020-02-18
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bharati mathur (08:41:38): > hi
Lauren Fitch (13:47:13): > http://bioc2020.bioconductor.org/ - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. June 24 - 27, New York City, USA.
Lauren Fitch (13:47:26): > the preview on this link is wrong somehow
Martin Morgan (17:11:23): > @Lauren FitchI’m not sure what you mean by ‘preview’ ? Maybe add an image (via the paperclip icon in slack) to illustrate?
Jared Andrews (17:26:03): > Circled info is incorrect, should be July 29 - 31, Boston, USA. > > Searching for it on google also provides the same incorrect preview info in the search results. Data in the page header is incorrect. Thedescriptionfield in the HTML needs to be updated. - File (PNG): image.png
Martin Morgan (18:05:14): > Thanks, I created a pull request on the underlying repository to fix thathttps://github.com/Bioconductor/BioC2020/pull/56 !
Aaron Lun (18:06:36): > I see someone took out all the fun parts in my biography.
2020-02-19
Dan Bunis (00:46:28) (in thread): > Oh? What had you put????
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2020-02-20
Mike Smith (07:12:58) (in thread): > https://github.com/Bioconductor/BioC2020/commit/92bb6befd98026d5637fa257d34b16de4e36e785#diff-1a523bd9fa0dbf998008b37579210e12
Aaron Lun (11:31:20) (in thread): > That’s just copy-and-pasted from the book. I had written a cooler, newer one, it seems that never even made it into the Git repo.
Ino de Bruijn (12:21:56): > Is Bioconductor part of GSoC2020 by any chance?
Martin Morgan (13:13:14): > No we don’t have a relationship
Ino de Bruijn (14:14:42): > :ok_hand:thank you!
Wendy Wong (18:56:29): > satRday DC is on March 28 and are calling for talk proposalssatRday > R conference in Washington, DC!
2020-02-21
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Stian Lågstad (07:13:10): > Question about a failing Travis build: Have anyone seen this error before? Things build fine locally. > > The command “Rscript -e ‘deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps\(package %in% installed.packages())) { message("missing: ", paste(setdiff(deps\) package, installed.packages()), collapse=“,”)); q(status = 1, save = “no”)}’” failed and exited with 1 during . > Fromhttps://travis-ci.org/stianlagstad/chimeraviz/builds/653423950
Lluís Revilla (08:33:21): > Slightly above that message there is another one related to a failed installation of S4Vectors or GenomeInfoDb. I would restart the build manually
Stian Lågstad (08:37:08) (in thread): > Thanks for looking. I’ve tried triggering the Travis build multiple times and on different branches and they all fail the same way. Locally it builds fine though. I’m confused
2020-02-22
Sean Davis (10:25:59): > We have a channel,#papersandpreprints, where we can share publications and preprints from the extended community. I just dropped some nice work by@Kasper D. Hansenon CpG island density and gene loss-of-function tolerance.
2020-02-23
Martin Morgan (03:28:28): > Many posts on the support sitehttps://support.bioconductor.org have R code that hasn’t been formatted in a markdown ‘fence’ or by selecting the text and clicking the 010010 icon. Why is that? It seems like the preview, and looking at the question after it’s posted, should indicate that there’s a problem. And there’s a tutorial linked to the new post page. Is it really that markdown is orthogonal to support site user skills, or is there a systematic problem with the support site that makes users think they’re doing the right thing when they’re not, or …? Are there similar challenges on StackOverflow / Biostars / … ? Any thoughts welcome!
Aaron Lun (03:38:20) (in thread): > Could just bounce any posts where<-is not fenced in. That’s a pretty R-specific expression that probably won’t pop up anywhere else.
Charlotte Soneson (03:38:42) (in thread): > Maybe it would help to explicitly mention code formatting on the new post template page? Like, “In particular, make sure to enclose all code in code blocks” or something like that. Now it says “please paste all the commands that produce the error and the full error text”, and if you don’t read the tutorial you may not think about that there’s anything particular about code.
2020-02-24
Aaron Lun (01:01:22): > Just noticed CRAN’s revdeps to Bioconductor have different colored links. What a nice touch.
FelixErnst (05:01:10) (in thread): > It is cache related. Delete the cache and it should work. Had the same issue yesterday.
Stian Lågstad (05:02:34) (in thread): > Thanks. How do I delete the cache?
FelixErnst (05:03:38) (in thread): > Right hand side is a menu from which you can trigger a new build (the three horizontal bars). Click on it, select cache, delete the cache with the bin button
Stian Lågstad (05:06:03) (in thread): > Thank you! I’ve deleted the cache and have triggered a new build now:https://travis-ci.org/stianlagstad/chimeraviz/builds/654336512 - Attachment (travis-ci.org): Travis CI - Test and Deploy Your Code with Confidence > Travis CI enables your team to test and ship your apps with confidence. Easily sync your projects with Travis CI and you’ll be testing your code in minutes.
FelixErnst (05:06:30) (in thread): > I like to add, that the formating is tricky onsupport.bioconductor.org . From recent experience, I have to say, that the preview produces a different result compared to message actually posted. This is largely due to missing empty lines and such. I haven’t looked at it in detail and probably cannot offer a more detailed description. I think this might be worth having a look at as a contributing factor.
FelixErnst (05:16:55) (in thread): > You don’t need to commit something to trigger a build on travis. You can just use the “trigger manual build” option in the menu I mentioned before. Keeps the history a bit cleaner
Stian Lågstad (05:18:02) (in thread): > Thanks for the tip, but that commit is for the bioconductor build to start:slightly_smiling_face:
Stian Lågstad (05:18:18) (in thread): > *was for
FelixErnst (05:18:50) (in thread): > Ah yes, just noted the time stamp…:expressionless::zipper_mouth_face:
Stian Lågstad (07:03:06) (in thread): > The build is green! Thanks again!
Mike Smith (08:39:18) (in thread): > I wonder if having the preview to the side, like in whatever software the RStudio community is built on, would have better success. Sometimes I forget that the preview is below. In full screen mode the bottom of the text box aligns perfectly with the edge of the screen, so it’s not obvious that a preview is being rendered below. - File (PNG): Selection_035.png
Leonardo Collado Torres (09:16:47) (in thread): > In RStudio when you create a new Rmd file, the file is filled up with a template explaining the format and all that. So maybe a “new question” (post) template that gets automatically populated and guides users on what to do would be a useful update@Martin Morgan
Shraddha Pai (11:50:26): > Hi all, when submitting a package-related paper to the F1000 BioConductor gateway, what is the latest recommended workflow if examples are generated via Rmarkdown? I see posts online about BiocWorkflowTools but these are from 2018, so don’t know if this information is still current. > Thanks!@Sean Davis?
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2020-02-25
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2020-02-26
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2020-02-27
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saskia (20:26:17): > I am wondering about the validity of analysing scATAC-seq data with the help of a SingleCellExperiment object. So far this has been working great for me, but I am running into problems when I am trying to annotate peaks to multiple genes (previously I have allowed peaks to be only annotated to their closest gene). This is because therowDataobject is restricted to contain as many rows as there are features. If multiple genes are assigned to one peak, the convention would be to duplicate the peak in theGenomicRangesobject. Obviously at the moment these two things are at odds with each other. I am just trying to see if I am missing something obvious, or whether there is a community consensus on where the data of scATAC-seq data is heading.
Peter Hickey (21:12:12): > you might store the peaks as a GRangesList. each top-level element is a peak and each sublevel element is a gene
saskia (21:12:34): > ahhh that is helpful
saskia (21:12:43): > thanks@Peter Hickey
Peter Hickey (21:14:53): > no worries. another option might be aIRanges::SplitDataFrameList(), basically one of theList-types and depending on how you store the peak and gene info
2020-02-28
Aaron Lun (00:15:23): > what he said.
2020-03-01
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2020-03-02
Jonathan Carroll (05:37:20): > I’m not sure if there’s a better channel for this but anyone able to help with a (possibly silly)edgeRquestion?https://twitter.com/carroll_jono/status/1234424379884199936?s=19 - Attachment (twitter): Attachment > Slightly more obscure (perhaps) R question… > > Any edgeR aficionados in the house? > > Say I have a few cohorts (A, B, C) of RNAseq samples…
Martin Morgan (09:56:20): > That’s really whathttps://support.bioconductor.org is for…
Kasper D. Hansen (20:54:24): > Any idea on the apprx. time for next release?
2020-03-03
Stian Lågstad (02:23:17) (in thread): > Seehttps://bioconductor.org/about/release-announcements/ and see if there’s a pattern:slightly_smiling_face:
Lori Shepherd (07:32:36) (in thread): > We are waiting for R to announce the R 4.0 release. We can’t schedule our Bioconductor release until after the R release. It generally happens sometime in April (as early as later march and as late as early may) - The Bioconductor release is generally about a week after the R-release
Arshi Arora (11:07:20): > I see two dates for notifications to be sent by, after submitting the abstract for BioC 2020, March 24 and May 31. Which one is the correct one?
Leonardo Collado Torres (13:03:08): > Hi, does anyone know a way of getting automatic messages on Slack for comments on a particular GitHub issue thread? > > In particular, I would like to add an automatic integration to get messages likehttps://github.com/Bioconductor/Contributions/issues/1393#issuecomment-593510693 on theregutoolschannel at CDSB’s Slack. From readinghttps://github.com/integrations/slack I’m not that’s possible to do with that tool. > > Thanks!
Sridhar N (13:06:16): > did you try RSS feed?
Leonardo Collado Torres (13:11:48): > Can you expand a bit? I’m not finding an answer when I google search about RSS feeds for github issues. I see some stuff likehttps://github.community/t5/How-to-use-Git-and-GitHub/RSS-feeds-for-GitHub-projects/td-p/298 - Attachment (github.community): RSS feeds for GitHub projects > How to get the rss feeds for GitHub projects ? For example, RSS feed for new issue created in https://github.com/mapstruct/mapstruct/issues
Sridhar N (13:25:36): > https://slack.com/help/articles/218688467-Add-RSS-feeds-to-Slack - Attachment (Slack Help Center): Add RSS feeds to Slack > Have a favorite blog or news site? You can use Slack to subscribe to both RSS and Atom feeds and get updates in the Slack channel of your choice. Note: If you get an error when trying to add a fee…
Sridhar N (13:26:31): > there are other add hoc github projects which are out there for this but installing it would be PTA, first pass would be set up RSS feed add the link from that issue and that should do the job IMO
Hervé Pagès (19:31:04): > PTA? Wow! To the other non-native english speakers out there: basic googling won’t help, you’ll have to use the amazing urban dictionary for that one:https://www.urbandictionary.com/ - Attachment (Urban Dictionary): Urban Dictionary, March 3: ate that > did a great job; pulled it off well; had a lot of success with something. Used by teens in the projects of Queens, NY, and probably elsewhere in NYC.
Aaron Lun (19:40:16): > OTL
Hervé Pagès (19:52:55): > Also on the urban dictionary:wink:
Aaron Lun (19:54:01): > yeet
2020-03-05
Pierre-Luc Germain (06:01:20): > @Pierre-Luc Germain has joined the channel
Sean Davis (13:58:02): > For folks interested in training and education, I started a dedicated channel,#education-and-training. Post your own materials, discuss processes, announce courses, and perhaps do some collaborative curriculum/material development.
Leonardo Collado Torres (22:02:14): > Hi BioC! > > We just made the announcement of our CDSB 2020 workshop (Cuernavaca, Morelos, Mexico August 3-7 2020) athttps://support.bioconductor.org/p/128868/ + Twitter & Facebook (both in English and Spanish).@Joselyn Chávezand@Rob Amezquitawill be among our instructors. Thank you Bioconductor Foundation for the support! > > Please help us spreading the word around. Also, if you have any contacts that you think might be interested in sponsoring the workshop, please let us know. Athttps://comunidadbioinfo.github.io/niveles-de-patrocinio/ we answer the questionwhy should you support us? Thanks! > > Best, > Leo
Leonardo Collado Torres (22:51:42): > Hi Bioconductor Slack, > > Since 2018 I’ve been interacting with rOpenSci’s organizers. For those that don’t know,r OpenSci is a non-profit that aims to > > > make scientific data retrieval reproducible. Over the past seven years we have developed an ecosystem of open source tools, we run annual unconferences, and review community developed software. > > (taken from their about page) That is, they are in some ways similar to Bioconductor and that’s why they want to build a bridge between the two communities. > > Stefanie Butland, their community manager, invited me to be a part of a community call (webinar) on the topic of Maintaining an R Package in order to bring in a little bit of the Bioconductor perspective. They have a pretty nice system where they take questions before hand through a GitHub issue page, so please feel free to chime in. I think that besides the Bioconductor side, I bring in a bit of the CDSB perspective (the work we do to help others in Mexico and Latin America). In any case, feel free to tune in to the webinar (details below) as well as share the information with anyone who might be interested.https://support.bioconductor.org/p/128869/ Best, > Leo - Attachment (ropensci.org): rOpenSci > Open Tools and R Packages for Open Science
2020-03-06
Mariam Malik (15:37:08): > @Mariam Malik has joined the channel
Shraddha Pai (16:11:21): > Hi all, I’m trying to use bioc-devel in a Docker instance, and when I try to run a java .jar resource, I get an “Illegal reflective access” error. I don’t get this error on my ubuntu 16.04 workstation, nor from the nightly build (my package has been accepted and is in bioc-devel). > > I suspect it has to do with the version of jdk installed on the Debian buster Docker image used for bioc-devel but wondering if anyone knows how to address this error? > Thanks! > > EDIT: Callingjava -versionon the Docker instance returnsopenjdk version "11.0.6"whereas on my workstation it returnsjava version "1.8.0_211".
Sridhar N (16:23:11): > is that a error or warning?
Sridhar N (16:23:47): > can you paste build ess code block from the dockerfile for installing java
Shraddha Pai (17:01:14): > @Sridhar NIt says warning but then the vignette doesn’t build (and it does build on my workstation). This is the error: > > root@14bd994320e3:/tmp# R CMD build netDx > Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help > * checking for file 'netDx/DESCRIPTION' ... OK > * preparing 'netDx': > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ... ERROR > --- re-building 'BuildPredictor.Rmd' using knitr > WARNING: An illegal reflective access operation has occurred > WARNING: Illegal reflective access by net.sf.cglib.core.ReflectUtils$2 (file:/tmp/Rtmp5WWUo6/BiocFileCache/4052707a4f0_genemania-cytoscape-plugin-3.5.0.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) > WARNING: Please consider reporting this to the maintainers of net.sf.cglib.core.ReflectUtils$2 > WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations > WARNING: All illegal access operations will be denied in a future release > Quitting from lines 368-376 (BuildPredictor.Rmd) > Error: processing vignette 'BuildPredictor.Rmd' failed with diagnostics: > object 'dat' not found > --- failed re-building 'BuildPredictor.Rmd' >
Shraddha Pai (17:04:06) (in thread): > @Sridhar NRe your comment on the Dockerfile. I’m not installing java. Rather I’m starting with the Docker image for bioc devel, which itself is based on the rocker image. > This is my Dockerfile: > > FROM bioconductor/bioconductor_docker:devel > # Install required Bioconductor package > RUN R -e 'BiocManager::install(c("RCy3","biomaRt","MultiAssayExperiment","curatedTCGAData","BiocFileCache","GenomicRanges","GenomeInfoDb","IRanges"))' > #install additional packages > RUN install2.r \ > -d TRUE \ > -r "[https://cran.rstudio.com](https://cran.rstudio.com)" \ > ROCR \ > pracma \ > ggplot2 \ > glmnet \ > igraph \ > reshape2 \ > parallel \ > stats \ > utils \ > graphics \ > drDevices \ > methods \ > bigmemory \ > doParallel \ > foreach \ > combinat \ > rappdirs > > RUN apt-get update && apt-get install -y git vim > > And here is the Dockerfile for bioc-devel. It seems to install a default jdk:https://github.com/Bioconductor/bioconductor_docker/blob/master/Dockerfile
Sridhar N (17:06:13) (in thread): > what is the name of docker image asking to pull
Shraddha Pai (17:08:08) (in thread): > Not sure I understand the question. I’m making a new docker image on my machine, called “netdx_biocdevel”, which has the Dockerfile as pasted above. It is pulling from the bioc-devel docker image.
Sridhar N (17:08:30) (in thread): > what does this return > > apt-cache show default-jdk >
Sridhar N (17:09:03) (in thread): > for bioc-devel
Sridhar N (17:09:24) (in thread): > docker pull xxx/bioc-devel:tag?
Shraddha Pai (17:10:20) (in thread): > > bioconductor/bioconductor_docker:devel > > Is this what you mean? I don’t use apullcommand. I take the Dockerfile above and I just saydocker build -t mynewimagename .
Sridhar N (17:12:11) (in thread): > that works
2020-03-07
Vince Carey (05:58:58): > I think this is getting too deep in the weeds for the general channel. I will post to@Shraddha Paiseparately. We can then communicate resolutions back to interested parties.
2020-03-09
Stian Lågstad (08:58:31): > (tldr: Can anyone help me with a failing Travis build?) > > I have a Travis build error (cannot coerce type 'S4' to vector of type 'double') that I haven’t been able to figure out yet:https://travis-ci.org/stianlagstad/chimeraviz/builds/660090246 . The error comes when building the vignette: > > E> Quitting from lines 663-676 (chimeraviz-vignette.Rmd) > E> Error: processing vignette 'chimeraviz-vignette.Rmd' failed with diagnostics: > E> cannot coerce type 'S4' to vector of type 'double' > E> --- failed re-building ‘chimeraviz-vignette.Rmd’ > E> > E> SUMMARY: processing the following file failed: > E> ‘chimeraviz-vignette.Rmd’ > E> > E> Error: Vignette re-building failed. > E> Execution halted > > Locally the vignette builds fine, using bothbioconductor_docker:develandbioconductor_docker:release. I did notice the different R versions however: > - Travis build: 2020-03-09 r77918 > -bioconductor_docker:devel: 2020-01-28 r77738 > -bioconductor_docker:release: 3.6.2 (2019-12-12) > > I looked athttps://developer.r-project.org/blosxom.cgi/R-devel/NEWS to see if I could see any relevant changes since the “2020-01-28 r77738”-version, but I don’t see anything. > > Right now I’m attempting to create a docker image with the same R version as the Travis build is using, because I want to reproduce the error locally. - Attachment (travis-ci.org): Travis CI - Test and Deploy Your Code with Confidence > Travis CI enables your team to test and ship your apps with confidence. Easily sync your projects with Travis CI and you’ll be testing your code in minutes.
David J. Goldstein (09:27:50): > @David J. Goldstein has joined the channel
Martin Morgan (09:43:13) (in thread): > I’d probably pay more attention to package version differences…
Stian Lågstad (09:45:32) (in thread): > Good idea, thanks!
FelixErnst (12:57:34) (in thread): > did you try clearing the cache?
2020-03-10
Stian Lågstad (03:54:13) (in thread): > My list today: > - clear cache and try again > - compare package versions:slightly_smiling_face:
Stian Lågstad (04:45:09) (in thread): > Its was the cache! Thanks again@FelixErnst. Next time: Delete the cache before asking questions.
Lori Shepherd (09:37:39): > The Bioconductor Release 3.11 (tentative) Schedule has been posted. Please see the following for important deadlineshttp://bioconductor.org/developers/release-schedule/ . We encourage all maintainers to be active in fixing any package ERRORs in release 3.10 and 3.11 ASAP. Cheers.
2020-03-11
ZedaoLiu (01:58:53): > @ZedaoLiu has joined the channel
Martin Morgan (03:41:40): > The R Consortium2020 ISC call for p roposals (thanks Vince for catching the error) is open, providing funding opportunities to improve infrastructure and build for long term stability – maybe there are projects in the Bioc community that would be appropriate?
Stian Lågstad (08:19:37): > Does anyone know if the development version of R is available as a conda package somewhere? I’ve only foundhttps://anaconda.org/r/r .
Jared Andrews (09:26:31): > I looked pretty extensively and could not find a channel with it. There’s probably one out there, but if so, it’s not well advertised.
USLACKBOT (09:28:55): > This message was deleted.
Stian Lågstad (09:35:08) (in thread): > I was note aware of the Biostars Slack. Thanks!
Mike Smith (10:02:30): > Does anyone know how to fix the following warning reported byR CMD check? > > * checking line endings in shell scripts ... WARNING > Found the following shell script(s) with CR or CRLF line endings: > configure.ac > Non-Windows OSes require LF line endings. > > The offending file is athttps://github.com/grimbough/rhdf5filters/blob/master/configure.ac The warning is only printed on Windows, and as far as I can tell the file doesn’t have CR pr CRLF line endings.
Nicholas Knoblauch (10:11:19): > doesconfigure.acnot go in.Rbuildignore?
Kasper D. Hansen (10:17:32): > I would not put configure.ac there. While it is not needed during the build process, I do think of it as part of the package code, but thats just my opinion.
Mike Smith (10:26:13): > That would be an interesting way of circumventing my issue without solving it. Putting it in.Rbuildignorewould mean it wasn’t included with in the package source tarball, right? If so, I’m with Kasper that I like it being there, I certainly find it useful to check in other packages sometimes. I also haven’t had to do that for any other package.
Mike Smith (10:29:47): > In fact, adding it to.Rbuildignoreleads to: > > * checking top-level files ... WARNING > Found a 'configure' file without source file 'configure.ac' or > 'configure.in' . An Open Source package must include its autoconf > sources. > > That seems like a more severe warning to me!
Vince Carey (10:35:00) (in thread): > call for “proposals” – the tidy bioc and the build system tasks could serve as bases for proposals? do we need to start with budgets and plans?
Nicholas Knoblauch (11:25:54): > oh well that’s good to know!
Kasper D. Hansen (11:59:11): > oh man, they have thought of everything
Kasper D. Hansen (11:59:41): > but if you’ve ever tried to debug a configure script you know you don’t want to look atconfigure
Hervé Pagès (12:05:21): > Maybe usednlinstead of#for comments. At least that seems to help thefilecommand recognize the .ac file for what it is: > > hpages@spectre:~$ file configure.ac > configure.ac: M4 macro processor script, ASCII text > > (right now it just says “ASCII text”) > BTW would be better to ask this on bioc-devel
Hervé Pagès (12:33:04) (in thread): > right, would be like trying to debug a C program by looking at its executable:fearful:
Martin Morgan (15:57:22): > When I check out the repository I see > > rhdf5filters master$ ls -al configure* > -rwxr-xr-x 1 ma38727 wheel 152554 Mar 11 15:55 configure > -rwxr-xr-x 1 ma38727 wheel 3069 Mar 11 15:55 configure.ac > -rwxr-xr-x 1 ma38727 wheel 760 Mar 11 15:55 configure.win > > with the execute bit set; is that triggering a false positive?
Hervé Pagès (16:37:01): > The execute bit should probably be avoided on aconfigure.acfile but we have other software packages that have it (e.g. CoGAPS) and they don’t get the warning.
Hervé Pagès (16:40:25): > mmh butconfigure.acin CoGAPS also uses#instead ofdnlfor comments so that doesn’t seem to be the problem either…:thinking_face:
Martin Morgan (16:43:41): > The code generating the warning is athttps://github.com/wch/r-source/blob/bd86d79d163a5b21ae7a182c4bfc55d501703a09/src/library/tools/R/check.R#L2839-L2850 but running under R-devel on a mac doesn’t produce TRUE > > > f = "configure.ac" > > contents <- readChar(f, file.size(f), useBytes = TRUE) > > grepl("\r", contents, fixed = TRUE, useBytes = TRUE) > [1] FALSE >
Hervé Pagès (16:44:46): > Windows should not be allowed to tell what other OSes require or don’t require anyway. Hey Windows, mind your own business!
2020-03-12
Mike Smith (05:57:03): > Thanks for all the suggestions. I’m starting to think something ingit cloneaffects the line endings, but I’ve never seen this behaviour anywhere else. I’ve been flipping the execute bit, to see if that had any effect but it didn’t seem to. I’ve also run it throughdos2unixand no changes happen. I’ve run the code Martin shows above fromRcheck readLines(),file(open='wb', sep='\n'),writeLine()on that same Windows box to regenerate the file, and that passes the test. Commit that to git and it fails on the Github Actions Windows build with the same warning, so I’m pretty stumped right now.
Alan O’C (08:16:51): > There’s a setting for handling line endingshttps://stackoverflow.com/questions/10418975/how-to-change-line-ending-settings#10419350 - Attachment (Stack Overflow): How to change line-ending settings > Is there a file or menu that will let me change the settings on how to deal with line endings? I read there are 3 options: Checkout Windows-style, commit Unix-style Git will convert LF to CRLF w…
Mike Smith (09:17:45): > Amazing! Default behaviour of git on Windows is to change the line endings on checkout. Addinggit config --global core.autocrlf falseto my Github Workflow switched that off and now it passes check. Thanks a lot@Alan O’C!
Alan O’C (09:18:17): > np, the problem sounded vaguely familiar :)
yue hu (11:44:17): > @yue hu has joined the channel
Sangram Keshari Sahu (13:35:00): > @Sangram Keshari Sahu has joined the channel
2020-03-13
cigdemak (03:39:09): > @cigdemak has joined the channel
Shraddha Pai (16:28:34): > Hi all, my package build is failing because of a timeout error for fetching data fromexperimenthub.bioconductor.org . > Indeed, loading this website on the browser is a bit slow. > > > brca <- curatedTCGAData("BRCA", > + c("mRNAArray","RPPA*","Methylation_methyl27*"), > + dry.run=FALSE) > Error in curl::curl_fetch_memory(url, handle = handle) : > Timeout was reached: [[experimenthub.bioconductor.org](http://experimenthub.bioconductor.org)] Operation timed out after 10001 milliseconds with 0 out of 0 bytes received > > Is there ongoing maintenance? I can’t find a recent thread reporting this issue on the bioc-devel mailing list.
Vince Carey (16:40:06): > See if you can use localHub=TRUE because you may already have copies of what you need. I am finding that AnnotationHub is not responding either.
Vince Carey (16:42:09): > x = curatedTCGAData("ACC", "RNASeq2GeneNorm", localHub=TRUE, dry.run=FALSE)will work if you have acquired that assay on that tumor in the past and have not cleaned your cache in the mean time.
Vince Carey (16:42:56): > It might be nice to have a failover component … if hub request fails, retry with localHub=TRUE@Marcel Ramos Pérez?
Martin Morgan (17:05:37) (in thread): > You could try to visithttps://experimentub.bioconductor.org in your web browser; it’s in the amazon cloud and seems responsive enough… I don’t know about the specific resource that you’re trying to rerieve
Shraddha Pai (17:07:56) (in thread): > Hi Martin, I did just that and for me the browser had a bit of lag in bringing up the URLexperimenthub.bioconductor.org .
Shraddha Pai (17:08:37): > Thanks@Vince Carey,didn’t know about localHub=TRUE. That is generally useful to add.
Martin Morgan (17:09:09) (in thread): > I think that’s a rendering issue, not something that would lead to a timeout?
Martin Morgan (17:11:24) (in thread): > but hmm, something is wrong…
Hervé Pagès (18:14:09): > Right, useful for interactive use but in the context of the nightly builds you should not assume that the data is already in the cache.
Hervé Pagès (18:20:46): > @Vince Carey@Marcel Ramos Pérez@Lori Shepherd@Martin MorganThe failover mechanism sounds generic and seems like it could be used any time an ExperimentHub or AnnotationHub resource is being accessed. Would it make sense to implement the mechanism in these packages?
Lori Shepherd (18:25:59): > @Martin Morganbelieves this is affecting more than justannotationhub.bioconductor.org andexperimenthub.bioconductor.org and that there could be a larger issue at hand… but in generally the failover mechanism could be worthwhile
Lori Shepherd (18:30:33): > I thought I had implemented something at aaron’s request to do a localHub in the background of the hub constructors if it failed but I can look into this again too.
Shian Su (18:47:15): > What’s the most painless way to set up R dev these days? I need to do some bug fixing and the BioC Docker page looks different to when I last looked at it.
Kevin Rue-Albrecht (19:06:48): > Depends what you consider painless, for me it’s downloading the source fromhttps://cran.r-project.org/sources.html (the linkR-devel.tar.gz ) and then compiling from source as inhttps://github.com/kevinrue/Bioinformatics/blob/master/R/make/macOS.sh You might need a few system libraries or dependencies that I usual install/upgrade withbrew
Shian Su (19:07:19): > Compiling from source I consider to be painful.
Shian Su (19:08:03): > Painless is ideally a quick command I can run, get some coffee and come back to a working R-dev installation.
Kevin Rue-Albrecht (19:09:36): > well, having written my own script to compile from source, it acts for me as …. > > a quick command I can run, get some coffee and come back to a working R-dev installation.
Kevin Rue-Albrecht (19:10:02): > modulo thesudocommand that requires a password, but hey
Shian Su (19:10:49): > Thanks Kevin, I’ll try it out and hope I have the right dependencies already
Kevin Rue-Albrecht (19:11:32): > Good luck. Nice thing is that dependencies are mostly a one-off cost. Sometimes one or the other needs an upgrade though, but that’s just part of the job
Hervé Pagès (20:00:19): > If you are on Windows or Mac, no need to compile anything. Just grab the latest binary from CRAN (for Windows) or fromhttps://mac.r-project.org/ (for Mac).
Marcel Ramos Pérez (20:01:32) (in thread): > I’ve implemented this here:https://github.com/waldronlab/curatedTCGAData/commit/abfbfe33fd950c8b723d2bd64e1ada0645a4a224 version1.9.6.. it might take a week to build on the builders:persevere:
Hervé Pagès (20:07:26): > If you are on Linux, the download+extract+configure+make sequence takes < 10 min (1-2 min for download+extract+configure and 6-7 min for make) which should be perfect for a coffee. But that doesn’t include installing the bunch of packages you will need for your debugging session (in my experience that’s always the most time consuming part).
2020-03-14
Stian Lågstad (07:40:34) (in thread): > The Docker image is still the easiest IMO
Vince Carey (07:41:54): > Apropos docker:https://github.com/bioconductor/bioconductor_docker and have a look athttps://github.com/waldronlab/bioconductor The disciplines described there really help get around the system dependency problems, but you will be running R within a linux environment. Thus some errors encountered in nonlinux platforms can’t be directly diagnosed in that approach. Furthermore I don’t think the linux environment would be identical to that of the central build system, but I wonder if we could move in that direction@Hervé Pagès?
Martin Morgan (10:05:38) (in thread): > Alsohttp://bioconductor.org/help/docker/ , where the ‘quick start’ > > docker run \ > -e PASSWORD=bioc \ > -p 8787:8787 \ > bioconductor/bioconductor_docker:devel > > gets us a Bioc-devel environment without giving us time for coffee. I’d opt for the slightly more complicated but equally quick ‘Mounting Additional Volumes’ instructions, e.g., > > docker run \ > -v /home/my-devel-library:/usr/local/lib/R/host-site-library \ > -e PASSWORD=password \ > -p 8787:8787 \ > bioconductor/bioconductor_docker:devel > > to run docker but with a persistent cache of installed packages
2020-03-15
Hervé Pagès (06:38:56) (in thread): > > without giving us time for coffee > That command took about 10 min to complete for me! (It downloads a lot of stuff). It gave me an R devel installation from 2020-01-28 so not too far behind the build system but since it’s different it could still give you different results (there’s been many important changes to R devel in the last 3 months).
Hervé Pagès (07:08:06): > @Vince CareyIf we want the Linux environment provided by the docker image to beidentical to that of the build system, it would need to run Ubuntu 18.04 LTS instead of Debian GNU/Linux 10, include TeX Live soR CMD buildcan build Sweave vignettes, provide an R devel that gets updated every time we update it on our Linux builder, and have the latest versions of all Bioconductor software and experiment packages pulled and installed directly fromgit.bioconductor.org . There are probably a few other things but that would be a good start. However, if you look at the “Goals for new container architecture” athttp://bioconductor.org/help/docker/ , one goal was “to keep the image size being shipped by the Bioconductor team at a manageable size”. I’m afraid that aiming at identical environments wouldn’t be compatible with that goal.
Vince Carey (09:46:39): > I hear you@Hervé Pagèsand I wonder about the necessity of TeX Live long term as a component of a genomic analysis ecosystem. Were we to fall back to HTML as theonly obligatory format for compiled vignettes, would pandoc be sufficient, and is this more economical in terms of container size/maintenance effort than pandoc+TeX? I am not sure it is, but I do think that errors arising from text formatting should not get in the way of code testing, interpretation of package build errors, and code revision. IMHO the main – and crucial – purpose of vignettes for the build system per se is to provide a runnable code base that provides information on reliability and interoperability. Publication-quality PDF formatting of vignettes could conceivably be factored out.
Hervé Pagès (16:13:00): > I hear you too but as maintainer of the build system that’s not my call. Taking care of the builds is basically satisfying the package needs, not the other way around. Some useful numbers before the advisory boards decide to ban PDF vignettes from Bioconductor: we still have~1282~1199 PDF vignettes vs~1225~1174 HTML vignettes in the software packages at the moment.Edit:
Alan O’C (16:22:55) (in thread): > Making a script to install the libraries you require as well turns it into a very extended (~30 mins, ymmv) coffee break
Moheb (16:25:22): > @Moheb has joined the channel
Alan O’C (16:26:13): > I assume nobody wants to go through old packages written entirely with Sweave and rewrite them in RMarkdown
Hervé Pagès (16:41:51) (in thread): > Yep, it’s more like a lunch break. Can include coffee after lunch depending on how fast you eat lunch.
Aaron Lun (17:12:17): > no.
Aaron Lun (17:12:48): > Well, if the book builder becomes available, I may consider moving csawUsersGuide to use bookdown.
Federico Marini (17:15:35): > FWIW: I started to work on a spinoff for the goodtopGOvignette as Rmd->html, moving away from Sweave
Federico Marini (17:16:29): > One side I like(d) of pdf vignettes was the fact of having them as full regular documents as they are, not after converting them to pdf
Alan O’C (17:16:45): > If you’re rewriting the documentation for topGO, can you make it less unwieldy to use as well?:sweat_smile:
Federico Marini (17:20:42): > :stuck_out_tongue:I said docs, not theRfolder
Federico Marini (17:21:23): > I think the unwieldiness is due to its long existence. Problem is that if you change now the API, lots of code chunks will break
Federico Marini (17:21:43): > not saying we needtopGO2, tho
Alan O’C (17:28:44): > Aye of course, just frustrated as GOstats and topGO both have… questionable UIs. I rewrote the former to be parallel in my last job but unfortunately it’s proprietary code and I cba redoing
Kasper D. Hansen (21:15:27): > Re: TexLive, I have for quite a while run BasicTex for my Mac, with a few (~30) packages installed additionally. That is a much smaller footprint; the installation package is 73MB
Vahid (21:52:09): > What is the recommended way of getting a list of all Bioconductor packages? > Is it reasonable to use the following? > > packages <- BiocManager::available() > packages_vector = strsplit(packages, " ") >
2020-03-16
Simina Boca (00:12:52): > There’s a package for this!
Simina Boca (00:12:53): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584971/ - Attachment (PubMed Central (PMC)): BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem > Motivation: The Bioconductor project, a large collection of open source software for the comprehension of large-scale biological data, continues to grow with new packages added each week, motivating the development of software tools focused on exposing …
Moheb (00:54:38): > May I ask, where do I post if I have questions about errors I am getting ? > I am new to R, and I am trying to get some single cell RNA-seq data analysis done. > Thanks in advance
Stuart Lee (00:55:28) (in thread): > support.bioconductor.org is probably the best place
Moheb (00:55:57) (in thread): > ok, thanks
Mike Smith (08:31:26): > As part of this month’s Developers’ Forum I thought would be good to guage peoples opinions on the type of topic we’ve been covering and the direction we should take things in the future. If you’re curious about what the Developers’ Forum is, or want to shape it’s future direction come join#developers-forum - Attachment: Attachment > The next Bioconductor Developers’ Forum is scheduled for Thursday 19th March at 09:00 PST/ 12:00 EST / 18:00 CET > > We will be using BlueJeans and the meeting can be joined via: > > https://bluejeans.com/114067881 (Meeting ID: 114 067 881)
Shraddha Pai (09:36:44) (in thread): > I agree that the Docker image is the easiest. Installing R-dev from source kept failing at the make stage for me, and took hours to get to the bottom of every objection it had.
Martin Morgan (10:02:00) (in thread): > I don’t think thestrsplit()is necessary? Also, it depends a bit on what you mean by ‘all’ and ‘Bioconductor’.available()returns all the Bioconductor software, annotation, and experiment data packages and all the CRAN packages available for your version of R. > > For finer control, look at > > > BiocManager::repositories() > BioCsoft > "[https://bioconductor.org/packages/3.11/bioc](https://bioconductor.org/packages/3.11/bioc)" > BioCann > "[https://bioconductor.org/packages/3.11/data/annotation](https://bioconductor.org/packages/3.11/data/annotation)" > BioCexp > "[https://bioconductor.org/packages/3.11/data/experiment](https://bioconductor.org/packages/3.11/data/experiment)" > BioCworkflows > "[https://bioconductor.org/packages/3.11/workflows](https://bioconductor.org/packages/3.11/workflows)" > CRAN > "[https://cran.rstudio.com](https://cran.rstudio.com)" > > which shows the repository locations where R looks when installing packages. So if you wanted to know just the vector of Bioconductor software packages, you could select that repository > > biocsoft <- BiocManager::repositories()["BioCsoft"] > > and then use R’s built-inavailable.packages()to get a matrix of available packages from that specific repository, e.g., > > > biocsoftpkgs <- rownames(available.packages(repos=biocsoft)) > > length(biocsoftpkgs) > [1] 1805 >
Vahid (11:46:01) (in thread): > @Martin Morganthank you.
Vahid (11:49:37): > @Simina BocaThank you.
Sridhar N (21:56:13): > can i fire up rstudio from with in LSF + docker?
Sridhar N (21:56:22): > or no i need to buy server pro for this?
Sridhar N (21:56:58): > i remember for Bioc2019 there was something similar to this rstudio + aws i guess?
2020-03-17
Federico Marini (04:14:55): > Maybe I misunderstood the question, but isn’t it the case for the quickstart here?
Federico Marini (04:14:56): > > docker run \ > -e PASSWORD=bioc \ > -p 8787:8787 \ > bioconductor/bioconductor_docker:devel >
Federico Marini (04:15:01): > http://bioconductor.org/help/docker/
Federico Marini (04:16:07): > > RStudio will be available on your web browser athttps://localhost:8787 . The USER is fixed to always beingrstudio. The password in the above command is given asbiocbut it can be set to anything.
Sergi Sayols (06:33:13) (in thread): > in addition to@Federico Mariniinstructions, you should submit an interactive job to LSF with > > bsub -I docker ... > > See bsub entry here > > Tho if you have LSF, your backend is probably an HPC cluster, which may mean you don’t have root access (which you need in order to run docker containers). > Your friend then is Singularity, which is well explained here also:http://bioconductor.org/help/docker/
Giuseppe D’Agostino (07:24:13): > @Giuseppe D’Agostino has joined the channel
Sridhar N (10:54:27): > @Federico Marinithanks, with LSF it gets tricky
Sridhar N (10:54:41): > this is what i had to use to invoke rstudio
Sridhar N (10:55:02): > > LSF_DOCKER_VOLUMES='/home/user:/home/userr' PATH=/home/user:$PATH LSF_DOCKER_PORTS='8787:8787' bsub -Is -G compute-research -q general-interactive -R 'select[port8787=1]' -a 'docker(rocker/verse)' /bin/bash >
Sridhar N (10:55:13): > the problem that i have now is i cannot change ports
Sridhar N (10:55:46): > @Sergi Sayols^
Sridhar N (10:56:09): > i was following thishttps://support.rstudio.com/hc/en-us/articles/200552316-Configuring-the-Server - Attachment (RStudio Support): Configuring the Server > RStudio Server: Configuring the Server Overview RStudio is configured by adding entries to two configuration files (note that these files do not exist by default so you will need to create them if …
Sridhar N (10:56:21): > to change ports incase there are many people using it
Sridhar N (10:56:50): > rstudio.conf file already exists but i cannot change it
Sridhar N (10:57:16): > looking at the dockerfile in case to see if i can expose some ports there
Sergi Sayols (11:03:13) (in thread): > you only need to change the port in the host machine, not the port Rstudio is listening from inside the container (this doesn’t conflict with anyone). Don’t touch the Dockerfile nor the rstudio.conf file. > Try changing the > > LSF_DOCKER_PORTS='8787:8787' > > variable to something else. This is controling which port in your host is mapping the port inside the container where RStudio is listening to. Also, set the appropriate resource in bsub to match the selected port in the host > > -R 'select[port8787=1]' > > Say, for instance, you set > > LSF_DOCKER_PORTS='50000:8787' > > , then you’d call bsub with > > `-R 'select[port50000=1]' > > and open Rstudio in your browser in the url > > [https://localhost:50000](https://localhost:50000) >
Sridhar N (11:04:32) (in thread): > duh
Sridhar N (11:04:34) (in thread): > that easy
Sridhar N (11:04:39) (in thread): > lemme try
Sridhar N (11:15:26) (in thread): > that worked
Sridhar N (11:15:30) (in thread): > thanks@Sergi Sayols
Sergi Sayols (11:15:45) (in thread): > excellent! you’re very welcome:slightly_smiling_face:
Sridhar N (11:18:07) (in thread): > one last question
Sridhar N (11:18:14) (in thread): > how can i add username and passsowrd
Sridhar N (11:18:43) (in thread): > i used that port and asked my friend to connect when i was live, my session got disconnected
Sridhar N (11:18:55) (in thread): > wondering if i can add username and password to avoid this
Sergi Sayols (11:20:14) (in thread): > to attach rstudio to a authenticate through eg. Active Directory, you need the licensed version of RStudio for this (not 100% sure though, please ask around)
Sergi Sayols (11:20:55) (in thread): > one think you can do is open >1 RStudio containers listening to different ports of your host (eg. 50000 as you did before, but then open another in port 50001, 50002, etc)
Sridhar N (11:21:21) (in thread): > true
Sergi Sayols (11:21:21) (in thread): > all this will be isolated rstudio instances running in their own private container area
Sridhar N (11:21:27) (in thread): > but we have a range > > 8000 and 8999 >
Sridhar N (11:21:38) (in thread): > also there are around 150 users
Sergi Sayols (11:21:43) (in thread): > ok then pick aport within this range
Sridhar N (11:22:02) (in thread): > if i pick 8000 and a diffrent user picks the same
Sridhar N (11:22:20) (in thread): > i am sure i will get disconnected if they land on the same blade
Sergi Sayols (11:22:53) (in thread): > I guess LSF will manage this resource, so port 8000 doesn’t get attached to 2 different processes
Sergi Sayols (11:24:28) (in thread): > But afaik only licensed rstudio server will allow you multiple users authenticated against an active directory
Sergi Sayols (11:24:53) (in thread): > and not the free rstudio desktop bundled in the rocker image
Sridhar N (11:31:01) (in thread): > I see
Sridhar N (11:31:09) (in thread): > that is a question i will post to IBM guys
Sridhar N (11:31:11) (in thread): > thanks
Sridhar N (11:31:14) (in thread): > once again
Sergi Sayols (11:36:12) (in thread): > you’re welcome. > maybe ask in the general channel, perhaps someone knows if this is possible with the rstudio desktop version bundled within the rocker image
Federico Marini (11:36:39) (in thread): > -> maybe this example can also be added as use case to the Docker user cases on Bioc@Lori Shepherd? I don’t know how many can be interested into it tho
2020-03-18
FelixErnst (09:25:49): > I have got a problem debugging current build issue for Bioc devel. There are a few package, which suffer from thecannot coerce type 'S4' to vector of type 'double'error. Since the Bioc Build system was upgraded tor77934I guess there is a difference tor77738, which is currently available in the docker imagebioconductor/bioconductor_docker:devel. I have updated the image yesterday and this is the ID I get > > [docker.io/bioconductor/bioconductor_docker](http://docker.io/bioconductor/bioconductor_docker)devel cea26025fd36 11 days ago 3.73 GB > > Since the docker images are based onrocker/rstudio:devel, which was updated 2 month ago, the problem appears to be upstream betweenrocker/r-ver:develandrocker/rstudio:devel. Does anyone know, when an update is triggered and who to contact to maybe fastforward this?
Stian Lågstad (09:28:23) (in thread): > Not a cache-thing this time? (As it was for me here:https://community-bioc.slack.com/archives/C35G93GJH/p1583758711067900 :slightly_smiling_face:)
Alan O’C (09:28:42) (in thread): > > I guess there is a difference to `` > Did you miss something between the backticks?
FelixErnst (09:29:15) (in thread): > No, forgotShiftto add a new line:neutral_face:
FelixErnst (09:31:14) (in thread): > Nope, sadly not a cache issue. I switched toFedoraand usedpodman, so there is no chance, that this was a cache issue:grin:
FelixErnst (09:40:37) (in thread): > With the With therstudiodocker image you will only get one user per docker instance. So you will get kicked out, if you access the session via a different browser. > > In addition, If you have multiple container running and try to open them in the same browser, they will also close on you (especially, if you use the same user names). This happens to me frequently, if I want to debuglatestvsdevel
Vince Carey (14:02:56) (in thread): > @FelixErnstcan you give specific code that generates the error …
FelixErnst (14:10:36) (in thread): > plotROCin theRNAmodRpackage and derivatives.plotROCis a wrapper around functions from theROCRpackage. Without having changed the code since release, I am unable to debug this, since the code works locally usingr77738
FelixErnst (14:14:02) (in thread): > It also breaks the Travis build, so I guess it is not some race condition, but a genuine problem. But currently I am a bit unable to get an idea, for what type of error I should look in my code.
FelixErnst (14:14:56) (in thread): > https://bioconductor.org/checkResults/3.11/bioc-LATEST/RNAmodR/malbec2-buildsrc.html
FelixErnst (14:19:56) (in thread): > https://github.com/FelixErnst/RNAmodR/blob/master/R/Modifier-roc.R
FelixErnst (14:34:33) (in thread): > Since the problem does not appear on theROCRbuild reports from CRAN (https://cran.r-project.org/web/checks/check_results_ROCR.html ) can mean hree things: I am usingROCRin the wrong way, I stumbled upon an error inROCRor with R versionr77988the problem solves itself. If you have an addition idea, I am all ears
Vince Carey (16:21:37) (in thread): > I can reproduce the error in your package in the vignette RNAmodR.Rmd … the failure is in the call to ROCR::prediction that occurs in a Map within RNAmodR:::.plot_ROCR … I cannot dig further … > > R Under development (unstable) (2020-03-17 r77988) > Platform: x86_64-apple-darwin15.6.0 (64-bit) > Running under: macOS Mojave 10.14.6 > > Matrix products: default > BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.0.dylib > LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats4 stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] ROCR_1.0-7 gplots_3.0.3 RNAmodR_1.1.10 > [4] Modstrings_1.3.11 RNAmodR.Data_1.1.2 ExperimentHubData_1.13.1 >
Steffen Neumann (16:26:15): > Hi, I am trying to help Egon Willighagen with his problem, see[Bioc-devel] help with Win10 TLS problem?. Istokay1https://bioconductor.org/checkResults/3.11/bioc-testing-LATEST/ ?
Steffen Neumann (16:43:10) (in thread): > Minimal reproducible exampledownload.file("https://zenodo.org/record/3611238/files/PubChemLite_14Jan2020_tier0.csv?download=1 ", "dummy.csv")
FelixErnst (16:43:25) (in thread): > Thank you@Vince Carey. I will have a look, whether the input is explicit enough or not.
Hervé Pagès (16:55:06) (in thread): > That’s really a question you should be asking in the#bioc-buildschannel.
2020-03-19
Lori Shepherd (10:15:03) (in thread): > Sorry I was off yesterday — I’ve seen this before too when a S3 plot method was not defined in the namespacehttp://bioconductor.org/developers/how-to/troubleshoot-build-report/#s3method – it could also be related to the plot() generic moving from graphics to base
FelixErnst (10:22:48) (in thread): > Hi Lori. Can you elaborate on this a bit? I am not trying to export and S3 method, but use it. So if it is not exported correctly fromROCRthen I am in trouble?
Lori Shepherd (10:29:33) (in thread): > i think so. But this could also be unrelated. I just thought I would toss it out there since I did see this alot initially and like the example above, it stemmed from not declaring the plot method they had created
Lori Shepherd (10:30:10) (in thread): > I would guess if you tried to use it that it would result in the same ERROR
FelixErnst (10:42:50) (in thread): > The weird thing is that ROCR does not have any build problems using R-devel (see link above)
Lori Shepherd (10:48:01) (in thread): > The probably related to the move of plot from graphics to base. The explanation we received was CRAN and Bioconductor had a few packages that “worked” because the right plot() was found in the normal search path, but now fail because it’s calling the one in base instead
FelixErnst (11:44:28) (in thread): > I guess this doesn’t have anything to do plotting. I am currently trying to get the latest R-devel to run, but if vinces suggestion holds true, that this is caused by callingROCR::predictionthen, plotting is not involved. I disabled the functions for now, until I have a working R-devel build, which I can use to reproduce the issue locally.
FelixErnst (14:28:56) (in thread): > Ok plotting is involved… -_- It was a call to the S4 plot method. I solved it by circumventing the call and went straight to the underlying function. I informed the maintainer.
FelixErnst (14:29:45) (in thread): > So no back to the original question: Who do I have to contact to get the rocker/rstudio:devel docker image updated?
FelixErnst (14:32:48) (in thread): > @Nitesh TuragaHi Nitesh just saw your posts on GitHub. Thanks for asking directly at the source.
FelixErnst (14:34:32) (in thread): > Regarding PCRE2: the package for PCRE2 support is calledlibpcre2-dev(instead oflibpcre3-dev). This makes a lot of sense:thinking_face::dizzy_face:
FelixErnst (14:39:11) (in thread): > Athttps://github.com/FelixErnst/biocdevel/tree/master/buildah you can find a complete buildsystem for r-ver, rstudio and bioc. I didn’t test it thoroughly, but it should work and got me to the point of fixing the bug mentioned above.
Moheb (15:01:53): > Hi, > I am trying to install R through the Anaconda environment > > I use the cmd line:conda install -c r rstudio Preparing transaction: done Verifying transaction: done Executing transaction: done
Martin Morgan (15:06:30) (in thread): > please seek help on the conda support channels rather than here…
Moheb (15:08:05) (in thread): > yes, sorry. > I was’t sure if I can ask here.
2020-03-20
Peter Allen (14:42:36): > @Peter Allen has joined the channel
2020-03-23
Edgar (10:15:03): > @Edgar has joined the channel
Sean Davis (10:25:26): > I didn’t see a proteomics channel, so added#proteomics.
Shian Su (21:26:52): > Is the BioC Dev Docker image suppose to have tex2pdf? My instance seems to be failing when I try to test a package.
2020-03-24
Vince Carey (01:36:12): > which image exactly are you using
Shian Su (02:06:47): > bioconductor/bioconductor_docker:devel
Steffen Neumann (06:43:07): > Hi, are there best practices how to create thepkg/data/*.rdafiles ? In the past I created and saved them manually. Where do people place, document and trigger an R script to handle that ?
Stuart Lee (06:59:49) (in thread): > I’m a fan ofusethis::use_data(data)and having an associateddata.Rthat documents it.
Steffen Neumann (07:22:51) (in thread): > Cool, thanks. Will that add a dependency to the package ? The script is still manually triggered, so maybe not ?
Steffen Neumann (07:23:00) (in thread): > https://usethis.r-lib.org/reference/use_data.html
Alan O’C (07:59:25) (in thread): > This can be considered best practice I thinkhttp://r-pkgs.had.co.nz/data.html
Vince Carey (08:50:37) (in thread): > This is something to be addressed to@Nitesh Turaga… from my scan of the dockerfile there is no tex installation, and it is not in the rocker image on which bioc containers are built. You may have to do a manual tinytex installation to make progress
Steffen Neumann (08:53:00) (in thread): > Thanks everyone, faahKO 1.23.2 and later have that now:wink:
Nitesh Turaga (09:06:03): > @Shian SuI invited you to the#containerschannel.
Jake Wagner (17:09:01): > @Jake Wagner has joined the channel
USLACKBOT (17:11:52): > This message was deleted.
Nicholas Knoblauch (17:29:05) (in thread): > Was this at the Channing Lab?
2020-03-25
brian capaldo (13:02:43): > @brian capaldo has joined the channel
2020-03-26
Aaron Lun (01:17:10): > Fixed an absolutely brutal bug with nested DelayedArray parallelization inside BiocParallelbplapplycalls.
Aaron Lun (01:18:45): > Whoops. will continue this conversation in#delayed_array
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2020-03-27
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2020-03-28
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2020-03-29
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2020-03-30
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Lori Shepherd (11:22:32): > Important Deadline Reminder: The new package submission deadline is this Friday April 3rd. The release branch of Bioconductor 3.10 will be frozen April 14th All code changes should be committed by April 13th. After this date there will be no updates to Bioconductor 3.10 packages in Bioconductor. All packages should be passing R CMD build and check in devel Bioconductor 3.11 by Friday April 24. The devel branch will be frozen on Monday April 27 to make the release 3.11 branch.
Lori Shepherd (12:21:33) (in thread): > I implemented a tryCatch when the database is checked for updates in 2.19.8. hopefully as long as the hub database has been downloaded at least once successfully if it becomes unreachable somehow to check for updates or download the latest, it will at least use the already downloaded/cached version and print out a warning – cheers
Benilton S Carvalho (13:37:10): > @Benilton S Carvalho has joined the channel
2020-03-31
Helena L. Crowell (03:18:02): > Can anyone help out with / give any insights re the following:BiocCheckusing R-devel/Bioc3.11 gives me > > This is BiocCheck version 1.23.1. BiocCheck is a work in progress. > Output and severity of issues may change. Installing package... > * Checking Package Dependencies... > * Checking if other packages can import this one... > * Checking to see if we understand object initialization... > * Checking for deprecated package usage... > * Checking for remote package usage... > * Checking version number... > * Checking for version number mismatch... > * Checking version number validity... > * Checking R Version dependency... > * WARNING: Update R version dependency from 4.0 to 4.1. > > I then changedDepends: R (>= 4.0)to4.1in theDESCRIPTION, after which all ran cleanly. But the Bioc server build fails withERROR: this R is version 4.0.0, package 'muscat' requires R >= 4.1. Now I could just ignore the error locally… but this is really confusion still. ShouldBiocCheckbe giving this warning?
Martin Morgan (06:40:37) (in thread): > yeah, that seems wrong! R-4-0-0 alpha was created in the SVN repository on Friday, and forms the basis for the next Bioconductor release and devel cycle. It looks like the Single Package Builder is running R-devel stilll@Lori Shepherd
Raphaël Bonnet (07:39:47): > @Raphaël Bonnet has joined the channel
Lori Shepherd (08:24:58) (in thread): > Until we update R on the daily builders then this will occur.
Raphaël Bonnet (10:23:54): > Hi all, I’m struggling to solve a git related issue in my first bioc package and I could use some advices. The package on the devel branch is currently passing bioc checks but it is 1 z bump ahead of my local/git version (1.1.0 on master branch DESCRIPTION / 1.1.1 on bioc devel check) due to reverting to an older commit. > > I tried syncing with fetch-merge but I only get ‘everything up to date’. > > Also the commit 8d8b0b7 which is the one shown by bioc devel check results does not appear in my git log. > > I feel I’m missing some readouts to tackle this issue, any advice? > > thx, > R
Lluís Revilla (10:52:20): > What commands did you run?git pull upstream?
Raphaël Bonnet (10:53:55): > hi Lluis, > following this :http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ steps 3 to 9
Lluís Revilla (10:56:42): > So did you merge from upstream?
Alan O’C (10:58:32): > Do you need togit merge upstream/devel?
Raphaël Bonnet (10:58:53): > I think I did: usinggit merge upstream/master
Raphaël Bonnet (11:15:02): > all I get is ‘everything up to date’
Lluís Revilla (11:22:28): > Could you provide the github url if you have the repository there?
Raphaël Bonnet (11:26:53): > yep,https://github.com/Peyronlab/MACSQuantifyR
Lluís Revilla (11:29:31): > If you want to syng your github repository with bioconductor devel you first need togit pull upstream(to get and merge the version bump from devel) followed bygit push(to update the repository on github)
Raphaël Bonnet (11:31:23): > I thought that the fetch/merge was another way to do this, I’ll give it a try right away.
Alan O’C (11:33:20): > git pull originis the same as doinggit fetch originthengit merge origin/<mybranch>(master in this case) so should be…?
Lori Shepherd (11:49:53): > Bioc2020 is proceeding with planning for the conference to be held July 29-31, with contingency planning for an online-only conference if necessary.https://bioc2020.bioconductor.org/ As part of the program we want to encourage community involvement and interactive projects. This may take the form of birds-of-a-feather discussion topics (like an open forum discussion) but could extend to ideas like short hack-a-thon projects (e.g., create a Pull Request for feature x in package y) or the compilation of short FAQ/how-to topics (e.g., how do I liftover hg19 coordinates to hg38 with Bioconductor resources). We encourage submissions from novice R/Bioconductor users and minority groups. > > We want to have some of these sessions planned and will also encourage spontaneous sessions to form on the day of the conference (pending an in-person meeting). In an effort to schedule topics that are of most interest to the Bioconductor community at large, we encourage submission of session ideas on the bioc2020 github as an open issue. (https://github.com/Bioconductor/BioC2020/issues ) > > Please include in the issue title if it’s a birds-of-a-feather (BOF), hack-a-thon (HAK), or how-to/FAQ (FAQ), and include a short description of the goals of the session. > For example: > (BOF) Annotation harmonization > (HAK) Add metadata column to package > (FAQ) How to do a lift over from hg19 to hg38 > > Please announce your session suggestion in the Bioconductor slack channel#bioc2020. This will encourage the Bioconductor community to contribute to the session. > Thank you > Lori Shepherd on behalf of the Bioc2020 planning committee - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 29 - 31, Boston, USA.
Matthew Carlucci (11:51:04): > @Matthew Carlucci has joined the channel
Raphaël Bonnet (12:37:43) (in thread): > I ‘m still getting ’everything up to date’ ..
Lluís Revilla (12:41:40) (in thread): > But did you check if the DESCRIPTION file changed?
Raphaël Bonnet (12:52:38) (in thread): > I did, nothing changed
Raphaël Bonnet (12:53:41) (in thread): > still 1.1.0
Lluís Revilla (12:55:25) (in thread): > Could you show the result ofgit remote -vandgit branch?
Raphaël Bonnet (13:21:23) (in thread): > git remote -v > originhttps://github.com/Peyronlab/MACSQuantifyR.git (fetch) > originhttps://github.com/Peyronlab/MACSQuantifyR.git (push) > upstream git@git.bioconductor.org:packages/MACSQuantifyR.git (fetch) > upstream git@git.bioconductor.org:packages/MACSQuantifyR.git (push)
Raphaël Bonnet (13:21:46) (in thread): > git branch > RELEASE_3_10 > * master
Lluís Revilla (13:27:05) (in thread): > Ok, I cloned the repository from bioconductor and there seems to be an error somewhere. The description indeed shows 1.1.0 but the landing page 1.1.1
Lluís Revilla (13:27:19) (in thread): > That’s seems a problem when building the landing page
Lluís Revilla (13:27:41) (in thread): > You did everything correctly but apparently the problem is elsewhere
Raphaël Bonnet (13:35:44) (in thread): > Do you know where the landing page gets its version ? directly from the DESC file or from the propagation of successive commits?
Raphaël Bonnet (13:35:59) (in thread): > thanks for taking the time btw
Lluís Revilla (15:35:15) (in thread): > In theory yes, from the DESC when a build is succesful
Hervé Pagès (16:41:02) (in thread): > From the DESC file of the latest versionthat propagated higher Packagedfield). You’ll also see that this was after commit 8d8b0b7 from Jan 13. Strangely,git logdoesn’t show this commit in master so it seems that some of the git history was altered at some point. > > Anyway, the propagation script won’t replace this with the current version (1.1.0). The only way to trigger a new propagation is to bump the version to 1.1.2.
Raphaël Bonnet (18:14:54) (in thread): > nice, I’ll get this in order, many thanks. Is it normal that the git pull upstream master does not replace my local version to 1.1.1, though?
Hervé Pagès (19:58:22) (in thread): > When yougit pull upstreamyou get what’s currently at git@git.bioconductor.org:packages/MACSQuantifyR.git and right now the package is at version 1.1.0 there. So that is expected. As mentioned earlier, what is not expected is that around Jan 14 it must have been at version 1.1.1 there because that’s the only way to explain how the build system could have built and propagated the version you see on the landing page. As I said, I don’t know how version 1.1.1 ended up atgit.bioconductor.org or why now it’s back to 1.1.0 there, or whygit logdoesn’t show any trace of a 1.1.1 version. If the git history was rewritten at some point (was it? by you or someone else?) there is no way for me to know.
2020-04-01
Raphaël Bonnet (06:25:39) (in thread): > I did commit a change that was reverted to an older commit that could explain the 1.1.1. At some point, I must have deleted and recreated the upstream branch, that’s maybe why I can’t find the current bioC commit in the log.
2020-04-02
Duy Pham (04:17:02): > @Duy Pham has joined the channel
2020-04-03
Helena L. Crowell (08:22:40): > Dear all, for all Bioconductor packages on MacOS Catalina (version 10.15.4) withBiocManager::version() > '3.11'``version > 'R version 4.0.0 alpha (2020-04-01 r78130)')I’m getting the below… Any suggestionshighly chooseBioCmirror()s, and various suggestions on google didn’t help…) > > > BiocManager::install("edgeR") > Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 alpha (2020-04-01 r78130) > Installing package(s) 'edgeR' > also installing the dependencies 'limma', 'locfit', 'Rcpp' > > Warning: unable to access index for repository[https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0](https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0): > cannot open URL '[https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/PACKAGES](https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/PACKAGES)' > Warning: unable to access index for repository[https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0](https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0): > cannot open URL '[https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0/PACKAGES](https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0/PACKAGES)' > Warning: unable to access index for repository[https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0](https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0): > cannot open URL '[https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0/PACKAGES](https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0/PACKAGES)' > Warning: unable to access index for repository[https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0](https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0): > cannot open URL '[https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0/PACKAGES](https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0/PACKAGES)' >
Charlotte Soneson (10:48:21) (in thread): > I think that’s all fine, you can install the packages from source.
Leonardo Collado Torres (12:36:41): > https://twitter.com/jtleek/status/1246097335244947458?s=12 - Attachment (twitter): Attachment > James was a scientific giant, dedicated to sharing what he knew with everyone no matter their background and one of the kindest people I knew. We will miss @jxtx https://twitter.com/deniswirtz/status/1246096452129918977 - Attachment (twitter): Attachment > Our hearts are heavy. James Taylor has passed away.https://pbs.twimg.com/media/EUsExGmUYAATQkn.png
Federico Marini (13:29:48): > Oh no:disappointed:
Federico Marini (13:30:04): > This is so sad to read
Hervé Pagès (13:57:30) (in thread): > This isinstall.packages()(the workhorse behindBiocManager::install()) complaining that it cannot find Mac binary packages in the BioC 3.11 repos. This is expected (we’re not producing those binaries yet) so you can ignore the warning for now. Later today I’ll make a small change to make the warning go away. No Mac binaries will be available but at least the repo where they’re supposed to be will exist (and will be empty) and that should makeinstall.packages()happy.
Elana Fertig (14:59:19): > https://bio.jhu.edu/2020/04/03/in-memoriam-professor-james-taylor/ - Attachment (Department of Biology): In Memoriam, Professor James Taylor | Department of Biology > It is with great sorrow that the Krieger School of Arts and Sciences shares that James Taylor, Ralph S. O’Connor Professor of Biology and Professor…
Michael Love (16:25:35): > This is devasting. So sorry for everyone’s loss, and I’m thinking of all the people here who were working closely with James to do this very important work of democratizing computational biology.
Rob Patro (16:43:30): > It’s unbelievable, honestly. He was such a great, fun, humble, down-to-earth guy. Obviously, a hugely impactful scientist too. He was 40!!! This is so tragic.
2020-04-04
Helena L. Crowell (03:16:31) (in thread): > Just to add that installing from source has lot’s of other issues (probably all Mac Catalina related…). E.g. > * /usr/local/include(C header .h files) no-longer exists and everything fails. A symlink from the developer tools resolves that, so far. > * BiocManager::install("x", type = "source")works, but when asked to update something, it resorts again to looking for the binaries and fails. > * manually installing each thing and it’s dependencies works, but is tedious for >500 packages… the perfect quaRantine activity! > * I triedtype = "source" / dependencies = T/F, update = T/F, ask = T/F… but none runs without failing or prompting me after less than a minute. > Not sure at this point if I’m doing everything wrong of whether Catalina is just really messed up…
Martin Morgan (08:30:21) (in thread): > There’s a globaloptions(pkgType = "source")that might make the second point better. Also BiocManager::install(type="source", ask = FALSE) with no package arguments will update the current installation, and might be a first step before installing new packages. I would also suggest (maybe unhelpfully) careful scrutiny of the current ‘R-admin’ manualRShowDoc("R-admin")orhttps://cran.r-project.org/doc/manuals/r-devel/R-admin.html - Attachment (cran.r-project.org): R Installation and Administration > R Installation and Administration
Aedin Culhane (12:07:02): > So tragic. So so sad.@Martin Morganhad written has started a tribute to him from Bioconductor, if you wish to add your tributes to him
Martin Morgan (18:14:25): > Bioconductor remembers the inspiration and leadership of Prof.James Taylor . Please see also theGalaxy Community Hub .
2020-04-05
Helena L. Crowell (01:30:19) (in thread): > Thank you, Martin, I’ll give these a try!
Charlotte Soneson (06:17:32) (in thread): > @Helena L. Crowell- in case it helps somehow, I can install Bioc packages from source with the same R alpha release that you have, on Catalina, but in order to make this work I removed (based on the note onhttp://mac.r-project.org/ ) all clang-related paths and flags from my Makevars file (keeping them, I got compilation errors from not findingstring.h).
2020-04-06
Hervé Pagès (05:37:31) (in thread): > The “unable to access index for repository…” warnings should be gone now. > I would advice against usingtype="source". The default (type="both") will try to install package binaries first and, in case they are not available, will offer to install packages from source. So even though there are no Bioconductor binary packages yet, at least you’ll be able to install all their dependencies from CRAN without the need to compile any of them (some of them are tricky to compile).
Anna Lorenc (06:40:16): > @Anna Lorenc has joined the channel
Yuzhu Duan (20:24:48): > @Yuzhu Duan has joined the channel
2020-04-08
Leonardo Collado Torres (16:20:44): > FYI, for those of you struggling with R 4.0.0 on macOS 10.15.4 like I was, I see that binaries are live now for CRAN packages:smiley:Note that Simon Urbanek recommends that we don’t use~/.R/Makevarsanymore. More athttps://github.com/s-u/rJava/issues/216#issuecomment-611126265
Hervé Pagès (17:03:35): > They should be live for Bioconductor packages too very soon. Stay tuned…
Shian Su (19:49:36): > Thanks for the heads up Leo, so we’re not meant to use custom clang version anymore? IIRC the clang bundled with Xcode doesn’t have openMP support, this might be pretty annoying.:thinking_face:
Peter Hickey (19:53:36): > technical discussion of openMP on macOS here:http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-Apple-Clang-does-support-OpenMP-if-libomp-is-available-td458.html#a461 This summary by Kevin Ushey is more understandable to me at least (albeit related to data.table’s use of openMP ):https://github.com/Rdatatable/data.table/issues/4348#issue-593486932 - Attachment (r-sig-mac.29524.n8.nabble.com): R-SIG-Mac - [R-SIG-Mac] Apple Clang does support OpenMP (if libomp is available) > [R-SIG-Mac] Apple Clang does support OpenMP (if libomp is available). Dear all, Lack of OpenMP support in Apple’s build of Clang is cited as one reason for not using it in CRAN builds, but this is…
Hervé Pagès (19:58:27): > Also this recent thread on R-SIG-Machttps://stat.ethz.ch/pipermail/r-sig-mac/2020-April/013340.html confirms that, by adopting the official Apple toolchain for R 4.0.0, the CRAN folks are dropping support for OpenMP on Mac. Luckily we seem to have only 1 software package (runibic) in Bioconductor that uses OpenMP on Mac, and adjusting it should be easy.
Aaron Lun (19:59:32): > Thank god I didn’t embark on my “OpenMP’ing everything” project.
Shian Su (20:19:12): > That’s a shame, because OpenMP was such a painless and high performance way to get parallelism in C++.
Shian Su (20:21:52): > It’s probably still worth writing OpenMP code as it’ll work fine on Unix machines where most heavy lifting is done anyway.
Aaron Lun (20:22:11): > yeah, on real computers.
Kasper D. Hansen (20:35:37): > I am not sure I would describe OpenMP as painless
Kasper D. Hansen (20:35:42): > Perhaps I am a wimp
Aaron Lun (20:36:26): > well, relative to refactoring it to use intel’s TBB.
2020-04-09
Federico Marini (08:16:32): > As if 2020 did not start on a wrong foot already:https://twitter.com/Rebeccatennan10/status/1248184282197176325?s=20 - Attachment (twitter): Attachment > @Protohedgehog
Sean Davis (11:35:04): > I wanted to highlight@Laurent Gattos recent post in#education-and-trainingabout getting training to be a teacher for the Carpentries and to contribute to Carpentry Bioconductor material.
Ian Williams (13:29:37): > @Ian Williams has joined the channel
Hervé Pagès (17:00:40): > As you’ve probably noticed already the builds on Mac are back:https://bioconductor.org/checkResults/3.11/bioc-LATEST/ The build target is High Sierra, like for the official Mac built of R 4.0.0 alpha (available herehttps://mac.r-project.org/ ) and the Mac binary packages available on CRAN. This means that the binaries we produce are only compatible with High Sierra or higher,as long as you’re using the official Mac built of R 4.0.0 BiocManager::install()with the Mac built of R 4.0.0 will pick up binary packages from CRAN and Bioconductor 3.11. It will fallback on source packages only when the binaries are not available. Please let us know here or on the bioc-devel mailing list if you run into any problem with this. > > Thanks to those of you who participated to the early testing of these new binaries.
Leonardo Collado Torres (20:07:52): > Awesome, thanks Hervé!
2020-04-10
Leonardo Collado Torres (01:29:42): > Looks like the recent Rccp issues are now fixed (so we can install from CRAN again instead of from source through GitHub or the linux binaries from Dirk’s drat)https://twitter.com/eddelbuettel/status/1248425917535289346?s=21 Reading several of the recent issues and pull requests (some are mentioned negatively but not linked to from the blog post) I saw that Dirk was annoyed by things that could be improved with more explanation & wording of the GitHub contributing.md doc.It feels to me like it’s probably useful to come up with a template that helps guide new contributors. Maybe we could have one, and an issues one. I guess usethis is likely the best home for these templates (some exist there already I think).Kind of related, I would likely not make a PR about R’s macOS docs despite how confusing they were for me recently. Who wants to be called out negatively?I do like what I’ve heard about the tidyverse developers day where many submit PRs, starting as small as a typo. I guess that they teach attendees how to make a PR the tidyverse devs would like to receive. - Attachment (twitter): Attachment > Rcpp 1.0.4.6 on CRAN > Seamless R and C++ Integration > http://dirk.eddelbuettel.com/blog/2020/04/09#rcpp_1.0.4.6 > #rcpp #rstats https://pbs.twimg.com/media/EVNMTx5U4AEVgj1.png
Pariksheet Nanda (10:50:27) (in thread): > If you’re using C++, when you the execution header with gcc, it will link to tbb for you.https://en.cppreference.com/w/cpp/header/execution
Pariksheet Nanda (10:50:36) (in thread): > For example:https://github.uconn.edu/HPC/parallel-intro-cpp/blob/master/hello-world/hello-world.cpp - Attachment (GitHub Enterprise): HPC/parallel-intro-cpp > Contribute to HPC/parallel-intro-cpp development by creating an account on GitHub.
Aaron Lun (11:49:34) (in thread): > I would say that’s not really the problem, it’s refactoring the for loops into classes to get it parallelized.
Aaron Lun (11:49:53) (in thread): > By comparison, openMP just allows me to slap a#pragmaon top and it’s done.
Aaron Lun (11:52:45) (in thread): > TBB also has UBSAN problems, which is concerning at least for CRAN devs.
Sherlock_Fan (19:48:02): > @Sherlock_Fan has joined the channel
2020-04-12
Shubham Gupta (21:50:59): > Rcpp does not build code from the subdirectories. How to tell it to get those files as well? > I am using > > devtools::load_all(".", recompile=TRUE) > > In the output, I can see that it is readingsrc/subdirectory/file3.hhowever, at the end I see following output at the Console: > > g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o package.so RcppExports.o file1.o file2.o -L/usr/lib/R/lib -lR > > I do not seesubdirectory/file3.o. Is there any way to tell it to compile them? I have included all the path infile1.cpp
Aaron Lun (22:03:41): > You’ll have to fiddle withMakevars. Seehttps://cran.r-project.org/doc/manuals/r-release/R-exts.html#Compiling-in-sub_002ddirectories . - Attachment (cran.r-project.org): Writing R Extensions > Writing R Extensions
Aaron Lun (22:04:20): > If I were you, I would reconsider the need to have files in subdirectories. I did it once, way more trouble than it’s worth.
Aaron Lun (22:06:10): > Generally speaking I would onlycontinue to do it if it was a requirement that was imposed from without, e.g., you’re distributing some library (e.g., HDF5lib, HTSlib) in an R package. Then you have no choice, but hopefully it’s as simple as calling theirMakefilewhile passing all the necessary flags.
Shubham Gupta (22:16:00): > Thanks. I have decided to remove subdirectories. Not worth the pain
2020-04-13
Zinian Wang (15:12:57): > @Zinian Wang has joined the channel
2020-04-15
Xinran Tian (12:32:31): > @Xinran Tian has joined the channel
Al J Abadi (19:54:27): > Hi everyone, > Are package maintainers supposed to receive emails on the BioC builds, or at least when they fail?
Lambda Moses (19:56:36): > Yes, when they fail
Aaron Lun (20:01:44): > I occasionally get them for BioC-release.
kipper fletez-brant (20:02:27): > I only get emails around next-BioC-release-dates
Al J Abadi (20:08:56): > That’s strange. Is it something that can be opted into / out of through BioC account, possibly?
Martin Morgan (20:40:55): > During most of the year, messages are sent on a schedule (once weekly, I think), and when specific conditions are met in the RELEASE builds (failure in the previous evening builds), to the package maintainer (‘cre’ field in Authors@R) as listed in the DESCRIPTION file. For instance,@Al J Abadiis listed as ‘ctb’ but not ‘cre’ in mixOmics, so would not receive automated email. > > The devel builds are not included during the regular cycle because the devel branch is, well, for development where things can go wrong and the person doing the breaking is keeping track of the changes anyway… We add the devel build emails and up the frequency when we get closer to each release. > > Core team members may reach out to individual maintainers, or others in the DESCRIPTION file if the maintainer is not responsive, as the release becomes imminent and packages will not propagate. > > Other uncertainties are the vagaries of email and spam detection, local filter rules, and of course problems with our code. Github is almost entirely irrelevant to the build system.
Al J Abadi (20:46:35): > Thanks@Martin Morgan. Yes thecrecorrespondent also did not receive email and that was strange to me, but as you mentioned it was the devel version so that was probably why. I think it would be nice if maintainers could opt-in/out of such emails for different build because for example we check the build on Travis, but at times such as this Travis build works but BioC’s does not.
Aaron Lun (20:47:33): > There were RSS feeds at some point. But I ended up building a page with the Bioc build badges so that I could see a wall of green and feel good about it.
Aaron Lun (20:47:53): > Though that’s never actually happened. Some green, mostly yellow, and spots of red.
Martin Morgan (20:58:51): > I like the wall of green idea; the information is pretty easily available programmatically > > > library(dplyr) > > rpt = BiocPkgTools::biocBuildReport(version="3.11") > > rpt %>% filter(pkg %in% "mixOmics") %>% select(pkg, last_changed_date, node, stage, result) > # A tibble: 11 x 5 > pkg last_changed_date node stage result > <chr> <dttm> <chr> <chr> <chr> > 1 mixOmics 2020-04-13 10:17:04 malbec2 install OK > 2 mixOmics 2020-04-13 10:17:04 malbec2 buildsrc OK > 3 mixOmics 2020-04-13 10:17:04 malbec2 checksrc ERROR > 4 mixOmics 2020-04-13 10:17:04 tokay2 install OK > 5 mixOmics 2020-04-13 10:17:04 tokay2 buildsrc OK > 6 mixOmics 2020-04-13 10:17:04 tokay2 checksrc ERROR > 7 mixOmics 2020-04-13 10:17:04 tokay2 buildbin NA > 8 mixOmics 2020-04-13 10:17:04 machv2 install OK > 9 mixOmics 2020-04-13 10:17:04 machv2 buildsrc OK > 10 mixOmics 2020-04-13 10:17:04 machv2 checksrc ERROR > 11 mixOmics 2020-04-13 10:17:04 machv2 buildbin OK >
USLACKBOT (20:58:52): > Did you mean:%/%
Hervé Pagès (21:34:15): > @Al J AbadiTo clarify: we activated automatic build failure notifications for the devel software builds (BioC 3.11) about 1 month ago. They’re senttwice a week on Linux kimanh.lecao@unimelb.edu.au in the case of mixOmics). You can’t opt out. I looked at the logs and I don’t see that any email was sent on Monday for mixOmics, probably because the package was not failing that day (based ongit logthe package has changed a lot since last Sunday, with more than 14 commits). BTW questions/discussions about the builds should happen in the#bioc-buildschannel.
Al J Abadi (22:43:48): > Hi@Hervé Pagès, > Thanks for your clarifications and the tip. I just joined the build channel.
Al J Abadi (22:46:35): > @Aaron Lunyes for instance[http://bioconductor.org/shields/build/devel/bioc/\({pkg_name}.svg](http://bioconductor.org/shields/build/devel/bioc/\) {pkg_name}.svg)shows you the devel build badge and it can be useful to have it for example in the README, but at the same time an email triggered by a build anomaly seemed equally useful. Although the twice-weekly scheduled emails should now do, thanks to the BioC team.
Aaron Lun (22:58:43): > I have so many stochastic Windows failures that I just deleted the auto-generated emails unless they were personally addressed to me. “Dear Aaron, I hope this letter finds you well…”
Hervé Pagès (23:02:03): > Not sure what auto-generated emails you are talking about but we don’t send emails for failures on Windows.
Aaron Lun (23:02:36): > Really?
Aaron Lun (23:03:03): > Hm. Guess that makes sense!
Aaron Lun (23:03:26): > Otherwise I’d be getting a lot more emails.
Hervé Pagès (23:04:21): > yep, the idea is to maximize the signal/noise ratio
2020-04-16
Modeline Longjohn (00:02:45): > @Modeline Longjohn has joined the channel
Modeline Longjohn (00:04:42): > Hello everyone, I am new here and new to working with bioconductor. I am trying to figure out what tools to use for differential expression analysis of miRNA microarray data. Any got any ideas? Thanks in advance.
Dario Strbenac (04:30:48): > It depends on the brand of microarray you have. Some of them will have one probe for each miRNA whereas others will have multiple probes of different lengths for each miRNA. The shorter probes are less specific to the miRNA and the longer probes are more specific to the miRNA. How you should summarise them is anyone’s guess. > > Once you have a single number per miRNA and per sample, the differential expression analysis is also challenging. There will only be a small number of miRNA expressed and it seems dangerous to use a method like quantile normalisation on such a small number of features. Many experiments have spike-ins.
Mike Smith (04:34:08) (in thread): > Here’s my ‘Wall of (hopefully) green’https://msmith.de/dashboard.html I think I stole the idea from you!
Alan O’C (05:34:12) (in thread): > limma’s certainly been used for this. I’d look at the literature and see what normalisation people are using:slightly_smiling_face:https://scholar.google.com/scholar?q=limma%20microrna&btnG=Search&as_sdt=800000000001&as_sdtp=on
Alan O’C (05:35:45) (in thread): > Also preprocessing as Dario mentioned. For some you’ll need to merge probes somehow
Pariksheet Nanda (06:37:24): > IsSeqinfo(genome = "hg19")working for anyone else? It works for hg38 but with hg19 I get the attached error. MyBiocManager::valid()is true. - File (R): snippet.R
Martin Morgan (06:41:40) (in thread): > BiocManager::version()? If it’s 3.9 or less then unfortunately this is a change in UCSC that cannot be fixed on our end without updating to the current release (3.10; note that 3.11 is due at the end of this month…)
Dylan Harwood (09:26:26): > @Dylan Harwood has joined the channel
Martin Morgan (11:21:02) (in thread): > Seems like there’s a DataTable.js generalization in there, where the default is a mega-table of build results, and the user can select particular packages, builds (release vs. devel) and stages, perhaps with a way to capture preferences via a URL? Update on a Github crontab action or on status change? (I think BiocPkgTools consultshttps://bioconductor.org/checkResults/3.11/bioc-LATEST/STATUS_DB.txt instead of scraping the build report…)
Jenny Drnevich (12:42:24): > What is everyone’s take on R 4.0 - is the switch going to be relatively pain-free or is going to be a big adjustment? R news here:https://cran.r-project.org/doc/manuals/r-devel/NEWS.html and here’s one blog post:https://blog.revolutionanalytics.com/2019/12/preview-of-r-400.html . Any other info would be appreciated! - Attachment (Revolutions): R 3.6.2 is out, and a preview of R 4.0.0 > R 3.6.2, the latest update to the R language, is now available for download on Windows, Mac and Linux. As a minor release, R 3.6.2 makes only small improvements to R, including some new options for dot charts and better handling of missing values when using running medians as a smoother on charts. It also includes several bug fixes and performance improvements. But big changes are coming to R with version 4.0.0, which is expected to be released not long after R’s official 20th birthday on February 29, 2020. (The CelebRation 2020 conference will mark the occasion in Copenhagen.) The…
Alan O’C (12:48:48) (in thread): > Better colours is a huge improvement! The only thing I’m concerned about is stringAsFactors changing and silently breaking things (not sure if this is in 4.0.0 or soon after). Actually it seems like 3.5 should probably have been v4, since it was the biggest set of breaking changes.
Dan Bunis (13:22:44) (in thread): > Are they better colors to you@Alan O’C? For protanomalous me, in the base colors, I can’t tell the 3rd and 7th apart for R4 as well as I can for R3. And then with things muted in the ggplot2 default palette, 2 vs 5 vs 8 (red vs gray vs gray-pink?) && 3 vs 7 would all be hard for me if these were dots.
Alan O’C (13:25:07) (in thread): > Interesting, I’m not colourblind (assuming that’s still a reasonable term to use) and had assumed they’d done some research on best practice (no shortage of good, colourblind-safe palettes at this point…). Disappointed in that case
Alan O’C (13:25:56) (in thread): > The default colours are currently awful for a number of reasons, eye bleed from excessive brightness being only one. I’d hope they’d do a lot of thinking before settling, though
Dan Bunis (13:32:40) (in thread): > It’s incredibly hard to make a good colorblind friendly palet period let alone with extra thoughts included like you mentioned. (and yes, the colorblind term isn’t charged at all; I was just being more specific.) And then if you need more than 8 colors….. There are actually far fewer color blind-friendly palets than one might think!
Jenny Drnevich (13:32:46) (in thread): > Personally I am happy with the default stringsAsFactors changing because the very first line of all my codes isoptions(stringsAsFactors = FALSE). But I can see how flipping the default could be a widespread problem
Alan O’C (13:34:00) (in thread): > I like the factors change massively, I’m just afraid that some packages/scripts silently depend on the current (awful) setting.
Alan O’C (13:35:11) (in thread): > Interesting, I thought that changes in luminance should make it easy to spot differences even if unable to distinguish colour
Alan O’C (13:35:39) (in thread): > In general palettes with <8 colours is tricky, though there are obviously poor choicescough
Dan Bunis (13:37:09) (in thread): > Luminance can indeed be helpful! But the problematic R4 colors don’t look very different in luminance to me:man-shrugging:
Alan O’C (13:39:07) (in thread): > Yeah I think they went for equal luminance, which is obviously going to make things tricky, and is maybe slightly weird as it’s not hugely important for qualitative palettes to be equal luminance. I think some of the colorbrewer palettes are a bit better at least? They certainly advertise colourblind-friendliness
Dan Bunis (13:43:25) (in thread): > They do have targeted ones. Just a few are for discrete data though: - File (PNG): image.png
Alan O’C (13:45:22) (in thread): > Good to know, I’d forgotten which were recommended. I try to use Paired mostly, and when n>12 (hello scRNAseq) it getsvery
Dan Bunis (13:46:11) (in thread): > I ended up making my own for my dittoSeq color-blindness friendly RNAseq Viz package based off of the panel inWong B, “Points of view: Color blindness.” Nature Methods, 2011 . But now that I’m getting into shameless self-promotion, maybe we’ve killed the topic lol - Attachment (Nature Methods): Points of view: Color blindness > Points of view: Color blindness
Dan Bunis (13:47:57) (in thread): > Essentially just added in darker and lighter versions after the required number of colors grows past 8. Not perfect, but:man-shrugging:.
Alan O’C (13:52:22) (in thread): > Cool, would you consider putting the palette(s) in a CRAN package? Or I could, it’s probably max a few hours of work. I’m keen to encourage people to use decent palettes (to the point where I made a PR to stop Seurat from using the default ggplot2 ones in lieu of pals::alphabet)
Dan Bunis (13:58:00) (in thread): > Oh sure! I’d gladly do that. I just don’t have enough time atm… If you could help point me towards any how-tos specifically for palette packages, if there are any, that would certainly help with the time issue.dittoSeq itself is a BioC package as of the coming release, but the color panel could easily be separated.
Alan O’C (14:06:31) (in thread): > Time is at a premium these days alright! I know dittoSeq, so I might see if I can pull things together this weekend:slightly_smiling_face:
Dan Bunis (14:08:25) (in thread): > Fine with me! All you should need, if you don’t know already, isdittoColors.
Jenny Drnevich (14:11:46) (in thread): > Coincidentally, the One R Tip a Day on twitter points to a “Fundamentals of Data Visualization” and you might find this chapter useful, particularly section 19.3:https://serialmentor.com/dataviz/color-pitfalls.html - Attachment (serialmentor.com): Fundamentals of Data Visualization > A guide to making visualizations that accurately reflect the data, tell a story, and look professional.
Dan Bunis (14:22:39) (in thread): > Wonderful chapter! Definitely some good points. I’m certainly biased, but I do think dittoSeq does an okay job on each. For example, offering shaping and faceting as alternatives to color when possible.
Martin Morgan (18:09:43) (in thread): > I think the transition to R-4.0 for people with extensive collections of scripts & hacks (i.e., long-time users) will be very disruptive. > > This is because there are almost certainly many implicit uses that rely onstringsAsFactors = TRUE. It won’t be enough to set a global option, because that’ll just propagate the problems into the future and confuse anyone you share your script with. > > There are other disruptive changes, too, especiallyclass(matrix())which will cause many conditional statements written asif (class(matrix() == "matrix"){}to generate an error (useis(matrix(), "matrix")orinherits()instead. > > Lori (primarily) has collated this developer-orientedhelp page .
Alan O’C (18:30:20) (in thread): > class(matrix())is stillmatrix(though now length 2), and I guess there’s much moreis.matrix(x)than the former
Modeline Longjohn (19:11:57) (in thread): > @Alan O’CThanks for your response. I will look at those papers. Thanks again
Shian Su (20:12:59) (in thread): > I’ve been hit by both the colour change and the stringsAsFactor change.:cry:
Shian Su (20:16:41) (in thread): > The annoying part is not updating things, but making tests and functions work without assuming people are up to date.
Shian Su (20:16:55) (in thread): > Lots ofif (getRversion() >= "4.0.0")
2020-04-17
Lori Shepherd (13:45:22): > Bioconductor is excited to announce an opportunity to recognize those making significant outstanding contributions to the Bioconductor community. The Bioconductor project proudly launches the first call for Bioconductor Awards, honoring various forms of contributions to the project. Four awardees will be selected, each having contributed to the project in an outstanding way based on one or more of the criteria foundhere Please fill out the nomination form by June 15 :Nomination Form
2020-04-19
Shubham Gupta (00:37:26): > .datapronoun doesn’t work withdplyr::lst()? > > zone <- c(rep(10,4), rep(20, 4), rep(30, 4)) > value <- c(4.5,4.3,4.6, 5,5, rep(3,7)) + round(rnorm(12, sd = 0.1),1) > df <- data.frame(zone, value) > # Works > dplyr::group_by(df, .data$zone) %>% dplyr::summarise(var3 = dplyr::lst(value)) %>% dplyr::ungroup() %>% as.data.frame() > # Error > dplyr::group_by(df, .data$zone) %>% dplyr::summarise(var3 = dplyr::lst(.data$value)) %>% dplyr::ungroup() %>% as.data.frame() > > Is there a way to fix this? Otherwise I get a warning in R CMD check that value has no visible binding for global variable value.
Vince Carey (10:30:56): > @Shubham Guptathis is not a bioconductor question – please pose to r-help, perhaps?
Shubham Gupta (14:15:45): > Thanks. I will post there.
Stuart Lee (21:59:08) (in thread): > it might also be appropriate for the rstudio help site too
2020-04-21
Pariksheet Nanda (16:03:13) (in thread): > Yeah, it is 3.9. Thanks for the explanation ^^
2020-04-22
Kelly Eckenrode (09:24:17): > @Kelly Eckenrode has joined the channel
Kelly Eckenrode (12:38:31): > Hi all! > > I am new to this community and have introduced myselfhere today. I am a postdoctoral researcher with@Levi Waldron. > > I’d like to invite you to a newly formingjournal club about single cell multimodal (SCMM) data here .Please fill out this doodle to help us schedule our first meeting time: https://doodle.com/poll/3ry8kg66yv3rsbvq Join us in the#education-and-trainingchannel. This is where I will post SCMM journal club updates. > > In addition to the journal club, if you are interested in sharing a SCMM dataset of yours or one of interest, please share with us. To streamline our database curation, please read the following guidelineshere . Parties interested in contributing would have to make a pull request to the repository. > > I’m looking forward to reading with you! - Attachment: Attachment > Hi everyone! > > I am a molecular biologist (PhD, at City University of New York) who is learning bioinformatics in my postdoc (with @Levi Waldron at School of Public Health at City University of New York). > > My research interests include bacterial biofilms (specifically how bacterial communities form. This could be pathogenic types or commensal human microbiomes) and developing packages for single cell multimodal datasets. > > I am a new Bioconductor user and enthusiastic about digging in. - Attachment (doodle.com): Doodle: Single Cell Multimodal Journal Club > A weekly single cell multimodal literature club
Levi Waldron (13:37:45) (in thread): > Thanks@Kelly Eckenrode! Also take a look at this preliminaryjournal club page with a list of papers and table for a schedule, and theSingleCellMultiModal data package by@Marcel Ramos Pérezwhich will be released with Bioconductor 3.11 as a way to help Bioconductor developers develop methods and data classes for these types of data, and which we’d love to get help with in adding benchmark datasets, as per the link Kelly posted above. It’s in the “curated” ExperimentHub style (ie a simple interface similar to curatedTCGAData, curatedMetagenomicData, HMP16SData).
Alex Tong (15:21:03): > @Alex Tong has joined the channel
Shraddha Pai (15:23:01): > Hi all, our package netDx builds successfully on the Win and Unix systems of bioc-devel but fails due to a Java error on the Mac system. netDx pulls a jar file, which changes based on whether the detected java version is 11 or other. This works for me on java 8 and java 11 systems (tested on Debian 10). > . > My understanding is that the Mac bioc-devel system uses Java 11 and the others use Java 8. > . > Any thoughts on why the build is still failing? I’d like for this issue to be resolved before the upcoming release. Thanks
Lucy (15:29:22): > @Lucy has joined the channel
Martin Morgan (16:07:03) (in thread): > Running on my local mac I see > > > out <- suppressMessages( > + buildPredictor( > + dataList=brca,groupList=groupList, > + makeNetFunc=makeNets,outDir=outDir, > + numSplits=2L,featScoreMax=2L, > + featSelCutoff=1L, > + numCores=1L, > + logging="none") > + ) > |======================================================================| 100% > > WARNING: An illegal reflective access operation has occurred > WARNING: Illegal reflective access by net.sf.cglib.core.ReflectUtils$2 (file:/Users/ma38727/Library/Caches/netDx/540c43bed3_genemania-netdx.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) > WARNING: Please consider reporting this to the maintainers of net.sf.cglib.core.ReflectUtils$2 > WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations > WARNING: All illegal access operations will be denied in a future release > Warning in file(file, "rt") : > 'raw = FALSE' but '/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T//Rtmp3MHAGj/pred_output/rng1/LumA/GM_results/' is not a regular file > Warning in file(file, "rt") : > cannot open file '/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T//Rtmp3MHAGj/pred_output/rng1/LumA/GM_results/': it is a directory > Error in inherits(dat, "try-error") : object 'dat' not found > > If I run the command interactively and without thesuppressMessages(), I see > > Java 8 detected > QueryRunner time taken: 0.0 s > > so it does not seem to be a java version-specific issue.traceback()after the error occurs tells me I should look atcompileFeatureScores() > > debugonce(compileFeatureScores) > > and then re-running thebuildPredictor()command I get to > > Browse[2]> > debug: try(dat <- read.delim(fName, sep = "\t", header = TRUE, as.is = TRUE, > skip = 1), silent = TRUE) > Browse[2]> > Warning in file(file, "rt") : > 'raw = FALSE' but '/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T//Rtmp3MHAGj/pred_output/rng1/LumA/GM_results/' is not a regular file > Warning in file(file, "rt") : > cannot open file '/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T//Rtmp3MHAGj/pred_output/rng1/LumA/GM_results/': it is a directory > debug: ctr <- ctr + 1 > Browse[2]> fname > Error: object 'fname' not found > Browse[2]> fName > [1] "/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T//Rtmp3MHAGj/pred_output/rng1/LumA/GM_results/" > Browse[2]> dir(fName) > [1] "CV_1.query" "CV_2.query" > > Again it doesn’t look particularly like a javaa error?
Hervé Pagès (16:19:01) (in thread): > @Shubham GuptaThe link you gave is for the check result on Windows. But it’s about the build failure on Mac right?
Shraddha Pai (16:20:49) (in thread): > @Martin MorganThe reason the file is missing is because a previous step which uses java has failed.sigh
Shraddha Pai (16:21:50) (in thread): > @Hervé PagèsYes, the issue is indeed on the Mac - sorry sent the wrong link because I was just looking at the summary table at the top.
Hervé Pagès (16:24:32) (in thread): > > The reason the file is missing is because a previous step which uses java has failed > An immediate improvement, and hopefully an easy one, is to have that step fail harder. Failing early with a clear error message is always better than failing late with an obscure error message:wink:
Shraddha Pai (16:31:44) (in thread): > Yes. I should do a test to see if a file exists and if not stop(“error”)
Shraddha Pai (16:31:50) (in thread): > (but more descriptive message)
Martin Morgan (19:02:47): > I’m delivering a spontaneous ‘QuaRantine’ introductory R course (https://mtmorgan.github.io/QuaRantine ). After getting through the very basics of R, there’s a brief foray scheduled for ‘Bioinformatic analysis with Bioconductor’ and I’m looking for some simple things that the participants could do, hopefully ending with a pretty picture. Any suggestions? It really can’t be complicated. We could doBiostrings::readDNAStringSet(), maybe translate strains to AAStringSet and find that mutations are mostly silent; or do something with the ape package showing strain genealogy from an existing tree (but ape ain’t Bioconductor). Any suggestions (with available data that does not require too much munging) for avenues that might be interesting? - Attachment (mtmorgan.github.io): 40 Days and 40 Nights > An ad hoc course to learn R for bioinformatics, using the COVID-19 epidemic as an excuse.
Aaron Lun (19:03:27): > is a multiple sequence alignment too hard?
Christopher Eeles (19:04:41): > @Christopher Eeles has joined the channel
Martin Morgan (19:10:20) (in thread): > If it’s (almost) a one-liner, then the complexity & sophistication of the analysis isn’t important… It would be really great to have a punch-line, and I’m not sure that multiple sequence alignment per se would deliver that? But then that’s why I’m asking, looking for my blind spots!
Aaron Lun (19:12:48) (in thread): > Looking at sequence divergence at critical positions seems pretty cool to me. I don’t know how much knowledge of the viral proteins we have to mark out the epitopes, though.
2020-04-23
Devika Agarwal (05:55:18): > @Devika Agarwal has joined the channel
Charlotte Rich-Griffin (06:00:05): > @Charlotte Rich-Griffin has joined the channel
Robert Castelo (14:55:13): > @Martin Morgancalculate GC content .. maybe too simple? i think the nature paper of 2001 of the human genome has a figure about that distribution; extract splicing dinucleotides of introns and notice that most of them are GT - AG.
Al J Abadi (22:10:29): > If integration of multi-omics data does not seem too complicated ( I can create a ready to use short example ), our package can create nice circos plots for supervised analyses which can possibly be of interest? Here’s a detailed example which can be made shorter by omitting the tuning parts:http://mixomics.org/mixdiablo/case-study-tcga/
2020-04-24
Martin Morgan (06:11:36) (in thread): > thanks for the offer and nice case study; I’ll look in detail. My initial feeling is that it requires quite a bit of biology / statistics / informatics which could be daunting to the (remote) audience…
Chengyang Ji (10:01:31): > I’d recommendggtree, a Bioconductor package (not my package but I use it a lot) for visualizing a phylogenetic tree. Based on ggplot2, pretty easy to usehttps://yulab-smu.github.io/treedata-book/ - Attachment (yulab-smu.github.io): Data Integration, Manipulation and Visualization of Phylogenetic Trees > Data Integration, Manipulation and Visualization of Phylogenetic Trees
Nicholas Cooley (15:43:27): > I have a general question abouttranslate()’sif.fuzzy.codonargument; will it translate to any of the amino acid ambiguity codes if appropriate?
Hervé Pagès (16:19:37): > Please ask on the support site. Thanks!
Hervé Pagès (16:26:33): > (It’s all documented in?translate. If there is something unclear about the documentation, please be specific when you ask on the support site.)
Anthony (20:06:54): > @Anthony has joined the channel
Preethy (21:26:36): > @Preethy has joined the channel
2020-04-27
Jonathan Hicks (13:48:25): > @Jonathan Hicks has joined the channel
Kelly Eckenrode (15:48:22): > For those of you interested in the Single-Cell Multimodal journal club, please see the post in#education-and-traininghttps://community-bioc.slack.com/archives/CUKAPEE1Y/p1588012080023400 - Attachment: Attachment > For those of you interested in the Single-cell Multimodal (SCMM) journal club, thank you so much for filling out the Doodle poll. According to consensus, Monday at 8am - 9am EDT / 2PM - 3PM European Central Time , is the best time. > > Our first meeting will be next Monday, May 4th on Zoom . And also add the invite to your calendar here!) > > We will introduce ourselves and get acquainted with the meeting format. In addition to introductions, I will also present a review paper, “A secret life of cells” by Michael Eisenstein. You can find a PDF attached here and on the SCMM journal club wiki > > Here you can find the agenda and where the meeting notes will be recorded: SCMM meeting notes > > I look forward to meeting all of you and beginning a thoughtful conversation about single cell multimodal data!
2020-04-28
Minoo (07:09:35): > @Minoo has joined the channel
Matt Paul (11:48:58): > If anyone has 10 minutes for a survey, I have a friend who does research on archiving, with a specific focus on the how people are preserving their work using Git.https://nyu.qualtrics.com/jfe/form/SV_5ArtYnx6kWMXYNv - Attachment (nyu.qualtrics.com): Investigating the Scholarly Git Experience Survey > Qualtrics makes sophisticated research simple and empowers users to capture customer, product, brand & employee experience insights in one place.
Anamaria Elek (12:56:54): > @Anamaria Elek has joined the channel
Lori Shepherd (18:51:28): > Bioconductor 3.11 is Released! Thank you to all developers and community members for contributing to the project! lease see the full release announcement:https://bioconductor.org/news/bioc_3_11_release/
Peter Hickey (18:59:39) (in thread): > A big thank you to everyone on the core team!
2020-04-29
Anthony Sonrel (03:45:24): > @Anthony Sonrel has joined the channel
Dominik Szabo (05:06:38): > @Dominik Szabo has joined the channel
Jeff Leek (09:05:16): > @Jeff Leek has joined the channel
caglarberkel (11:57:19): > @caglarberkel has joined the channel
Lambda Moses (14:30:47): > I do still want to push some changes to the release branch. The output ofgit branch -ris still this today: - File (PNG): Screen Shot 2020-04-29 at 11.29.54 AM.png
Lambda Moses (14:31:02): > When do we get theRELEASE_3_11branch?
Aaron Lun (14:31:15): > It’s been out since a few days ago. I mean, I’ve got it.
Lambda Moses (14:32:13): > OK, I didgit fetch --alland got it
Robert Ivánek (17:16:04): > I wanted to useseqLogo package and realised that it fails check in both release and devel. I could fixed it for myself. I sent an email to listed maintainer but so far no response. Is there a way how to send PR or fix it tohttps://git.bioconductor.org/packages/seqLogo ? Since 2011 the only commits in repo are bumped versions by core team.
Sridhar N (20:31:27): > is there a reason not to use another package if all else fails?
Sridhar N (20:31:56): > seqLogo was a workhorse for me until i found thishttps://www.bioconductor.org/packages/release/bioc/html/motifStack.html - Attachment (Bioconductor): motifStack > The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.
2020-04-30
Robert Ivánek (03:24:47): > Thanks for the tip. suremotifStackis an option.
Robert Ivánek (03:33:13): > ButseqLogois used by many other packages so I believe it is worth to be fixed.
Federico Marini (04:27:22): > FWIW,DESeqis also failing on all systems
Robert Ivánek (04:50:18): > IsDESeqdeprecated now? I thought it was replaced byDESeq2
Federico Marini (04:57:24): > not that I know
Federico Marini (04:57:31): > it is “just” a build error
Charlotte Soneson (04:59:56): > DESeqis deprecated (was in Lori’s email from March 30)
Lori Shepherd (09:21:05): > Yes DESeq is deprecated in favor of DESeq2. It is rare case where we are leaving it deprecated an extra release (3.12) because of its large reverse dependency chain. Having DESeq and DESeq2 caused a lot of confusion esp on the support site and since the later is the replacement for the former it made sense to finally deprecate it with permission from the maintainers.
Lori Shepherd (09:23:43) (in thread): > General if a package is failing in release and devel with an inactive/unresponsive maintainer the package will be marked for deprecation. I see you have submitted a patch to us which martin applied – we will also reach out to the maintainer – hopefully they are responsive – if they remain unresponsive you can request to take over as maintainer of the package if you are interested
Federico Marini (09:48:31): > Thanks@Lori Shepherd! I just noticed that without the successful build, some packages indeed are also not installing in the newer version of R I installed (yes, I like to carry them over from release to release:slightly_smiling_face:)
Federico Marini (09:48:51): > Is the vignette error going to be fixed or will that be left as it is?
Lori Shepherd (09:49:10): > Not sure – up to the DESeq maintainers
Federico Marini (10:37:43): > Ok, thanks:wink:
2020-05-03
Nitin Sharma (12:17:43): > Hello everyone, I have created a channel#singlecell-queriesfor more general queries regarding single-cell analysis.
Jack Zhao (19:59:34): > @Jack Zhao has joined the channel
Dario Strbenac (21:30:05): > Could someone reproduce this error? Is it a bug? > > library(VariantAnnotation) > fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") > vcf <- readVcf(fl, "hg19", param = ScanVcfParam(info = NA, geno = NA)) > > subset(vcf, FILTER == "PASS") # Works well without param setting above. > Error: subscript is a logical vector with out-of-bounds TRUE values > vcf[rowRanges(vcf)$FILTER == "PASS", ] # Workaround >
2020-05-04
Nils Kurzawa (04:35:36): > @Nils Kurzawa has joined the channel
Hervé Pagès (05:05:14) (in thread): > Yup, I can reproduce this. Can you please open an issue herehttps://github.com/Bioconductor/VariantAnnotation/issues ? (withsessionInfo()) Thx!
Nadine Bestard-Cuche (05:38:52): > @Nadine Bestard-Cuche has joined the channel
Nadine Bestard-Cuche (06:11:39) (in thread): > Hi! Your channel is not visible on the Channels list unless clicking on your comment. I am relatively new to Slack and I just joined this group so I don’t know if this is on purpose. However, I have seen other groups where all the existing channels available to join are listed on the left pannel. If there is a way of doing that it might be a good idea. Your message will soon be lost in the clutter and it would be a shame such an interesting channel remains unnoticed.
Nitin Sharma (06:18:44) (in thread): > Thanks for your message and joining the channel. > This was not done on purpose. Pinning#singlecell-querieswith existing channels will be a good idea but I am not sure how to do that as I am relatively new to slack as well. Maybe one of the admins of the workspace such as@Sean Davisor@Marcel Ramos Pérez**** ****can help us with this.
Nadine Bestard-Cuche (06:21:01) (in thread): > I just noticed there is a Channel browser with quite a lot of channels available; so it might actually be on purpose. Let’s see what they say.
Nitin Sharma (06:22:10) (in thread): > I am sure lot of interaction at#singlecell-querieswill promote it
Zhiyuan Hu (09:06:03): > @Zhiyuan Hu has joined the channel
Sean Davis (10:46:06): > When users join slack, there are a limited number of “default” channels that folks are automatically subscribed to. There is not really the concept of “pinning” a channel; a user has joined a channel or not. > When creating new channels, you may “invite” folks to the channel and they will automatically be added. You can announce the creation of the new channel on#general(in another more specific channel). > In terms of creating channels designed for “general questions” about a topic, I’d suggest to consider asking questions on the support site as a first option. The user community there is MUCH bigger than here. Also, any questions and answers here are likely to serve a pretty small community of folks. There is a balance and use of slack vs more traditional communication approaches is an evolving topic. These editorial comments are not meant to discourage use of slack for Q&A, but just to point out that there are both strengths and weaknesses of using slack in this context.
brian capaldo (10:50:14): > I’ll also point out slack is fleeting
brian capaldo (10:50:38): > stuff doesn’t stick around for ever
Martin Morgan (12:00:53) (in thread): > fwiw this slack is ‘permanent’; but I agree that the support site is much more user-facing and the correct place for user-oriented posts
brian capaldo (12:01:37) (in thread): > oh, good to know
MarieV (12:19:30): > @MarieV has joined the channel
Sanchit Saini (15:43:52): > @Sanchit Saini has joined the channel
Shraddha Pai (17:25:28) (in thread): > Hi@Martin Morganand@Hervé PagèsI’m still having this issue of netDx not building on the BioC machv2. > > Since the thread above, I’ve tested it on my Mac Air which has java 8, as well as on a Docker running Debian 10 with java 8. So on all my machines the package builds and runs correctly. > > I’m unable to debug the reason it doesn’t work on machv2. Any help would be great; this is the last niggling issue to get resolved so I can announce the package release in BioC. > > Any help would be great, thank you! It would be great to get that “build:error” badge gone
Norbert Tavares (18:17:43): > NSF Opportunity:Conferences for Building Computational Literacy in Biological Sciences
Hervé Pagès (19:54:50) (in thread): > The BuildPredictor.Rmd vignette fails for me trying to download a file that doesn’t seem to exist: > > hpages@spectre:~/git.bioconductor.org/software/netDx/vignettes$ R CMD Stangle BuildPredictor.Rmd > Output file: BuildPredictor.R > > Then from R: > > > source("BuildPredictor.R", echo=TRUE) > ... > ... > ... > > ## ----eval=TRUE---------------------------------------------------------------- > > head(groupList[["clinical"]]) > $age > [1] "patient.age_at_initial_pathologic_diagnosis" > > $stage > [1] "STAGE" > > > > ## ----------------------------------------------------------------------------- > > makeNets <- function(dataList, groupList, netDir,...) { > + netLis .... [TRUNCATED] > > > ## ----eval=TRUE---------------------------------------------------------------- > > set.seed(42) # make results reproducible > > > outDir <- sprintf("%s/pred_output",tempdir()) # location for intermediate work > > > # set keepAllData=TRUE to not delete at the end of the predictor run. > > # This can be useful for debugging. > > out <- suppressMessages( > + buildPre .... [TRUNCATED] > bfcdownload() will overwrite exisiting files, continue? (yes/no): y > |======================================================================| 100% > > Warning: download failed > web resource path: '[http://download.baderlab.org/netDx/genemania-cytoscape-plugin-3.5.0.jar](http://download.baderlab.org/netDx/genemania-cytoscape-plugin-3.5.0.jar)' > local file path: '/home/hpages/.cache/netDx/file7574709eeabe' > reason: Not Found (HTTP 404). > Warning: bfcdownload() failed > rid: BFC2 > file: '[http://download.baderlab.org/netDx/genemania-cytoscape-plugin-3.5.0.jar](http://download.baderlab.org/netDx/genemania-cytoscape-plugin-3.5.0.jar)' > reason: download failed > Error: download failed; see warnings() >
2020-05-05
Shraddha Pai (09:51:52) (in thread): > Ooh that is outdated.
Shraddha Pai (09:52:24) (in thread): > Let me confirm that I performed agit push upstream master
Shraddha Pai (10:22:15) (in thread): > H’m. I just performed a git clone fromhttps://git.bioconductor.org/packages/netDx and it seems to have the latest code, which doesn’t download the jar file you mention above. How can I check when that github repo was last updated? If I visitgit.bioconductor.org I don’t see any timestamp…and get an error message if I try to open the url above in a web browser. > > Sorry if this should be more obvious.
Martin Morgan (10:28:59) (in thread): > git log on the checked out repo?
Shraddha Pai (10:37:11) (in thread): > Thanks@Martin Morgan. OK, I don’t understand now why@Hervé Pagèsgets the error above. I updated the path to the jar on April 21, and thegit logcommand on the checked out repo fromgit.bioconductor.org shows a last update date of April 27. So the issue of Java 8 vs 11 detection should have been resolved?
Hervé Pagès (13:29:42) (in thread): > I see “bfcdownload() failed” so it looks like you’re relying on BiocFileCache for downloading the jar file. Maybe I have something stale in my cache? How do I know? It means other people might run into the same problem.
Jonna Heldrich (15:11:16): > @Jonna Heldrich has joined the channel
2020-05-06
Shraddha Pai (12:25:10) (in thread): > Thanks@Hervé Pagès. I updated the BiocFileCache code that downloads the jar. I was previously using > > if (!isFALSE(bfcneedsupdate(bfc,rid))){ > bfcdownload(bfc,rid,ask=FALSE) > } > > but that wasn’t enough to download the file if the URL had changed. So now I added this: > > urlChanged <- rid_rec$fpath != fileURL > if (urlChanged) { > message("File path changed. Updating...") > bfcupdate(bfc, rid, fpath=fileURL, ask=FALSE) > } > > I ran a test aftermv-ing the target file and renaming thefileURLin my code (so download would fail if it tried to find the “old” file). This seems to work and catch all update scenarios. > > Updated master, let’s see what happens.
Aaron Lun (15:55:47): > Any old-timers around here who worked with human/mouse sequencing data before a reference genome came out? I need some history to fill in the preface to a book.
Dan Bunis (20:34:27): > This’ll probably come off as annoying and very SF LGBTQ+ of me,:pride:, … but just to acknowledge and be inclusive of any nb or trans folks who may be here, a non-binary inclusive way of saying “s/he” is simply = “they”
Aaron Lun (20:35:17): > Hm. Well, okay, wasn’t that important anyway.
Dan Bunis (20:35:29): > (I’m sure you didn’t mean anything or even think of it, but just for everyone’s acknowledgement)
Aaron Lun (20:35:34): > Just wondering whether we had someone right here immediately, but whatever.
Hervé Pagès (20:46:08) (in thread): > Makes a lot of sense when speaking. However the written form “s/he” is not binary if you see it as the interval with bounds “she” and “he”:nerd_face:
Dan Bunis (20:48:40) (in thread): > True! Not sure it’s what many people would think of, but still valid!
2020-05-07
Aedin Culhane (10:25:01): > Hi Aaron I know people who can help.. what exactly do you need to know. Sanger sequencing/ Staden alignment/ Contigs etc
Shubham Gupta (12:33:53): > Hi I just found a bug in my package that is available with this release. Is it possible to check-in fixes? or do I have to wait till next release?
Henrik Bengtsson (12:38:37) (in thread): > Singular “they” is grammatically correct. It’s in the Chicago Manual of Style (CMOS) since 2017.
Aaron Lun (12:39:48): > Great, now it looks like@Dan Buniswas referring to my comments.
Dan Bunis (12:45:26): > Oh man. There was no attack or blame meant to anyone whether it was directed at you or the now retracted comment. I still say “he or she” occasionally myself without thinking about it!
Hervé Pagès (12:45:40) (in thread): > Yes, please fix in both, the master and RELEASE_3_11 branch. For the latter, make sure to not introduce any disruptive change i.e. changes that could possibly break code that is using your package (e.g. change in argument or function names, or change in function behavior). Thanks!
Aaron Lun (12:46:04): > We should use threads more, that’s the problem with having two conversations in parallel.
Dan Bunis (12:47:15) (in thread): > Push instructions here:http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
USLACKBOT (12:47:16): > This message was deleted.
Shubham Gupta (12:59:35) (in thread): > Thanks very much. It says that commit format should be > > git commit -m "bug fix: my bug fix" > > I don’t have this format for commit i just write “fixed xyz” > Would that cause any problem?
Dan Bunis (13:02:45) (in thread): > I don’t generally use command line git, but I think the quoted bit is just the name for the commit and shouldn’t matter for the actual code/package much. But I’m not a core team member so perhaps someone else can confirm?
Shubham Gupta (13:05:50) (in thread): > Thanks! I think that this is for best practices only
Leonardo Collado Torres (17:14:28) (in thread): > I agree, it’s just hard to do this. I have seen it well executed in one other Slack, but I guess many of us started using Slack before threads were a thing.
Levi Waldron (17:17:18): > FYI<!channel>, BioC2020 will be a virtual conference - discussion in the#bioc2020channelhttps://community-bioc.slack.com/archives/CLAEUFVAA/p1588885599025100 ; planning will be very active in the next few weeks, details to come. - Attachment: Attachment > <!channel> it is official that BioC2020 will be an online-only conference, during the same week as planned. We on the BioC2020 committee are actually pretty excited, because we have time to design it well and to develop an innovative, interesting, productive, inclusive, community-building online conference. It is not too late to get involved if you are excited about planning a great online conference. A couple things: > 1. If you’d like to take part in some brainstorming, check out https://app.sli.do/event/gvh5mzfq/live/questions (# 52549) to toss out ideas and up/down-vote, read/add to our more detailed brainstorming document at https://docs.google.com/document/d/12mBgGjQRsmbxj3g8Qi73k1fMAckJHxJbHtdMn7S4Jgc/edit?usp=sharing , or write your thoughts here in this channel. > 2. if you already registered, we’ll be in touch about your refund. The online conference fee is TBD but will be significantly less expensive.
James MacDonald (17:31:30) (in thread): > Listening to Mariah Carey sounds like a lot of work. Do you get paid double for that?:grinning:
Vivek Das (17:51:41): > I would definitely try to join it this year if possible. Thanks for the information
2020-05-08
Daniel Piqué (01:19:01): > @Daniel Piqué has joined the channel
Martin Morgan (02:56:32): > Join us for ‘BiocCheck-a-thon’, a week-long virtual hackathon to improve BiocCheck and the consistency and quality of Bioconductor packages! Seehttps://github.com/Bioconductor/BiocCheck/wiki for details; starting May 18.
Waldir Leoncio (03:28:53): > @Waldir Leoncio has joined the channel
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Marcel Ramos Pérez (09:06:29): > Join the#bioccheck-a-thonchannel to participate
2020-05-11
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2020-05-12
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2020-05-13
Aaron Lun (03:57:45): > max.col’s defaults are crazy. > > In this case, the determination of a tie assumes that the > > entries are probabilities: there is a relative tolerance of 1e-5, > > relative to the largest (in magnitude, omitting infinity) entry in > > the row. > That’s anything but the maximum column value!
Shian Su (04:38:57): > Is this to account for complex numbers in some wacky way?
Shian Su (04:41:31): > I mean it’s “most likely” the maximum column value.:stuck_out_tongue:
Hervé Pagès (13:28:44): > Also why wouldn’t it supportna.rmlike any other matrix summarization method:face_with_rolling_eyes:@Henrik Bengtssonany chance you’d consider adding decentwhichRowMaxs()andwhichColMaxs()functions to matrixStats?
Henrik Bengtsson (13:33:01) (in thread): > Sounds like a good feature request. Please bring it up onhttps://github.com/HenrikBengtsson/matrixStats - otherwise it’s 100% certain it’ll be lost in the noise. Proof-of-concept examples illustrating what to expect are very helpful too, especially if they include corner cases (whatever they are in this case)
Hervé Pagès (15:32:04) (in thread): > Done:https://github.com/HenrikBengtsson/matrixStats/issues/176
Michael Lawrence (18:42:27): > A patch formax.col()would also be welcome.
Shian Su (20:08:06): > > mat1 <- matrix(rep(1e4, 24), nrow = 2) + c(0, 0, 1, 1) > max.col(mat1) # always even > > mat2 <- matrix(rep(1e5, 24), nrow = 2) + c(0, 0, 1, 1) > max.col(mat2) # could be anything >
Shian Su (20:12:27): > Should the tolerance be adjustable or an option to force exact comparison?
Dan Bunis (20:41:13): > I don’t think there should be a tolerance at all, at least not by default. Maybe it’s just my interpretation, but I think this was Aaron’s as well… The function name ismax.col, notnear/potentially/almost.max.col()
Aaron Lun (20:42:03): > Indeed.
kipper fletez-brant (20:47:47): > https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/all.equal ?
Alan O’C (20:55:31): > There’s already tolerance of ~2e-16 based on.Machine[["double.eps"]], surely? Floating point comparisons are already iffy without adding extra noise. It does bother me thatwhich.maxdoesn’t have comparable options and just gives you the first max
Alan O’C (20:57:31): > (which I think is also a bad default)
Aaron Lun (21:04:40): > Politely put, the currentmax.colbehavior is “surprising”.
Alan O’C (21:11:06) (in thread): - File (PNG): s_compat.png
2020-05-15
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Martin Morgan (08:59:50): > #bioccheck-a-thondetails have been posted to the slack channel; seehttps://github.com/Bioconductor/BiocCheck/wiki for additional detaiils
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2020-05-17
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2020-05-18
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Martin Morgan (11:03:16): > The item at the bottom ofhttps://cancerletter.com/articles/20200515_4/ is a funding opportunity for development of visualization software for cancer genomic data; thought it might be interesting to (US-based?) investigators on this list…
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2020-05-19
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2020-05-21
Pariksheet Nanda (08:16:32): > Hi folks, I’m trying to scope out the work I need to put into updating some packages. We use a set of packages from a collaborator’s lab that uses nVidia CUDA for doing SVM computations. But the packages never made it into Bioconductor. The past few times I’ve installed it I’ve had to hand editconfigure.ac because I needed to add some defines, fix the hard coded GPU architecture, incorrect detection of CUDA paths, and rerunautoreconf. Some of the other packages also need some tweaks. I’m expecting to leave the lab in a year and would rather fix this mess so that other grad students can install the packages more normally. The only example of a GPU or CUDA package I see in Bioconductor is gpuMagic. Is that the only approved CUDA / GPU package? Are there any others? I know one of Bioconductor’s philosophies is to prioritize cross compatibility on Windows, Mac OS and GNU Linux, so I imagine that may limit how many GPU packages make it in (edit: s/CPU/CUDA/).
Pariksheet Nanda (08:18:11): > I suppose I could try to add a dependency on gpuMagic and then think carefully about how to deal with the libsvm C++ dependency.
JiefeiWang (10:00:31): > Hi@Pariksheet Nanda, have you considered using the existing CUDA package likegpuR? This may make the configuring process less painful and the package more portable.gpuMagicis an OpenCL-based package but it does not provide SVM function, you need to manually write it. As far as I know, there is no GPU on Bioconductor servers, so any GPU-only solution will suffer. I would suggest making two versions of SVM, one for R and one for GPU, then you can automatically switch between them based on the availability, this can help you pass Bioconductor check.
JiefeiWang (10:08:59): > The point is not to make the GPU solution portable, but to make the package portable. As you said you have to manually edit configure file to make it work, I will suspect even Bioconductor accepts all the CUDA packages you’ve mentioned, there is no chance for the other grad students to install your package normally.
Pariksheet Nanda (10:55:13): > @JiefeiWangThanks for the suggestion of using gpuR. It looks like gpuR also uses OpenCL, and the gpuR author also wrote gpuRcuda, but that never made it into CRAN and was last updated 2 years ago. My collaborator’s implementation is tightly coupled to both libsvm and CUDA. At the minute it looks like there’s a lot of work to do with adding at least some unit tests, cleaning up the code, and fixing obsolete dependencies that I’ll have to sick with CUDA for now so that I have some test harnesses in place to start replacing CUDA. Also thanks for your valuable insight about having some fallback to non-GPU functionality. That fallback already exists within the package and can be toggled at runtime.
2020-05-22
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2020-05-25
Martin Morgan (12:41:49): > Bioconductor Technical Advisory Board Nominees, open until June 3. Details linked fromhttps://support.bioconductor.org/p/131307/
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2020-05-26
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2020-05-27
Shraddha Pai (11:08:34): > Hi all, I resolved a nightly build error on my package netDx using the BioC docker and R 4.0.0. The offending example now works and I pushed the commit to my github copy and then to BioC. But a subsequent build still finds the error. What am I missing?https://bioconductor.org/checkResults/3.11/bioc-LATEST/netDx/malbec2-buildsrc.html Just to be sure this morning I fetched the repo afresh usinggit clonehttps://git.bioconductor.org/packages/netDx within my Docker and ranR CMD build netDxwhich completed successfully. > > Thanks!
Lori Shepherd (11:11:39): > We do not see any changes pushed to thegit.bioconductor.org repository. Please try pushing to upstream again and note if there are any error messages. Also make sure there is a valid version bump
Lori Shepherd (11:12:32): > Remember to push to release 3.11 you need to be pushing to the RELEASE_3_11 branch (we do see changes pushed on the master / devel 3.12 branch but also with no version bump)
Shraddha Pai (11:14:20): > Thanks Lori. I will make the version bump and set my upstream to push to the RELEASE_3_11 branch. That’s probably my problem right there.
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2020-05-28
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Kozo Nishida (14:24:42) (in thread): > I copiedhttps://github.com/csoneson/ExploreModelMatrix/blob/master/.github/workflows/R-CMD-check.yaml (just like@Kevin Rue-Albrecht) > and applied it tohttps://github.com/afukushima/rRPMM/runs/705444057?check_suite_focus=true And I found this does not show GHA RED status even if there is WARNING. > Do these actions only catch ERROR (not catch WARNING) ?
Federico Marini (15:01:23): > AFAIK warning is still not a fail there
Federico Marini (15:01:37): > an the one action run you linked is all green
Federico Marini (15:01:40): > (now)
Kozo Nishida (15:16:52): > Thanks for the information. > I’ll manually check WARNING.
Lucy (16:04:25): > Hi all, > I am teaching a course on pathway analysis in R next week and I was wondering what everyone’s favourite pathway analysis packages for bulk RNA-seq and scRNA-seq are? > Thanks!
Dan Bunis (16:06:04): > I useclusterProfilerhttps://bioconductor.org/packages/clusterProfiler/ - Attachment (Bioconductor): clusterProfiler > This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.
Lucy (16:06:23): > Thanks, yes I like this one and was thinking about using it:+1:
Federico Marini (17:05:22): > I’d say topGO, goseq, reactomePA and fgsea
Federico Marini (17:07:16): > I’ll avoid the shameless plug forGeneTonicto be used after one running these tools (to explore in detail e.g. the relationships between expression values and gene signatures)
Federico Marini (17:07:32): > oh wait too late:smile:
Matt Ritchie (20:17:25): > I’m also biased, but you might findEGSEA useful (which also has an associated workflow packageEGSEA123 that could be handy if you need material for a hands-on practical - the associated workflow article is available athttps://f1000research.com/articles/6-2010 ). Happy to share some introductory slides on this if it is of benefit to you - Attachment (Bioconductor): EGSEA > This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. - Attachment (Bioconductor): EGSEA123 > R package that supports the F1000Research workflow article `Easy and efficient ensemble gene set testing with EGSEA’, Alhamdoosh et al. (2017). - Attachment (f1000research.com): F1000Research Article: Easy and efficient ensemble gene set testing with EGSEA. > Read the latest article version by Monther Alhamdoosh, Charity W. Law, Luyi Tian, Julie M. Sheridan, Milica Ng, Matthew E. Ritchie, at F1000Research.
Lambda Moses (20:40:50): > I like topGO, but I would like to try clusterProfiler
Kozo Nishida (23:47:31): > Is there any example of package transferred from CRAN to Bioconductor? > I’m one of the author ofhttps://cran.r-project.org/web/packages/DiffCorr/index.html . > I think Bioconductor might be a more appropriate place for distribution.
2020-05-29
Robert Castelo (02:55:42): > @LucyThe good oldGOstats is also very popular and my shameless plug isGSVA :sweat_smile: - Attachment (Bioconductor): GOstats > A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations. - Attachment (Bioconductor): GSVA > Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.
Lucy (03:58:26): > Thanks everyone for your great suggestions! I will have a go with some of them:slightly_smiling_face:
Martin Morgan (04:33:48) (in thread): > packages do occasionally make the trip from CRAN to Bioconductor. One important point is that a package can’t exist in two places at once, so there is some point (when it is added to the Bioc devel branch) where it is removed from CRAN. > > I think a major theme these days is robust interoperability in the Bioconductor ecosystem, so you’d likely need to think about how to re-use common Bioconductor data representationshttp://bioconductor.org/developers/how-to/commonMethodsAndClasses/ . ‘Real’ vignettes (with fully evaluated code chunks demonstrating package functionality) are also required. It’s also worth-while paying attention to packages that you depend on, and that depend on you; the twice-yearly Bioconductor release schedule and availability of separate repositories for each release can introduce challenges when there are extensive mixes of CRAN / Bioc dependencies.
Federico Marini (04:51:43) (in thread): > Is the output format “constrainable” into what is expected here?https://github.com/federicomarini/GeneTonic/blob/master/R/gs_shaker.R
Federico Marini (04:52:06) (in thread): > Because in that case I’m totally up for anothershakerfunction!
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Ludwig Geistlinger (11:18:54) (in thread): > Hi@Lucy: > > The annotation section ofhttps://www.nature.com/articles/s41592-019-0654-x lists a number of Bioconductor packages, partly already mentioned above, for bulk and > single-cell GSEA. > > If you like working with a SummarizedExperiment (or derivatives such as > DESeqDataSet and SingleCellExperiment), you might find the EnrichmentBrowser > package (https://bioconductor.org/packages/EnrichmentBrowser ) useful. > > Seamless access to 20 different set-based and network-based enrichment methods ( > comprehensively benchmarked here:https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbz158/5722384 ), that comes in the current release with additional > access to gene sets from the MSigDB for 11 different species, gene set libraries from Enrichr, > for 5 different species, and simplified application of legacy enrichment methods to RNA-seq data. - Attachment (Nature Methods): Orchestrating single-cell analysis with Bioconductor > This Perspective highlights open-source software for single-cell analysis released as part of the Bioconductor project, providing an overview for users and developers. - Attachment (Bioconductor): EnrichmentBrowser > The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.
2020-05-31
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2020-06-01
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Matt Ritchie (07:55:09) (in thread): > Not sure - great name for a package and the functions within it though!
Joan (13:35:01): > does anyone has recommendation on bioconductor packages on bulk rna-seq data analysis? I am new to bulk rna-seq and. looking for package(s) to start my first bulk rna-seq analysis. thanks ~
Alan O’C (13:36:34) (in thread): > DESeq2 is generally highly regarded
Joan (13:37:04) (in thread): > great, I will look into it. thanks Alan!
Stephanie Hicks (13:40:23): > @Joanthere a ton of great workflows for this on the bioc website
Alan O’C (13:42:44) (in thread): > I think the vignettehttps://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html and workflowhttps://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html are very helpful
Joan (13:43:47) (in thread): > checking the website … thanks for pointing out the direction!
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Federico Marini (14:59:39) (in thread): > can’t hide I am quite proud of the whole:smile:
Federico Marini (15:00:14) (in thread): > now I am working on a function that “compresses” the info, couldn’t avoid call itdistill_
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2020-06-02
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Lori Shepherd (08:34:23): > Friendly reminder: Please submit your nominations for Bioconductor Awards in by June 15 th. Nominations are open to the public. For more information and links to the nominating form please seehttps://support.bioconductor.org/p/130094/
Lori Shepherd (11:13:25): > Registration for Bioc2020 is Open. The virtual conference will be held July 27 - July 31. The cost of registration is $50 USD. Please see the Bioc2020 Event Website for more information:http://bioc2020.bioconductor.org/registration - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 29 - 31, Boston, USA.
Federico Marini (14:01:19) (in thread): > I’m in:heart:
2020-06-04
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2020-06-05
Lori Shepherd (08:23:04): > Have you received excellent assistance or troubleshooting on the support site? Don’t forget to nominate your assistant for a Bioconductor Support Site award! Nomination deadline June 15
2020-06-06
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2020-06-07
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Adewale Ogunleye (06:24:36): > Hi, any suggestions on lncRNA-specific annotation software after logFC calculations
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Sean Davis (10:10:12) (in thread): > @Adewale Ogunleye, this is a great question for the support site,https://support.bioconductor.org/ . Be as specific as you can about what you want to do, ideally including an example of what you want to annotate and an example of what kind of output you would like to see. The support site offers about 20x more people to answer your question and any answer is then publicly searchable for others with the same question.
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2020-06-08
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Danny Kearns (08:51:11): > Hi, I’m trying to find a weighted log odds ratio for a summarizedExperiment object. I’m using the tidylo package to do my analysis, but I’m getting some results. Anybody ever used this package?
Lori Shepherd (08:56:32): > Enjoying a new package submitted for Bioconductor 3.10 or Bioconductor 3.11?New Packages for Release 3.10 and 3.11 (see all tabs) Nominate it for a Bioconductor New Package Award! Nominations are open to the public and the deadline is June 15Bioc2020_newPkgAwards.png
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Ino de Bruijn (16:32:49): > Hey all - I’ve been trying to read up on what I can do within academia to support the Black Lives Matter movement. I think the #ShutDownAcademia on Wednesday 6/10 is a good first step:https://twitter.com/MiaDoesAstro/status/1268944608798466049 (https://www.shutdownstem.com/ ). Wanted to share here to encourage others to join
Dan Bunis (16:59:28): > Thanks for sharing! Sharing elsewhere myself as well
Ino de Bruijn (18:59:08) (in thread): > Thank you!
Dan Bunis (19:02:54) (in thread): > Kinda the least I can do for this, so certainly no thanks needed:man-shrugging:. I’ve been thinking of sharing other things here as well, myself, but haven’t been sure about breaking that wall.
Dan Bunis (19:10:07) (in thread): > I have been keeping a list of resources on things that we can all be doing in support of the BLM movement (USA-focused as that’s where I am, but not academia-focused). I’m unsure about fully breaking the professional wall here, so for now, anyone interested in the list, DM me and I will send it your way.
2020-06-09
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Lori Shepherd (08:51:26): > Have you come across a package that was so easy to use and everything documented and well organized? Now is the time to let that documentation shine! Nominate someone for outstanding documentation. Nominations are open to the public but the deadline is fast approaching. Please fill out theNomination Form by June 15th.
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2020-06-10
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Lori Shepherd (11:19:22): > Is there someone in your area actively involved in engaging and growing the Bioconductor community? Know someone hosting virtual or in-person Bioconductor outreach events? PleaseNominate by June 15th for the Bioconductor community engagement and outreach award. Nominations are open to the public.
Hervé Pagès (12:37:00): > No nomination for best package sticker?
Kasper D. Hansen (13:21:21): > I want to update an experiment data package. Where is that stored these days? I can see from the git documentation that annotation packages are stored “elsewhere”, but I couldn’t see experiment data packages mentioned
Kasper D. Hansen (13:21:51): > package in question isbsseqData
Lori Shepherd (13:22:04): > they are git tracked like software.git.bioconductor.org
Kasper D. Hansen (13:23:04): > oh yes
Lori Shepherd (13:23:06): > git@git.bioconductor.org:packages/bsseqData
Kasper D. Hansen (13:23:18): > I had a typo with/instead of:
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Kasper D. Hansen (19:08:35): > Who can I contact about an annotation package updating issue? I am re-designing the annotation stack for minfi and I would like to replace the annotation packages one time “soon” and another time before the next release, ie. a 2-stage update procedure.
Hervé Pagès (19:18:53): > Should be the same procedure as when you send your updated annotation packages before a release.@Daniel Van Twiskor@Kayla Interdonatoor@Lori Shepherdshould be able to provide the details. Maybe seize the opportunity to turn the packages into AnnotationHub-based data packages. In any case, make sure you get rid ofLazyData: yes.
Kasper D. Hansen (20:59:36): > Well, that’s only going to be partly solved right now. But I agree in principle
Kasper D. Hansen (21:00:40): > Anyway, if someone who is willing to work with me (and work with me here really means be willing with uploading a new version of ~5 packages soon (in the next week or so) and do it again in 2-3 months time) could DM me, that would be awesome
2020-06-11
Kozo Nishida (05:45:50): > Is there any Bioconductor pacakge that depends onhttps://cran.r-project.org/web/packages/tensorflow/index.html ?@Satoshi Kumeis trying to learn how to create a Bioconductor package that depends on tensorflow.
Shian Su (06:01:33): > You can see the packages that depend on it in the bottom of that page under “Reverse dependencies”.
Shian Su (06:04:04): > http://www.bioconductor.org/packages/release/bioc/html/scAlign.html seems to be an example but it’s literally failing to build right now because of tensorflow. - Attachment (Bioconductor): scAlign
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Kasper D. Hansen (12:02:14): > @Daniel Van Twisk,@Lori Shepherd,@Kayla Interdonatoin case you didn’t see my question: > > Anyway, if someone who is willing to work with me (and work with me here really means be willing with uploading a new version of ~5 packages soon (in the next week or so) and do it again in 2-3 months time) could DM me, that would be awesome
2020-06-12
Lori Shepherd (08:46:52): > Bioconductor Scientific or Informatic Technology Advancement Award. This award is for outstanding contributions enabling computational analysis or representation of data from new scientific technologies or new informatic technologies within the project via package development or other means. Have a good candidate (or multiple candidates)? PleaseNominate them by June 15. Applications are open to the public and any individual may submit more than one nomination.
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2020-06-14
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2020-06-15
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2020-06-16
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2020-06-17
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2020-06-18
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2020-06-19
Michael Love (10:55:54): > A number of BioC folks are at this BIRS multi-omics integration virtual meeting. One question that has come up today is, whether accessibility and specifically colorblind friendly plotting is or should be part of the submission checklist.
Michael Love (10:56:49): > Should we point new developers toward the cb friendly palette that is part of R 4.0?
Michael Love (10:58:29): - File (PNG): Screen Shot 2020-06-19 at 10.58.15 AM.png
Michael Love (11:00:11): > bottom left palette is specifically designed for accessibility
Martin Morgan (11:27:00) (in thread): > is there an easy programmatic way to check, or to encourage (maybe updating BiocStyle or something inbiocthis )?
Michael Love (11:37:48) (in thread): > i was thinking about this, but probably not so easy to check e.g. the vignette figures
Michael Love (11:43:37) (in thread): > but even just a bulletpoint on the submission checklist? e.g. “Please consider that some of your users may be colorblind and so elements with rainbow color schemes may not be easily discerned. You can check your plots using online colorblind simulators for e.g. red-green colorblindness. Note that the”Okabe-Ito” built-in palette in R >= 4.0 is designed to be colorblind friendly.”
Dan Bunis (12:20:33): > Okabe-Ito is what dittoSeq’s colors are based off of because they work for me / for the most common forms of color blindness (red-green). Very much a fan.
Dan Bunis (12:22:38): > Making legend icons larger can also be quite helpful for distinguishing “similar” colors. It helps to be able to at least figure out the proper label even when colors may still be hard to tell apart. So this could also be a part of the suggestion to consider colorblind audiences.
Martin Morgan (13:16:16) (in thread): > Maybe there should be a companion tohttp://bioconductor.org/developers/package-guidelines/ about visualization. Or maybe there is already an excellent guide in the R world? It’s not a bioc-specific challenge… (FWIW there is deep skepticism amongst some [ok, me] that the package guidelines / submission instructions are actually read; during my own submission I treated them essential as a EULA to be clicked through as quickly as possible; I’m just not sure ‘more is better’ in this context).
Michael Love (13:17:55) (in thread): > it’s true that a long list of todos will be ignored, but also would be good to have some way to tell developers the good way to do things
Michael Love (13:18:59) (in thread): > but maybe just adding a section to that with a few bulletpoints about visualization concerns
Michael Love (13:21:13) (in thread): > another would be, if you are plotting hundreds of thousands of points, you should probably switch to smooth scatter or hexbin
Michael Love (13:22:26) (in thread): > this is less on the importance scale that most of these package guidelines though
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Jim Hunter (14:55:38): > Is there any bioconductor package that calculates Dn/Ds ratios? There are some CRAN packages, but they don’t seem to provide the details my colleagues needs for their analysis of selection pressure by codon. Thanks.
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Simina Boca (15:48:09): > In terms of being colorblind-friendly - I think it would be great to include those palettes as defaults in some way
Simina Boca (15:49:03): > Or maybe to give them a name/alias that’s short and easy to remember
Simina Boca (15:49:30): > I always find myself switching to colorblind-friendly palettes towards the end of a project, sometimes I forget etc
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Atul Deshpande (17:10:13) (in thread): > Hi@Michael Love, I had made the original comment at BIRS. Thanks for relaying the accessibility concerns here.
Atul Deshpande (17:15:38): > @Dan Bunis, I have found a few color palette’s which work for me as well (red-green), but I was also making the comment from the perspective of reading/viewing other authors’ published work/presentations. I agree with you regarding larger legend icons. I also feel that in specific cases, we can use marker types in combination with the colors to provide more visual cues which are not entirely dependent on colors.
Atul Deshpande (17:19:31) (in thread): > +1 for colorblind-friendly palettes as default. It is likely that a majority of package users might choose to use the default visualizations. I think it would greatly help if the path of least resistance was also the most accessible one.
Dan Bunis (17:36:44): > Would love if more packages were colorblind by default. dittoSeq is, and it uses a version of the Okabe-Ito palette that’s been extended in an okay way, with lighter and darker versions, to allow more than 8 colors. I’m not sure what happens with the default Okabe-Ito palette after 9 colors are needed?
Dan Bunis (17:37:38): > When it makes sense, I also added letter overlay for the dots in my scatter plots or adjusting shapes (/ marker types, I think that’s what you meant@Atul Deshpande?).
Dan Bunis (17:39:14) (in thread): > What are these other panels?
Atul Deshpande (17:39:51) (in thread): > you mean palettes?
Atul Deshpande (17:40:43) (in thread): > I found colorbrewer’s colors to be pretty decent.
Atul Deshpande (17:42:36) (in thread): > I have seen umaps with 30 cluster assignments, every third color looks the same!
Dan Bunis (17:43:53) (in thread): > Okay so… it’s not perfect, butdittoSeq::dittoColors()
Atul Deshpande (17:44:24) (in thread): > Thanks, I’ll try that out.
Atul Deshpande (17:44:47) (in thread): > And as you said, we can adjust shapes to add more visual information beyond colors.
Dan Bunis (17:45:02) (in thread): > Lol just having it literally repeat kinda defeats the purpose of having the colors be distinguishable!
Atul Deshpande (17:46:05) (in thread): > I’m not sure if it repeats, but is pretty useless for me if I have to figure out which of the eight green-brown color legends pertain to a cluster of green-brown color.
Atul Deshpande (17:47:20) (in thread): > Maybe they are distinguishable to people who can identify the mythical color Mauve.:smile:(edit: I say mythical in jest, i know it is a color. One I have never seen.)
Simina Boca (18:36:14) (in thread): > Colorbrewer is good but it always takes me 3 steps to find a colorblind-friendly palette, copy the name, paste it in my ggplot etc. Like you were saying, it would be great to have it involve the least amount of resistance.
Aedin Culhane (18:39:18) (in thread): > @Atul DeshpandeGlad you found the channell. I suggested to Atul he submit a poster and an request for a Birds of Feature at Bioc2020 so we can actively discuss this. I think its really important with scRNAseq, UMAP clusters are typically visualized by color.
Aedin Culhane (18:39:47) (in thread): > @Atul Deshpandeand I discussed some approaches in the BIRS slack but there are probably better options .
Aedin Culhane (18:41:09) (in thread): > I suggested centroid labels, maybe a ggrepel for colors by xyz space of the UMAP (so colors that are similar are assigned to clusters that are far apart. We could also use ellicipse, density rather than points
Aedin Culhane (18:45:43): > http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/#a-colorblind-friendly-palette - File (PNG): Screen Shot 2020-06-19 at 6.44.46 PM.png
Aedin Culhane (18:47:18) (in thread): > Yes. I think Maftools package might
Aedin Culhane (18:49:17): > With UMAP and other scRNAseq approaches so dependent on a contrastive color platter to distinguish clusters.. is there a good color blind palette with as many clearly distinguishable colors as possible
Atul Deshpande (18:57:51): > I think a lot of concerns can be alleviated with labels on centers of gravity of the clusters instead of a legend, and then making sure that every adjacent color in the umap is as distinguishable from its neighbors as possible.
Atul Deshpande (18:58:45): > Frankly, I personally don’t even mind if colors actually repeat if I can identify cluster boundaries, and name each cluster.
Atul Deshpande (19:01:19): > I think whichever color palette we choose (@Dan Bunismentioned the Okabe-Ito palette,https://www.vwvj.be/sites/default/files/zien/zien_-_uit_voorbije_vorming/kleurzinonderzoekextratips.pdf ), beyond 8-9 colors, life is going to be tough if color is the only qualifier.
Atul Deshpande (19:01:50): > One could play around with hollow vs solid points, different point shapes, etc, depending on the number of points.
Atul Deshpande (19:02:27): > If there are too many points to distinguish the shapes, then an ellipse, or a “boundary” for a cluster might help.
Atul Deshpande (19:05:55): > Here is an example from the pdf document from Okabe-Ito linked above.. - File (PNG): image.png
Atul Deshpande (19:08:57): > In the case of using ellipses or earmarking areas in general, it would be beneficial if the geometrical shape has patterns in addition to color as an identifier. - File (PNG): image.png
Atul Deshpande (19:10:13): > This second figure also shows how color separation in the figure is also important in addition to using the right palette.
Dan Bunis (19:30:44) (in thread): > dittoSeq does labels too, with or without repelling away from each other/the plot bounds.dittoDimPlot(..., do.label = TRUE, label.repel = TRUE)
Dan Bunis (19:31:50) (in thread): > I know we’re talking more in general for other things too, but since we’re specifically on UMAP…
Atul Deshpande (19:33:46): > There’s also this article I found in dittoSeq’s README:https://www.nature.com/articles/nmeth.1618 - Attachment (Nature Methods): Points of view: Color blindness > Points of view: Color blindness
Simina Boca (20:05:50): > I feel like for interactive plots we can do something like just offering multiple palettes
Henrik Bengtsson (23:44:35): > Regarding color-blindness and accessibility in general: It would be neat if the end-user could set aaccessibility.preferencesoption that then packages and functions could/should acknowledge and be agile too, e.g.options(accessibility.preferences = c("deuteranopia", "high-contrast", "dark-mode")). Ideally, this type of configuration should really be a cross-platform standard at the OS level.
Simina Boca (23:52:19): > 100% agree
Simina Boca (23:52:52): > It wouldn’t help for static images in papers but would in other circumstances
Simina Boca (23:53:15): > Agree that there are multiple types of color-blindness/vision issue so a single palette won’t help them all
2020-06-20
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Alan O’C (08:51:36) (in thread): > alphabethas a large number of colours but with n >>> 10 it’s really difficult to design a good palette, doubly so one that’s colourblind-friendly
Alan O’C (08:51:39): > I think for scatterplots with >>> 100 points, shape becomes very hard to distinguish. Boundaries sounds like a good solution (eg, from a 2D gaussian)
Dan Bunis (12:11:26): > Using faceting by the same groupings as would get different shapes is another idea. (And I’ll keep dropping the dittoSeq inputs for these implementations withdittoDimPlot()cuz why not:shape.by,split.by,do.ellipse, and, as noted in a thread above,do.label)
2020-06-22
Alan O’C (04:46:28): > Yeah I find combinations of facet and colour easier to interrogate. I realise the boundaries idea implicitly assumes a 1-1 correspondence between reduced dims and and cluster labels so not really feasible
Vince Carey (06:58:04): > This is a really interesting discussion. I would like to know whether there is a role for plotly in enhancing accessibility in a few ways. First, when points on the plane are the main representation of the data in a graph, does text-on-hover help diminish impacts of altered color perception on data interpretation? We can use plotly fairly easily in any html rendering, and some interactivity in PDF should also be possible. Second, would text-to-speech-on-hover help even more for significant visual impairment? > > Is there research in this domain, and if not, can we sketch out an agenda? A quick search revealedhttps://www.prnewswire.com/news-releases/sas-enables-visually-impaired-to-visualize-data-300411767.html http://users.umiacs.umd.edu/~elm/projects/vis4nonvisual/vis4nonvisual.pdf - Attachment (prnewswire.com): SAS enables visually impaired to ‘visualize’ data > /PRNewswire/ – People with visual impairments are often shut out from hot careers in STEM fields, including analytics and data science. Why? Because the…
Sean Davis (07:31:30): > https://accessibility.18f.gov/tools/ - Attachment (accessibility.18f.gov): Tools | 18F Accessibility Guide > Tools we use to improve and test accessibility
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2020-06-23
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2020-06-24
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2020-06-25
USLACKBOT (09:38:11): > This message was deleted.
Mike Smith (09:50:17) (in thread): > If it’s single-cell data maybe that and/orhttps://www.nature.com/articles/s41592-019-0654-x - Attachment (Nature Methods): Orchestrating single-cell analysis with Bioconductor > This Perspective highlights open-source software for single-cell analysis released as part of the Bioconductor project, providing an overview for users and developers.
Stephanie Hicks (10:03:34) (in thread): > @Kevin BligheThere is another one with Gentleman as first author
Stephanie Hicks (10:03:36) (in thread): > let me dig it up
Stephanie Hicks (10:04:25) (in thread): > https://genomebiology.biomedcentral.com/articles/10.1186/gb-2004-5-10-r80 - Attachment (Genome Biology): Bioconductor: open software development for computational biology and bioinformatics > The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.
Stephanie Hicks (10:05:01) (in thread): > this is the reference cited for Bioconductor in the “Orchestrating high-throughput genomic analysis with Bioconductor” paper.
Shraddha Pai (16:06:19): > Hi everyone, > I still haven’t gotten to the bottom of the purported Java 8 incompatibility for our package “netDx” , which causes a BioC build failure specifically on OS/X. Some help would be awesome as I’ve been trying to resolve this issue for a while. > > Thank you! > Here is a snippet of my email to bioc-devel yesterday: > — > My package relies on a Java jar and detects whether the OS has Java 8 or 11, to be accordingly compatible. The error message from the BioC build failure is a symptom of Java 8 incompatibility. > > However, on my 2014 Mac Air which runs Java 8, the offending example (“Predict_CaseControl_from_CNV.Rmd”) runs through to completion with no errors (BioC 3.11 and R 4.0+). > — > Error: This is the error from the build result: > > WARNING: An illegal reflective access operation has occurred > > WARNING: Illegal reflective access by net.sf.cglib.core.ReflectUtils$2 (file:/Users/biocbuild/Library/Caches/netDx/763502120e4_genemania-netdx.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) > WARNING: Please consider reporting this to the maintainers of net.sf.cglib.core.ReflectUtils$2" > > > * Mac specs: MacBook Air early 2014; High Sierra 10.13.6 > * “java -version” output: > java version “1.8.0_31” > Java(TM) SE Runtime Environment (build 1.8.0_31-b13) > Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode) > * R version 4.0.2 ; BioC 3.11 > I’m happy to paste insessionInfo()output if it would help.
2020-06-26
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2020-06-28
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2020-06-30
Dario Strbenac (04:30:36): > Has anyone run the Bioconductor Docker container on a HPC system with an older operating system? The university’s HPC runs CentOS 6.9. I am running Singularity 3.5.3 and I got advice that > > You are correct that Singularity on the HPC cannot make use of User Namespaces. However, you should find that many containers can still be run using the setuid method. > I asked for explanation about what “the setuid method” is but didn’t get one > > Whilst we provide basic support for establishing access to the singularity toolset, support of containers themselves and the software stacks within are something to take up with the developer of the container. > Do I need to rebuild Bioconductor’s container with some different option perhaps?
Alan O’C (05:49:03) (in thread): > https://singularity.lbl.gov/docs-security - Attachment (singularity.lbl.gov): Security | Singularity > Security These docs are for Singularity Version 2.5.2. For older versions, see our archive Container security paradigmsFirst some background. Most container platforms operate on the premise, trusted users running trusted containers. This means that the primary UNIX account controlling the container platform is either “root” or user(s) that root has deputized (either via sudo or given access to a control socket of a root owned daemon process).Singularity on the other hand, operates on a different premise because it was developed for HPC type infrastructures where you have users, none of which are considered trusted. This means the paradigm is considerably different as we must support untrusted users running untrusted containers.Untrusted users running untrusted containers!This simple phrase describes the security perspective Singularity is designed with. And if you additionally consider the fact that running containers at all typically requires some level of privilege escalation, means that attention to security is of the utmost importance.Privilege escalation is necessary for containerization!As mentioned, there are several containerization system calls and functions which are considered “privileged” in that they must be executed with a certain level of capability/privilege. To do this, all container systems must employ one of the following mechanisms: Limit usage to root: Only allow the root user (or users granted sudo) to run containers. This has the obvious limitation of not allowing arbitrary users the ability to run containers, nor does it allow users to run containers as themselves. Access to data, security data, and securing systems becomes difficult and perhaps impossible. Root owned daemon process: Some container systems use a root owned daemon background process which manages the containers and spawns the jobs within the container. Implementations of this typically have an IPC control socket for communicating with this root owned daemon process and if you wish to allow trusted users to control the daemon, you must give them access to the control socket. This is the Docker model. SetUID: Set UID is the “old school” UNIX method for running a particular program with escalated permission. While it is widely used due to it’s legacy and POSIX requirement, it lacks the ability to manage fine grained control of what a process can and can not do; a SetUID root program runs as root with all capabilities that comes with root. For this reason, SetUID programs are traditional targets for hackers. User Namespace: The Linux kernel’s user namespace may allow a user to virtually become another user and run a limited set privileged system functions. Here the privilege escalation is managed via the Linux kernel which takes the onus off of the program. This is a new kernel feature and thus requires new kernels and not all distributions have equally adopted this technology. Capability Sets: Linux handles permissions, access, and roles via capability sets. The root user has these capabilities automatically activated while non-privileged users typically do not have these capabilities enabled. You can enable and disable capabilities on a per process and per file basis (if allowed to do so).How does Singularity do it?Singularity must allow users to run containers as themselves which rules out options 1 and 2 from the above list. Singularity supports the rest of the options to following degrees of functionally: User Namespace: Singularity supports the user namespace natively and can run completely unprivileged (“rootless”) since version 2.2 (October 2016) but features are severely limited. You will not be able to use container “images” and will be forced to only work with directory (sandbox) based containers. Additionally, as mentioned, the user namespace is not equally supported on all distribution kernels so don’t count on legacy system support and usability may vary. SetUID: This is the default usage model for Singularity because it gives the most flexibility in terms of supported features and legacy compliance. It is also the most risky from a security perspective. For that reason, Singularity has been developed with transparency in mind. The code is written with attention to simplicity and readability and Singularity increases the effective permission set only when it is necessary, and drops it immediately (as can be seen with the –debug run flag). There have been several independent audits of the source code, and while they are not definitive, it is a good assurance. Capability Sets: This is where Singularity is headed as an alternative to SetUID because it allows for much finer grained capability control and will support all of Singularity’s features. The downside is that it is not supported equally on shared file systems.Where are the Singularity privileged componentsWhen you install Singularity as root, it will automatically setup the necessary files as SetUID (as of version 2.4, this is the default run mode). The location of these files is dependent on how Singularity was installed and the options passed to the configure script. Assuming a default ./configure run which installs files into –prefix of /usr/local you can find the SetUID programs as follows:$ find /usr/local/libexec/singularity/ -perm -4000/usr/local/libexec/singularity/bin/start-suid/usr/local/libexec/singularity/bin/action-suid/usr/local/libexec/singularity/bin/mount-suidEach of the binaries is named accordingly to the action that it is suited for, and generally, each handles the required privilege escalation necessary for Singularity to operate. What specifically requires escalated privileges? Mounting (and looping) the Singularity container image Creation of the necessary namespaces in the kernel Binding host paths into the containerRemoving any of these SUID binaries or changing the permissions on them would cause Singularity to utilize the non-SUID workflows. Each file with -suid also has a non-suid equivalent:/usr/local/libexec/singularity/bin/start/usr/local/libexec/singularity/bin/action/usr/local/libexec/singularity/bin/mountWhile most of these workflows will not properly function without the SUID components, we have provided these fall back executables for sites that wish to limit the SETUID capabilities to the bare essentials/minimum. To disable the SetUID portions of Singularity, you can either remove the above -suid files, or you can edit the setting for allow suid at the top of the singularity.conf file, which is typically located in \(PREFIX/etc/singularity/singularity.conf.# ALLOW SETUID: [BOOL]# DEFAULT: yes# Should we allow users to utilize the setuid program flow within Singularity?# note1: This is the default mode, and to utilize all features, this option# will need to be enabled.# note2: If this option is disabled, it will rely on the user namespace# exclusively which has not been integrated equally between the different# Linux distributions.allow setuid = yesYou can also install Singularity as root without any of the SetUID components with the configure option --disable-suid as follows:\) ./configure –disable-suid –prefix=/usr/local$ make$ sudo make installCan I install Singularity as a user?Yes, but don’t expect all of the functions to work. If the SetUID components are not present, Singularity will attempt to use the “user namespace”. Even if the kernel you are using supports this namespace fully, you will still not be able to access all of the Singularity features.Container permissions and usage strategyAs a system admin, you want to set up a configuration that is customized for your cluster or shared resource. In the following paragraphs, we will elaborate on this container permissions strategy, giving detail about which users are allowed to run containers, along with image curation and ownership.These settings can all be found in the Singularity configuration file which is installed to $PREFIX/etc/singularity/singularity.conf. When running in a privileged mode…
Alan O’C (05:50:30) (in thread): > Slightly odd; I assume you don’t have root on your HPC so that sounds like it shouldn’t work? On our HPC we have to use namespaces/sandbox mode so I can’t tell you much
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Dirk Eddelbuettel (06:46:06) (in thread): > “The suid method” is likely referring to running Docker (which runs as root, or, in the lingo with “setuid” ie the set user id onroot). No change to the container or their build, simply acknowledging that CentOS 6.9.* is old and may require that.
000 (11:50:04): > @000 has joined the channel
Shian Su (23:29:34): > When did Biostrings print start looking this cool? - File (PNG): Screen Shot 2020-07-01 at 1.28.36 pm.png
2020-07-01
Levi Waldron (09:42:21) (in thread): > Have they installed Singularity, or did you somehow manage to do it in your user space? You shouldn’t have to rebuild Bioconductor’s container, you should be able to use it directly from Singularity-hub or DockerHub.
Dario Strbenac (10:00:30) (in thread): > No, I just didmodule load singularity.
Levi Waldron (10:31:27) (in thread): > OK, that’s good. And are you able to do things likesingularity pulldocker://bioconductor/bioconductor_full:release followed bysingularity shell bioconductor_full_release.sifthen continue working as your normal user? BTW here is the approach I’m using to replace all my usual commands with Singularized commands:https://github.com/waldronlab/bioconductor/wiki/Running-Bioconductor-in-Docker-using-Bulker
Levi Waldron (10:37:52) (in thread): > You shouldn’t have to worry about user issues, Singularity maintains your user and permissions. Probably the only thing you’ll have to do is to bind any directories outside of${HOME}that you need.
Dario Strbenac (11:30:09) (in thread): > That worked without a problem and I see a Singularity command prompt. Perhaps it has something to do with my use of Nextflow. Part of the configuration is > > process.container = 'bioconductor/bioconductor_docker:RELEASE_3_11' > process.module = 'singularity/3.5.3' > singularity.enabled = true > > Also, the container name is different to the one which you recommended.
Levi Waldron (11:31:13) (in thread): > I haven’t used it with Nextflow yet, although will in the near future…
Alan O’C (11:34:50) (in thread): > I had issues using snakemake and singularity together. When the job is launched it may not have loaded the singularity module (I think that was the issue for me). Can’t speak to nextflow at all unfortunately
Hervé Pagès (13:16:33): > Since BioC 3.11. Glad you like it:slightly_smiling_face:
2020-07-02
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Mike Jiang (17:58:37): > After searched in both slack and google, I haven’t found the relevant answer regarding to the best practice for renaming the existing bioc package, i.e.flowWorkspace–>cytolibr, my plan is to move the code base tocytolibr, which will be submitted as a new package, and makeflowWorkspaceimport/export everything fromcytolibrwith somedeprecationwarnings, so that the existing users will still be able to use it. Any better suggestions?@Hervé Pagès@Lori Shepherd
Hervé Pagès (20:39:24): > @Mike JiangSounds good to me. Probably the less disruptive path from an end-user point of view. Thanks!
Dario Strbenac (22:00:11) (in thread): > Is there a Bioconductor image with all Bioconductor packages pre-installed? It seems like only BiocManager and BiocVersion come with the image. That way, the environment is unchanging and doesn’t depend on packages installed in the user’s home directory (or on the user having administrator privileges to runsudo singularity shell --writable) It would be bloated, but get the job done by having everything in the immutable SIF.
Dirk Eddelbuettel (22:20:29) (in thread): > From hundreds of code packages? Plus Yuge data repo packages? You understand that that gets unwieldy? Plus Docker “is like legos”. Take the base container, add the five or ten or fifty BioC packages closes to your heart and createyour preferred container.
Dario Strbenac (22:30:23) (in thread): > Indeed, remarkably wasteful but I was thinking about large hard drives and broadband internet. So, it’s basically necessary to have a personal Linux installation you can usesudoon before you move it onto a HPC is what I’m understanding.
2020-07-03
Alan O’C (07:51:56) (in thread): > You can set up a github repo with a dockerfile to automatically build, you don’t need to make the image locallyhttps://docs.docker.com/docker-hub/builds/link-source/ - Attachment (Docker Documentation): Configure automated builds from GitHub and BitBucket > To automate building and testing of your images, you link to your hosted source code service to Docker Hub so that it can access your source code repositories. You can…
Alan O’C (09:28:38): > Are there any recommendations on parallel C++ code in Bioc? I gather there are some issues with OpenMP and OSX, and RcppParallel seems slightly more restrictive, so I want to pick the path of least pain before diving in properly
Nicholas Knoblauch (13:27:46) (in thread): > The TBB (which is vendored with RcppParallel) is about as good as it gets for performant, portable, general purpose parallel programming in C++
Pariksheet Nanda (14:14:51): > Trying to install Bioconductor packages chokes every so often with ” cannot open URL ‘http://bioconductor.org/config.yaml ’”
Aaron Lun (15:00:27) (in thread): > I thought they had solved the OpenMP problems with OSX.
Aaron Lun (15:03:07) (in thread): > In any case, OpenMP is what Rtsne uses for parallelization. Ridiculously easy to slap onto existing code, I would definitely use more of it if I weren’t already parallelizing via BiocParallel.
Alan O’C (15:29:24) (in thread): > Could well be that the OpenMP/OSX stuff is fixed, I just recall people grumbling about it. I think rstan uses OpenMP as well so must be at least pseudo-portable, and as you say much easier to slap on to existing code. Thanks!
2020-07-04
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2020-07-05
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Pariksheet Nanda (09:08:01): > The newNcpusoption forinstall.packages()
Pariksheet Nanda (09:08:56): > addsoptions(Ncpus = parallel::detectCores())to~/.Rprofile
Dirk Eddelbuettel (09:20:47) (in thread): > IIRC it isway older than R 4.0.*. But yes,incredibly useful . My command-line wrappers inlittleruse it too if set.
Martin Morgan (10:20:48) (in thread): > Either ingeniously clever:bulb:or an egregious hack:face_with_head_bandage:, R does this by translating the package dependencies to Makefile targets, and then runs make. Somewhere aroundhttps://github.com/wch/r-source/blob/576765c3b22ddeadd0854d3b042c21f4c1e90444/src/library/utils/R/packages2.R#L803
Dirk Eddelbuettel (10:24:39) (in thread): > Thanks! Always meant to look into it because I also like how R takes care of the stdout from the different builds (I am of course on Leeenucks) do not cross.
Alan O’C (10:26:14) (in thread): > Wow, that seems like something I’d consider as a quick hack, but if it works it works
Dirk Eddelbuettel (10:34:21) (in thread): > OpenMP is good, old (in the “very well standardized”) sense, mature and recommend. Also “too low level” and not trivial, so Intel TBB and hence RcppParallel are good. I say a few words about that in the preprint herehttps://arxiv.org/abs/1912.11144 that is now also out ashttps://onlinelibrary.wiley.com/doi/abs/10.1002/wics.1515 - Attachment (arXiv.org): Parallel Computing With R: A Brief Review > Parallel computing has established itself as another standard method for applied research and data analysis. The R system, being internally constrained to mostly singly-threaded operations, can…
Alan O’C (10:37:28) (in thread): > Thanks Dirk! Yeah I read that while waiting for replies here, it’s a very helpful paper. For the time being I’ve gone with OpenMP as it’s more drop-in and most of the use cases are embarrassingly parallel, but there are a few cases that I have had to avoid because of locking so TBB may be the long term solution
Dirk Eddelbuettel (10:37:37) (in thread): > But to this non-macOS user is seems like OpenMP gets lost “not infrequently” somewhere between Cupertino and the macOS toolchain for R. Very sad. Fixable with patience and elbow grease but it simply should not be that hard. Similarly Kevin had to tone down RcppParallel to not always try Intel TBB but I forget the details.
Dirk Eddelbuettel (10:38:43) (in thread): > Personally I just like higher abstraction levels. So I’d always recommend RcppParallel and BiocParallel first. “But it depends” as always and if you can make good use of OpenMP directly so reason not to:slightly_smiling_face:
Alan O’C (10:42:12) (in thread): > Yes, it seems that native code for a few prominent packages (Stan in particular) seems to have a biannual meltdown for OSX users. Then again I know a lot of musicians who seem to experience the same thing so it’s perhaps unsurprising. > > Indeed, I think the RcppParallel worker paradigm is more general and abstract, will definitely play around with it in future. Though there are a few other aspects of Rcpp I need to master first -wrapandasbeing next on the list
Dirk Eddelbuettel (11:30:05) (in thread): > You are mixing a few topics here, and it may be simpler to keep it at one topic at time. I only brought RcppParallel up because it gives us all the easy to use and performant heuristics for work stealing and what not from Intel TBB. You could also use it without Rcpp taking any worries about fancy use of the latter away for now.
Dirk Eddelbuettel (11:30:51) (in thread): > OpenMP is used in base R (as I mention in the little paper). (r)stan is one of few packages using it well, there are more (again, see paper).
Alan O’C (11:43:57) (in thread): > Ah, I missed the ref to base R in your paper - that would have likely answered my OSX question. Sorry, the wrap/as stuff was a complete aside. Not working on any standalone C++ stuff atm
Shian Su (19:54:38) (in thread): > Seeing how I’ve never had this fail on me, I’d say ingeniously clever.
2020-07-06
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Federico Marini (13:59:36) (in thread): > I do 2 less than the max, just to make sure 2 are left for whatever could come
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Pariksheet Nanda (14:32:33) (in thread): > Ah I see. On my end I’ve never had an issue with the Linux kernel scheduler noticeably slowing down my desktop experience under that load. Sometimes I oversubscribe cores when compiling to keep the cores busy while some workers are engaged in I/O.
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Henrik Bengtsson (17:59:09) (in thread): > Just make sure you don’t do this on a compute cluster with many users - unless you wanna get your sysadm’s attention.
2020-07-07
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Heather Turner (08:23:48): > useR! 2020 is kicking off this week! > > Here is the agenda for the live events:https://user2020.r-project.org/program/agenda/ That page includes iCal and Google calendars, so you can add the times to your calendar to make it easier to see when they are in your own timezone. > > Further details are gradually being added for the tutorials:https://user2020.r-project.org/program/tutorials/ . Playlists of contributed videos will be announced when they are ready.
Dirk Eddelbuettel (08:28:19) (in thread): > What’s the deal with titling on the tutorials page? Did old Europe and esp Austria take over with their mad admiration for formal titles? Asking for a “friend” Prof Dr ….
Dirk Eddelbuettel (08:28:45) (in thread): > Kidding aside, can we drop that? > > Also, if you know who edits that I too am slated for 2 hours rather than NA.
Heather Turner (09:20:58) (in thread): > I’ll pass the comment on about the titling. I’ve updated the Google doc that the tutorial page is built from to indicate that your tutorial is 2 hours.
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Simone Tiberi (09:38:11): > Hi, > does anyone know whether Bioc2020 conference will only be streamed live, or if the talks will remain online for a few hours/days ? > > Thanks, > Simone
Martin Morgan (09:54:03): > Check out the useR! conference free, online, and this weekhttps://user2020.r-project.org/program/agenda/
Levi Waldron (15:47:06) (in thread): > I believe the recorded versions become immediately available within the conference platform, and our intention is to organize and post them publicly online after the conference.
2020-07-08
Steffen Neumann (03:11:30): > Hi, I am currently using travis on github for some packages. For a new package I’d like to try github actions. Has anyone a link to a great gh actions setup to get inspiration (steal) from ?
Mike Smith (03:20:41): > Steffen, sounds like you need to join this months devel call! - Attachment: Attachment > The next Bioconductor Developers’ Forum is scheduled for Thursday 16th July at 09:00 PDT/ 12:00 EDT / 18:00 CEST - You can find a calendar invite at https://bit.ly/3gCsFXO > > We will be using BlueJeans and the meeting can be joined via: > https://bluejeans.com/114067881 (Meeting ID: 114 067 881) > > This month we’ll be focusing on continuous integration with Github Actions, led by @Sean Davis, and discussing how we can benefit from GA across a wide variety of development tasks, including cross-platform testing of code and website deployment.
Simone Tiberi (03:33:59) (in thread): > Ok, thanks Levi
Constantin Ahlmann-Eltze (04:56:45): > I had a good experience using the R-CMD-check.yaml from iSEE (https://github.com/iSEE/iSEE/blob/62617d6354614ba39b5e29bf8c911c67344dd63a/.github/workflows/R-CMD-check.yaml ) by@Kevin Rue-Albrecht. He did however recently change it, though I am not quite sure why :)
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Steffen Neumann (05:51:13) (in thread): > Yes, that’s what I found in rhdf5lib as well:slightly_smiling_face:Not sure if I’ll make it to the dev meeting, there is ISMB2020 as well. Thx, Steffen
Mike Smith (05:56:36) (in thread): > Hopefully we’ll get the recording of the meeting to work this month, so you should be able to watch it after the fact. There’s also some discussion and links to GA examples starting athttps://community-bioc.slack.com/archives/CLUJWDQF4/p1587164112094800 - Attachment: Attachment > @Nitesh Turaga @Charlotte Soneson @FelixErnst I now have a working GitHub actions workflow that uses the Bioconductor dockers (release or devel depending on the GitHub branch) , caches the R packages, runs BiocCheck, pkgdown, covr. Some things got tricky because of the docker containers vs the linux OS (like getting BiocCheck to work properly in that setting and configuration required by pkgdown). I’m sure there’s probably ways to make the code cleaner. > > Anyway, I’m quite happy with it and made suggestions in 5 different repos all linking to https://github.com/r-lib/actions/issues/84 . If they like the suggestions, I would make the related PRs too. > > I thought you would be interested too. If you feel inclined, please feel free to chime in the “issues” (suggestions) I made on GitHub so others not in this Slack can see your comments.
Kevin Rue-Albrecht (06:40:55) (in thread): > @Constantin Ahlmann-Eltzethanks for the feedback. The recent changes were due to issues related to bad interactions betweenactions/checkout@v2andJamesIves/github-pages-deploy-action@releases/v3https://github.com/iSEE/iSEE/commits/b373a95900c3f1310a0aa48b920e8251ac4daa5e/.github/workflows/build_check_deploy.yaml
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Heather Turner (16:28:27): > https://twitter.com/R_Forwards/status/1280947257173512192?s=20 - Attachment (twitter): Attachment > Succession and diversity were key topics in the #useR2020 R Core panel (https://youtu.be/X_eDHNVceCU ). We are putting a team together with @lawremi
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2020-07-09
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estepi (07:04:12): > Hello everybody!
estepi (07:04:24): > I need dome advice as bioc developer
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2020-07-10
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2020-07-11
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2020-07-12
Pariksheet Nanda (09:26:18): > Hi folks, I’m making the case for improving the quality of 3 GitHub packages developed by collaborators to be brought into Bioconductor, and was hoping to have citations to justify several months of PhD work for why it’s worth having things like tests, CI, more frugal memory management, better integration with Bioconductor infrastructure instead of calling ad-hoc command line tools (!), and improved maintenance from a larger developer community. Can anyone point me towards a citable resource talking about the benefits of having packages in Bioconductor that would convince the average non-programmer? I suspect there’s a broader, standard paper I should cite, in which case it would be nice to know what “catch phrases” are convincing over simply sharing code on GitHub, etc.
Martin Morgan (10:19:27) (in thread): > That’s a great question, and I look forward to the citable answers. > > There are many anecdotal stories, of course, including the ticker of citations mentioning Bioconductor athttp://bioconductor.org/help/publications/ where there are several citations to Bioconductor (usually as the source for a package) per week. Also following the link ‘PubMed Central’ at the top right of the page tells us that there are 38285 full text citations to ‘bioconductor’ in the scientific literature (a fraction of these are false positives). The annual reportshttp://bioconductor.org/about/annual-reports/ used to cite, pre- about 2010 (e.g., section 6.1), citations to individual packages, but this stopped when it became problematic [for me] to confidently claim citations to papers that, e.g., introduce a package but also significant statistical innovation, as a citation to the package. > > The download stats for Bioconductor packages are availablehttp://bioconductor.org/packages/stats/ and it would be very interesting to ask about downloads of packages that make use of core infrastructure (based on dependencies, for instance…) versus those that do not. This seems like a nice graph theory problem, too, removing packages whose downloads are because they implement core infrastructure. A nice problem for@Robert Casteloand other? > > It would be tempting to add to the narrative the success of individual Bioconductor packages, and the role this success had on the academic careers of the authors of those packages (there are more than a few examples of this) but it’s hard to know how to specify the control group, e.g., Seurat is obviously successful without being in Bioconductor…
Pariksheet Nanda (10:41:12) (in thread): > Thanks, Martin! The blurb I’m currently writing for my proposal is: “Research software projects that find enthusiastic adopters must grow from their original publication goals to also satisfy the specific experimental needs of those adopters. Growing the average GitHub software project requires improving mainability by adding unit tests and test oracles, unit test coverage reports, machine agnostic continuous integration, reduce bugs by reusing existing scientific software libraries, accommodating larger data sets with improved memory management, and thereby reach publication quality for the Bioconductor project. Bioconductor increases the visibility and lifespan of the project, and trust in the scientific integrity of the software calculations.”
Pariksheet Nanda (10:45:30) (in thread): > I think you’re right to look at the anecdotal stories for building the case initially, because sometimes that’s what needs to be done with these qualitative responses. I remember one of the first long term studies of the value of teaching programming by the Carpentries did an indepth analysis of the specific comments from their surveyed users. I wonder if similar survey responses from Bioconductor users or developers might provide better support for all of the value we need to convince the normies about:laughing:
Pariksheet Nanda (10:47:05) (in thread): > How would one use the more visible PubMed Central impact and downloads to compare packages in- vs out- of Bioconductor?
Martin Morgan (10:47:28) (in thread): > I’ll mention that unit tests were not at all common in Bioconductor (or the software community?) back at the dawn of time, and actually there was a certain antagonism toward developing unit tests at the expense of new software development. On the other hand there was deep appreciation of the value of what might be called the ‘integration’ tests of R CMD check and of runnable vignettes illustrating package functionality. At least from the core team perspective, the richness of the software, the depth of the dependency graph, and the temporal longevity of the code mean that unit tests have become basically essential to robust software – there is no way that a ‘bug report’ or pull request on a core package can be understood without reference to the unit tests that define current behavior.
Pariksheet Nanda (10:50:39) (in thread): > Yeah, discussing unit tests in academic software sometimes needs more nuance. I recently learned about the highway “guard rail” analogy of using unit testing to more to prevent catastrophic problems than to make testing itself a goal or overspecifying an API. I tend to find it valuable in self-documenting esoteric calculations.
Pariksheet Nanda (10:53:08) (in thread): > Yes, I should mention the package vignettes! I feel in some contexts they are superior to methods papers.
Pariksheet Nanda (11:12:05) (in thread): > Yes, the dependency graph is quite useful when comparing package maintainability. I like that you core developers like having the unit tests as a measure of package behavior. I’ve changed my wording from describing unit tests with jargony “maintainability developer features” to “productivity and computation integrity features”. (edits because spelling things is hard)
2020-07-13
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Sean Davis (08:14:50) (in thread): > I would just note that all software written by grad students does not need to be submitted to Bioconductor. Also, not all folks who fund software development want to invest time and resources into best practices. Perhaps helping your non-programmer collaborators (who are the funders/PIs?) to identify their rationale and goals for publishing the software can help to make the case for some of these items. CI and tests ultimately increase resilience and reduce maintenance burden and speed development; if long-term maintenance is not a goal, then making that case may be less valuable. Documentation can increase uptake, as can interoperability. Again, knowing what your collaborator expects and wants is important. Finally, some non-programmers do not know that having these “extras” are the mark of a thoughtful and academic research software package and softwares lacking at least some may be viewed less positively. In the same way that a good publication has high quality figures and tables that often require extra work, high quality software requires extra work.
Pariksheet Nanda (10:14:11) (in thread): > @Sean Davisthose are excellent points. I like your advice on discussing the long term maintenance goals and frame software engineering in that context, and making the comparison of how software quality is viewed back to how publications are viewed - that’s much more convincing than a citation.
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Pariksheet Nanda (12:04:10) (in thread): > If it’s useful to anyone, this is what I currently have in my introduction: > “Critical software packages for processing PRO-seq data require sustainability improvements. Limitations in funding and reward structures favor publishing scholarly results quickly over investing in development of sustainable software that reliably supports longer-term research (Katz et al. 2019, page 9). Sustainability improvements increase the quality of packages for publication in Bioconductor (Huber et al. 2015), and Bioconductor increases the trust, visibility, and lifespan of its member projects. Similar to how good paper publications show attention to detail in figures, software packages missing similar marks of quality are seen less favorably. I therefore propose extending the bare minimum work items (i) to (iii) required to publish in Bioconductor with items (iv) to (v): (i) add compatibility for Windows and Mac OS with continuous integration, (ii) reduce bugs by reusing existing scientific software libraries, (iii) add reproducible package vignettes for richer user training than relying on methods papers alone, (iv) add computation integrity and productivity features of unit tests and test oracles, unit test coverage reports, and (v) accommodate larger data sets with improved memory management.”
Pariksheet Nanda (12:04:52) (in thread): > Thanks for all your help Martin and Sean!
Sean Davis (12:33:11): > Promoting this out of the thread since I suspect it might be useful to others in similar circumstances. - Attachment: Attachment > If it’s useful to anyone, this is what I currently have in my introduction: > “Critical software packages for processing PRO-seq data require sustainability improvements. Limitations in funding and reward structures favor publishing scholarly results quickly over investing in development of sustainable software that reliably supports longer-term research (Katz et al. 2019, page 9). Sustainability improvements increase the quality of packages for publication in Bioconductor (Huber et al. 2015), and Bioconductor increases the trust, visibility, and lifespan of its member projects. Similar to how good paper publications show attention to detail in figures, software packages missing similar marks of quality are seen less favorably. I therefore propose extending the bare minimum work items (i) to (iii) required to publish in Bioconductor with items (iv) to (v): (i) add compatibility for Windows and Mac OS with continuous integration, (ii) reduce bugs by reusing existing scientific software libraries, (iii) add reproducible package vignettes for richer user training than relying on methods papers alone, (iv) add computation integrity and productivity features of unit tests and test oracles, unit test coverage reports, and (v) accommodate larger data sets with improved memory management.”
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2020-07-14
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2020-07-15
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Steve (10:02:31): > I have a funny situation deciding between laptops, where one is 6 cores @ 2.6GHz, and another is 8 cores at 2.3GHz. The latter is much more expensive, BUT I suspect R uses just one core the vast majority of the time, so funnily, the cheaper option is the better option (since 1 x 2.6GHz is better than 1 x 2.3GHz). > > If anyone has any ideas on this, I would be very keen to hear them / discuss!
Dirk Eddelbuettel (10:03:18) (in thread): > > R uses just one core the vast majority of the time, > Is plain wrong / it depends / is too narrow a view. > > For starters, R itself even uses a little OpenMP (on platforms where it can). Next up, you can pick BLAS that do all your matrix math in parallel. Next up is client code that can be threaded. > > Maybe (to me) most importantly: if I set Ncpu=6 on my six core desktop, I getinstall.packages()to install six packages in parallel. > > Ditto formake -j ...
Steve (10:04:18) (in thread): > Thanks Dirk!
Dirk Eddelbuettel (10:06:08) (in thread): > Now, the money question: you will likely never see or fee the difference between the two. Pick the cheaper one, or the one with “more ram”. Or the nicer keyboard.
Dirk Eddelbuettel (10:06:22) (in thread): > Lastly, and thatis
Steve (10:07:23) (in thread): > Great knowledge!
Steve (10:07:39) (in thread): > In this case, it’s macbook pro (Mac OS)
Steve (10:08:33) (in thread): > I asked a similar question (more specifically) here:https://stackoverflow.com/questions/62900601/do-r-sessions-always-use-one-core-unless-specifically-instructed-otherwise - Attachment (Stack Overflow): Do R sessions always use one core unless specifically instructed otherwise? > On occasions where heavy compute is required, I’ve used doParallel package to dispatch work over multiple cores. Random example: if (detectCores()-1 > 1) { cl <- makeCluster(detectCores…
Dirk Eddelbuettel (10:08:41) (in thread): > That changes things, and my lawyers tell me I am not allowed to say more here.
Steve (10:10:03) (in thread): > The specs are slightly different in the SO question (still undecided on 13 vs 16”), but the idea is the same - fewer cores @ higher clock speed vs more cores at lower clock speed
Dirk Eddelbuettel (10:15:36) (in thread): > I just carried it over to the SO question.
Dirk Eddelbuettel (10:16:45) (in thread): > Also, I learned just this week that apparently Docker also (comparatively speaking) sucks on macOS relative to Linux. So if youreally care about performance, maybe go with Linux?
Steve (10:17:44) (in thread): > Brilliant advice. Thanks so much Dirk!!
Dirk Eddelbuettel (10:18:27) (in thread): > (Funny side story: my older daughter accidentally spilled a large cup of coffee on her 2015 mac air, and it was declared dead. Got a new macbook (now pro) as it was in the middle of term, but it turned out the box just needed to dry more … and worked again. So I am now proud owner of a hand-me-down 2015 macbook air onto which I ….installed Ubuntu 20.04 just to see how it goes.:slightly_smiling_face:)
Dirk Eddelbuettel (10:19:26) (in thread): > I like the keyboard feel. Screen resolution is smaller than my desktops and my lenovo but it still has a nice usability to it. Now have ctrl+function swapped, and yesterday eve in a quick try go the camera to work. Need to blog about all those tweaks.
Steve (10:22:44) (in thread): > I recently read a (lengthly) linux vs mac discussion in a ruby on rails thread, the upshot was linux > macOS, BUT people were saying it takes a lot of time to set things up that they completely took for granted on mac. For yourself (who knows linux very well), it would probably be trivial, but for mortals, it sounds like the ‘apple tax’ is buying back time. I do love the idea of knowing the machine well enough to understand all its programs/dependencies, and that itself has auxillary benefits like being far more capable of running things (like shiny apps) in docker/k8s etc. Linux vs MacOS is a tough decision for me right now, since my knowledge on Linux is very limited
Steve (10:24:24) (in thread): > Which version of linux would be best for a complete linux beginner (and mostly R programmer) ?
Dirk Eddelbuettel (10:27:01) (in thread): > I may be biased but I’d say Ubuntu.
Dirk Eddelbuettel (10:28:04) (in thread): > Also came across this a few days ago:https://jorin.me/linux-impressions/ - Attachment (jorin.me): Linux Impressions > One year ago I still had a MacBook Pro for work and a MacBook Air at home. Now I have a Thinkpad T490 running Manjaro + KDE and a Dell XPS 13 running Ubuntu + Gnome.
Dirk Eddelbuettel (10:28:49) (in thread): > Itreally
Dirk Eddelbuettel (10:29:00) (in thread): > We could go on forever here with no resolution….
Steve (10:36:15) (in thread): > Just reading the article. Very promising. Definitely going to look into ubuntu
Pariksheet Nanda (12:01:22) (in thread): > If you’re looking into a Linux based machine, you might also consider laptops that already come with it instead of shoe horning it into a macbook. I’m pretty happy with my Purism laptop - they use a slightly modified version of Debian so you shouldn’t have a noticeably different experience than Ubuntu.
Steve (12:03:22) (in thread): > Great idea. My short term strategy is to set up ahttps://www.virtualbox.org/ with ubuntu (it seems to work happily with R/ruby) and dip my toe in the water that way.. I will take note of purism, as I do worry about security and the like
Alan O’C (17:17:48) (in thread): > Ubuntu used to run quite well on old Macbook Pros (I had a 2008 model). > > Coming from Windows/Mac, I found Ubuntu really easy to use for programming etc. It falls apart a bit for word processing etc (that’s what LaTeX is for:slightly_smiling_face:), and definitely for leisure applications
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2020-07-16
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Shubham Gupta (14:02:30): > I have a function in my package that uses tryCatch for condition handling. > > f <- function(){ > tryCatch(expr = warning("?!"), error = function(c) {message(c); 3}, > warning = function(c) {message(c); 4}) > } > > When I try to write a unit test for this with testthat, these warnings show up in mydevtools::test()output. > > test_that("test_f", { > suppressWarnings(output <- f()) > expect_equal(output, 4) > }) > > devtools::test() > OK: 201 > Failed: 0 > Warnings: 1 > > Does any one know how to suppress warnings? I triedsuppressWarningsbut this doesn’t work. > > version R version 4.0.2 (2020-06-22) > os Ubuntu 16.04.6 LTS > system x86_64, linux-gnu >
Henrik Bengtsson (14:14:08) (in thread): > Drop themessage(c):s?
Shubham Gupta (14:14:55) (in thread): > But then how to display the warning that has occured
Henrik Bengtsson (14:17:28) (in thread): > YourtryCatch()statement turns error and warning conditions into message conditions the way you currently do it. These are three different types of conditions classes.suppressWarnings()only suppresses warning conditions, so if you want to keep usingmessage(c)and suppress those later, you need to usesupressMessages()(because they’re no longer warning conditions.
Henrik Bengtsson (14:19:08) (in thread): > Also, be careful using tryCatch(expr, warning = ...). That will stop the evaluation ofexpras soon as a warning is produced. For example,y <- tryCatch({ warning("boom"); 42 }, warning=function(w) 0)}will return0andnot 42!
Nicholas Knoblauch (14:20:09) (in thread): > the testthat docs for expect_message have a pretty good example of what you’re supposed to do > > f <- function(x) { > if (x < 0) { > message("**x** is already negative") > return(x) > } > > -x > } > expect_message(f(-1)) > expect_message(f(-1), "already negative") > expect_message(f(1), NA) > > # To test message and output, store results to a variable > expect_message(out <- f(-1), "already negative") > expect_equal(out, -1) >
Shubham Gupta (14:37:39) (in thread): > I had triedsuppressMessages(),expect_message() and expect_warning().expect_warning(output <- f(), "?!")I keep getting the following text in thedevtools::test()output. > > test_get_global_fit.R:26: warning: test_f > ?! > > test_get_global_fit.R:25: warning: (unknown) > ?! >
Nicholas Knoblauch (14:43:21) (in thread): > have you tried both?
Shubham Gupta (14:45:16) (in thread): > yup. I triedexpect_message(output <- f(), "?!")
Shubham Gupta (14:46:15) (in thread): > Funny part is that it doesn’t consider output as message. > > failure: test_f > `output <- f()` did not produce any messages. >
Nicholas Knoblauch (14:46:55) (in thread): > testthat::expect_message(testthat::expect_warning(tryCatch(warning("oh my"), finally = message("Hello")),"oh my"),"Hello")
Shubham Gupta (14:49:36) (in thread): > Your code does not produce any warning in devtools::test()
Shubham Gupta (14:53:47) (in thread): > I replacedmessage(c)withprint(c). Now I don’t get that warning. I think i just need to be stick with it for now
Nicholas Knoblauch (14:55:39) (in thread): > I think the point is that if you add amessageyou need toexpectit, and also that if your code generates a warning, then you need toexpectthat too,tryCatchis not going to convert your warning into a message, it’s going to signal both
Shubham Gupta (15:03:34) (in thread): > Got that. This makes sense. Unfortunately, there is no function in testthat that can check both of them
2020-07-17
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Hervé Pagès (11:57:45) (in thread): > Note thatcat()is generally better thanprint()for printing a message.
Henrik Bengtsson (12:02:03) (in thread): > Though, you don’t want to usecat()orprint(), which output to stout, in packages, where you want to usemessage(), which ends up on stderr
Hervé Pagès (12:09:56) (in thread): > Right, but if for some reason I don’t want to usemessage()(@Shubham Gupta’s use case),cat()is a better alternative thanprint().
Shubham Gupta (12:47:38) (in thread): > Thanks for the suggestion. I will usecat()instead.
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2020-07-18
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2020-07-19
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Shubham Gupta (21:09:06): > Multiple messages intestthat::expect_message(obj, regexp)My function spits out multiple messages, is there a way to fit them in regexp? I am currently usingtestthat::capture_message(), but will preferexpect_message(). > I triedregexp=("m1"|"m2"|"m3"), however, this doesn’t work for string only works for numeric
Alan O’C (21:18:42) (in thread): > Seems like a good fit for stackoverflow? Though I’m sure there are plenty of testthat masters here too
Shubham Gupta (21:20:50) (in thread): > On the stackoverflow, I will probably get answers in the context of Unix. That’s why thought to post here.
Shian Su (21:53:42) (in thread): > I think you’re trying to do"m1|m2|m3"?
Shian Su (21:55:25) (in thread): > Though that test will pass if ANY of the 3 options are seen in ANY of the messages. Make sure that’s what you want. > > f <- function(){ > message("things are ok") > message("hold up... it's all gone wrong") > } > > f() > > testthat::expect_message(f(), "ok") >
Shian Su (21:57:12) (in thread): > You can use theall = TRUEoption to make sure all messages match. But that won’t catch if a message is missing.
Shubham Gupta (22:02:19) (in thread): > Thanks."m1|m2|m3"formatting works
2020-07-20
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Martin Morgan (08:29:34): > Join us today at 3:00 US Eastern time today, July 20 for a one hour mini-symposium updatingBioconductor / Human Cell Atlas https://docs.google.com/document/d/19iSMhzoZGzxQjYvO__fbAh7aH5nhAhEGdgJQGVld-3Y/edit?usp=sharing
Chris Vanderaa (09:24:18) (in thread): > Look’s great, but I can’t attend…:sob:Will it be recorded?
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Martin Morgan (10:57:36) (in thread): > yes we’ll try to remember to record it!
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Martin Morgan (14:34:47): > Happening in 30 minutes!Bioconductor/ HCA Seed Network mini symposiumhttps://docs.google.com/document/d/19iSMhzoZGzxQjYvO__fbAh7aH5nhAhEGdgJQGVld-3Y/edit?usp=sharing
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2020-07-21
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Vivek Das (19:23:53) (in thread): > I missed it:disappointed:
Martin Morgan (19:58:24) (in thread): > The recording is herehttps://chanzuckerberg-2.wistia.com/projects/0i6yz9gk2w/channel ; slides will be made available soon@Chris Vanderaa@Vivek Das - Attachment (fast.wistia.net): CZI Seed Networks Webinar Series > Monthly webinar series for the Seed Networks in support of the Human Cell Atlas. The first year will feature presentations that address common experimental and computational challenges in single-cell biology and HCA/Seed Networks communities. As we move forward and begin to generate data we will switch to presentations focused on the findings from Seed Network labs. Calendar of upcoming presentations
2020-07-22
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Vivek Das (09:03:16) (in thread): > Thanks:pray:
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2020-07-23
Martin Morgan (09:21:40) (in thread): > Slides and video are now also linked fromhttp://bioconductor.org/help/course-materials/ (thanks@Kayla Interdonato)
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Kasper D. Hansen (21:36:01): > The James Taylor Foundation is offering 10 scholarships for grad students to attend the 2020 Biological Data Science Conference @ CSHL. Applications are due Aug 1. No association with Galaxy is required. Please pass along to anyone who might be interested.https://galaxyproject.org/
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Simina Boca (22:36:32): > Is there a tweet advertising it@Kasper D. Hansen?
Hyun-Hwan Jeong (22:37:30): > @Simina Bocahttps://twitter.com/galaxyproject/status/1281249379974893573?s=20 - Attachment (twitter): Attachment > James Taylor memorial fund (JTech) and CSHL announce 2020 Biological Data Science Scholarship. 10 outstanding graduate students will be selected to attend the 2020 Biological Data Science Conference #biodata20 #usegalaxy: https://forms.gle/PAVeZCqhVJCidqtu6
Simina Boca (22:40:46): > There’s no deadline on the form or in the tweet
Simina Boca (22:41:13): > I’ll use Aug 1 as per Kasper’s note here in my retweet, but may want to add that in
Simina Boca (22:43:05): > I did find the deadline on the CSHL website
2020-07-24
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2020-07-26
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2020-07-27
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Jeroen Gilis (04:38:48): > Not sure where put this, but here goes; > On July 16th I successfully made the payment for the “Virtual Conference Rate - All Attendees” option. However, I did not receive an email frompathable.com with my login information to the virtual platform. Does anybody know who I should be in contact with for this? > King regards
Constantin Ahlmann-Eltze (04:44:11) (in thread): > Hi Jeroen, I assume your question is about the Bioconductor Conference starting today, right? In that case, I think the best place to ask this is the#bioc2020channel:slightly_smiling_face:
Jeroen Gilis (04:44:49) (in thread): > Perfect, thanks!
Heather Turner (04:48:53): > If you watched or participated in any useR! 2020 events please take a moment to fill out this survey:bit.ly/useR2020survey . > > It will help us make future useR! conferences better for more people!
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Nathan Sheffield (10:58:33) (in thread): > Hi@Pariksheet Nanda– sorry to resurrect an old thread, but just came across this and wanted to reach out. I agree with you comments and in your abstract, the PRO-seq analysis caught my eye. My group is also working on R packages for PRO-seq analysis and I thought it might make sense to join forces in your effort to improve the tools. We’ve been thinking about doing something similar with our R package.
Pariksheet Nanda (11:33:54) (in thread): > Hi@Nathan SheffieldThat’s awesome!! It was nice meeting you and John at BioC 2019. I have a graphviz chart tracking typical PRO-seq analysis that I’m planning on working on (attached) and it would be great to compare notes. I have my weekly video call with Leighton on Wednesday mornings at 9am: maybe the 3 of us can talk sometime? Or I can start an e-mail thread and we can find a convenient time for all of us. - File (PDF): proposal-page_6.pdf
Nathan Sheffield (11:44:03) (in thread): > Oh yeah, I remember that conversation now! Did you already see our preprint on peppro?https://www.biorxiv.org/content/10.1101/2020.02.27.956110v3
Pariksheet Nanda (11:45:18) (in thread): > Yes! Our lab read your PEPPro paper in a journal club a few days after we saw the pre-print appear. That was very similar to one of my PhD aims which I had to scrap in lieu of what I’m now doing!:joy:
Pariksheet Nanda (11:45:44) (in thread): > That was really nice work!
Nathan Sheffield (11:52:20) (in thread): > Wednesdays at 9 is generally open for me, I can join a call
Nathan Sheffield (11:52:32) (in thread): > just e-mail me details
Nathan Sheffield (11:53:34) (in thread): > Oh no, hope it didn’t cause too much of an issue! for that we made some new QC metrics in R, but haven’t polished/packaged it into a bioconductor package,
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Pariksheet Nanda (12:31:04) (in thread): > Ok great! I’ve messaged Leighton about adding you in to our call. No worries, I hadn’t really put much work into that aim. My approach was to add plugins into the MultiQC python package for PRO-seq specific steps. I was really happy seeing how well executed your work was, because my solitary work wouldn’t have been nearly as effective.
Pariksheet Nanda (12:33:53) (in thread): > I used this meme in my lab presentation when your paper came out: - File (JPEG): 3v2p2a.jpg
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bogdan tanasa (21:37:25): > Dear all, please may I ask for your suggestions about BioC packages that i could use to identify the TEMPORAL PROFILES/CLUSTERS of gene expression in scRNA-seq ? (we do have scRNA-seq data that has been collected at 5 different time points, and ideally, we would to define the sets of genes that are on the ascending trend, descending trend, oscillating trends or display other patterns). many thanks !
Koen Van den Berge (21:46:29) (in thread): > You may want to take a look attradeSeq, e.g. see Fig 1 and 5 of thepaper , and thecorresponding section in one of the vignettes. Monocle3 alsoprovides a way to do that . - Attachment (Nature Communications): Trajectory-based differential expression analysis for single-cell sequencing data > Downstream of trajectory inference for cell lineages based on scRNA-seq data, differential expression analysis yields insight into biological processes. Here, Van den Berge et al. develop tradeSeq, a framework for the inference of within and between-lineage differential expression, based on negative binomial generalized additive models. - Attachment (cole-trapnell-lab.github.io): Monocle 3 > Monocle - A powerful software toolkit for single-cell analysis
bogdan tanasa (22:16:19) (in thread): > thank you Koen, i am looking forward the tutorial on TradeSeq offered by the BioC conference. I did come across the benchmark article :https://github.com/dynverse/dynbenchmark , and congratulations and thank you for Slingshot/TradeSeq developments
bogdan tanasa (22:18:02) (in thread): > if I may, i may ask you for comments/suggestions as i am applying tradeSeq functionson our data
bogdan tanasa (22:20:08) (in thread): > i was just wondering if there is a way to explicitly include the time points (1,2,3,4,5) in TradeSeq or if using the pseudotime approach may be better (as it is unsupervised)
Jared Andrews (22:33:04) (in thread): > You can use your timepoints as the input to pseudotime (in place of clusters) if you’d like, and specify the start/end points. Then use the slingshot results for tradeSeq to visualize/ascertain the genes that change between the timepoints.
bogdan tanasa (22:34:39) (in thread): > that is an excellent suggestion, many thanks, Jared !
2020-07-28
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Alan O’C (05:09:47) (in thread): > GPLVM allows you to use known time as a prior for pseudotime inference as well I believe
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bogdan tanasa (20:21:33): > Dear all, a question about BioC in relation to Terra platform and WDL workflow language , particularly if there is any tool in BioC/a wrapper in R for WDL (to be used when writing and running the WDL pipelines on GCP or on Terra). thanks a lot:slightly_smiling_face:! (my question comes also after a workshop at BioC2020 that has presented the CNV annotation pipelines and pureCN that did run on Terra)
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2020-07-29
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Vince Carey (06:58:19) (in thread): > @bogdan tanasathere has been work on R:WDL interfacing by@Sean Davis… I also seehttps://github.com/FredHutch/fh.wdlR
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Chris Vanderaa (08:40:19) (in thread): > Thanks !!
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Matthew Carlucci (10:54:21) (in thread): > For an approach outside of single cell experiments I will plug my new package DiscoRhythm which offers traditional approaches to inference of oscillations with known time in SummarizedExperiment data. I will have a poster session this afternoon.
Koen Van den Berge (11:56:00) (in thread): > Interesting, I will make sure to drop in your poster meeting room!
Ludwig Geistlinger (12:39:59): > Just a heads-up for those that are interested in questions that couldn’t be answered due to limited time during the workshops. We are following up on them in the#bioc2020-workshopschannel. - Attachment: Attachment > <!here>: there were a number of questions in the enrichOmics workshop yesterday where time didn’t permit me to answer them, and which I collected and answered here. I am not sure how to best reach everyone who asked a question, but I am also pasting these answers in the chat section of the workshop of the pathable conference website.
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bogdan tanasa (15:24:47) (in thread): > Thank you Vincent. I will take a close look on the commands . I know that the folks from ENCODE started to develop a python wrapper for WDL (it is called CAPER :https://github.com/ENCODE-DCC/caper/blob/master/docs/conf_encode_workshop_2019.md ), and i thought that similar initiatives are currently ongoing in BioC community
Vince Carey (15:34:31) (in thread): > There are archives of WDL workflows atdockstore.org . Bioconductor is involved withanvilproject.org , and the AnVIL package can be used to drive workflows in Terra and for interacting with the dockstore API. If you’d like to discuss further just email me atstvjc@channing.harvard.edu
bogdan tanasa (15:40:10) (in thread): > thank you Vincent. i believe that it is going to be a workshop on Anvil package at BioC2020 ? i am looking forward to it :) I may email you at a later time point, when i could focus more on GCP and WDL (now in our department at Stanford, there are several projects on scRNA-seq and wil have to finalize some trajectory inference pipelines)
Sean Davis (15:44:31) (in thread): > https://liubuntu.github.io/Bioc2020RCWL/ - Attachment (liubuntu.github.io): Bioc2020 Rcwl > This workshop introduces the Bioconductor toolchain for usage and development of reproducible bioinformatics pipelines using packages of Rcwl and RcwlPipelines. The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of development, usage, and maintenance of CWL pipelines, and furthermore offers higher performance by intuitively supporting parallel work on high performance computing (HPC). hundreds of pre-built bioinformatics pipelines in CWL are included in RcwlPipelines. The tools and pipelines are highly modularized for easy customization of complex bioinformatics analysis. An scRNA-seq pipeline using STARsolo for alignment and quantification, DropletUtils for filtering raw gene-barcode matrix will demonstrate the typical use case of these two packages. More details for usage and examples are available on Rcwl website(https://hubentu.github.io/Rcwl/ ).
Sean Davis (15:47:39) (in thread): > @bogdan tanasa, I’d recommend taking a close look at Nextflow. And despite the fact that Nextflow doesn’t have a name as grandiose as Common Workflow Language, Nextflow is quite nice to use and actually MORE portable (run on laptop, HPC, multiple clouds, same workflow) than CWL or WDL.
bogdan tanasa (16:30:57) (in thread): > Dear Sean, thank you for your suggestions. yes, we would be interested in any workflow language that has been tested/well documented on GCP. The folks from ENCODE are located in a building near us in Palo Alto, and as they have been working on WDL for a long while, we are slightly more inclined towards WDL (and R:wink:. Although, we’d be happy with CWL or Nextflow too (especially as CWL has been used for a long time also on SevenBridges platform).
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2020-07-30
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Mireia Ramos-Rodríguez (09:49:52): > Hi all! > > I have implemented the Github Actions Workflow from the biocthis package (https://github.com/lcolladotor/biocthis ) into my own package. However, since I started using BiocFileCache to download some sample data for the examples and vignettes, it raises a weird error when running the examples (see first attached image). I do not get this error when I run rcmdcheck in my local machine. > > Also, unit tests raise an error that the files downloaded using BiocFileCache are not present (see second attached image), so I’m not sure why it can’t download the appropriate files when running examples and tests, but it works when running the vignettes, which use the exact same function (downloadUMI4CexampleData,https://github.com/Pasquali-lab/UMI4Cats/blob/master/R/makeUMI4Cexample.R ). > > Anyone has any insight on this or has encountered anything similar? - File (PNG): examples_error.png - File (PNG): test_error.png
sani (10:08:00): > Hi all, are there any specific channels for asking questions? My question is related to drawing a Bar chart to represent the contribution of each group to clusters.
Jared Andrews (10:42:37): > If it’s single cell related,#singlecell-queriesis your go to.
Leonardo Collado Torres (10:43:12) (in thread): > Hi@Mireia Ramos-Rodríguez,biocthisruns checks on the Bioconductor Docker#containers+ macOS + Windows. Let’s say that you see the error on the Docker environment. One thing you can try to use is the BioC docker, install your package and dependencies, then reproduce the error. Then you can use functions liketraceback()but also inspect in more detail their status and all that. Fromhttp://bioconductor.org/help/docker/ , use: > > docker run \ > -e PASSWORD=bioc \ > -p 8787:8787 \ > bioconductor/bioconductor_docker:devel >
Jared Andrews (10:44:16): > For general vis questions,#cool-visis what you want.
Jared Andrews (10:44:41): > Otherwise, it kind of depends.
Leonardo Collado Torres (10:45:21) (in thread): > Also, based on your screenshots, I see that on your machine you already had the data (BiocFileCachecached it), so maybe there’s an issue with the source of the data (gattaca.imppc.org ) that you are only seeing now on GHA since it doesn’t have a local cache of the data
Mireia Ramos-Rodríguez (10:55:32) (in thread): > Great, thanks! I will try to see if I can reproduce the error with the Docker image. However, I doubt is related to the data source, as I’ve tried in different computers with no cache of the data, and also after removing such cache, but still can’t get that specific error.
Liz Ing-Simmons (11:07:35) (in thread): > This might be more suitable for the support site (https://support.bioconductor.org/ ), which also has more users - I think channels here are more focused on package development than general usage
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Mireia Ramos-Rodríguez (11:43:17) (in thread): > Some news… I ran the checks on the Bioconductor Docker image with absolutely no problems whatsoever… My last guess would be that the timeout error has something to do with the Github Actions platform? I have no idea how to further explore this, might just avoid testing examples and unit tests for now…
Mireia Ramos-Rodríguez (12:26:47) (in thread): > I encountered the same error when activating the Test coverage section… This is very weird. :( - File (PNG): image.png
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Leonardo Collado Torres (12:58:45) (in thread): > are you working on a private repository? you are getting a connection error with codecov forcovr
Leonardo Collado Torres (12:59:14) (in thread): > anything you do with internet connections can fail randomly too
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Leonardo Collado Torres (13:00:08) (in thread): > so sometimes, I manually re-run all GHA jobs when I get errors like this (not immediately, but a few hours later, just to rule out random connectivity problems)
Leonardo Collado Torres (13:03:06) (in thread): > how big is the data that you are downloading btw?
Leonardo Collado Torres (13:03:34) (in thread): > https://docs.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners
Leonardo Collado Torres (13:03:48) (in thread): > > Each virtual machine has the same hardware resources available. > > 2-core CPU > 7 GB of RAM memory > 14 GB of SSD disk space >
Leonardo Collado Torres (13:04:12) (in thread): > a portion of those 14GB are used for the bioc docker image
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Mireia Ramos-Rodríguez (13:25:03) (in thread): > Data is ~200Mb so that should not be an issue… However the package has lots of dependencies, but I doubt they would occupy almost 10GB… Anyhow, the package just passed all the Bioconductor builds and checks, so I guess that is indeed something limited to GHA…
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Leonardo Collado Torres (20:39:50): > Hi! > > David@David Zhangand I are going to write a small R package that will be a wrapper for an external system (new) dependency that we’ll submit to BioC. I’ve never written an R package with explicit system dependencies. Fromhttp://r-pkgs.had.co.nz/description.html &https://docs.rstudio.com/rspm/admin/appendix/system-dependency-detection/ I understand that you need to a) add theSystemRequirementsfield and b) provide some README installation instructions. I like theblogdownapproach forhugo(https://github.com/rstudio/blogdown/blob/master/DESCRIPTION#L47 ) which seems to download ahugobinary (https://github.com/rstudio/blogdown/blob/master/R/install.R , I do seebrewcalls for macOS) that makes it simple for users. Would that be ok? Like maybe a function that downloads the binary + a link in the readme to the GitHub repo for the system dependency (that has the full compilation instructions for those that might need them). > > Our work is in collaboration with the author of the new system dependency and as such they have built macOS, Windows and Linux binaries. > > Best, > Leo
Aaron Lun (20:41:35): > Sounds like you could just distribute the dependency inside the package. Add aconfigureto pull it down and put it ininst/or something.
Aaron Lun (20:42:23): > I was going to mention TileDB, but I see Dirk is already typing.
Dirk Eddelbuettel (20:42:35) (in thread): > You generally can’t write on user’s file system though.
Aaron Lun (20:44:26) (in thread): > I was thinking to have it download the dependency’s binaries on R package install and put it in the R package installation directory; the path can then be used insystem2()or whatnot. Should be fairly innocuous for prebuilt executables. Shared libraries would probably be more painful.
Dirk Eddelbuettel (20:44:35) (in thread): > Touche:slightly_smiling_face:But that is a “temporary”: iflibtiledb(or its header are not found, and if build from source is not selected, then on macOS + linux we fetch a shared library. [ This sentence alone needs to become a paper detailing all this. ] We then use the libraryto build the package at hand and the downloaded content both a) vanishes from the temp build dir and b) lives on in the created package.
Dirk Eddelbuettel (20:45:03) (in thread): > Whereas@Leonardo Collado Torreswants to download “and keep” a binary. Can’t generally do that…
Dirk Eddelbuettel (20:45:45) (in thread): > Hm, maybe. Can’t think of an example that does that.
Aaron Lun (20:45:56) (in thread): > I just remembered that’s whatbasilisk
Aaron Lun (20:46:16) (in thread): > (Does it for miniconda)
Spencer Nystrom (22:58:47): > Hey Leo, I faced a similar issue with a package I developed, I’d be curious to hear answers to this. I wound up writing detailed install docs as a vignette. The tool I wrap doesn’t ship precompiled binaries and needssudoto install, so I couldn’t write an install function. I’m giving a lightning talk tomorrow about some tools I built to deal withsystem2calls. They might not be useful to you, but if so, happy to chat further.Check them out here . (this is what I mentioned at the happy hour I was thinking of throwing up on CRAN soon)
2020-07-31
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Hervé Pagès (01:36:17) (in thread): > Hi Leo, the Bioconductor tradition is to put the installation instructions in a file calledINSTALL. See packages ChemmineOB, eiR, flowWorkspace, HilbertVisGUI, rsbml, and xps for some examples.
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Leonardo Collado Torres (09:56:02) (in thread): > ohh, thx Aaron and Dirk! I’ll look into basilisk to see how it’s done. Thx again!
Leonardo Collado Torres (09:56:38) (in thread): > Interesting, thanks for sharing! I’ll look into your package^^
Spencer Nystrom (09:58:37) (in thread): > You might not have similar issues as I did. Since you & the tool developer are collaborating, you’ll probably have more say in the interface.
Spencer Nystrom (09:59:31) (in thread): > Looking at Aaron’s solution using theconfigurescript is interesting, and might actually work for me, so I might give this a try & report back on how it goes.
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Dirk Eddelbuettel (10:12:34) (in thread): > Sounds good. I just double check and the CRAN Repository Policy has “Source packages may not contain any form of binary executable code.” so downloading to circumvent may not work. But you could offer a helper function that downloads, and have your package useSys.which()to see if the program is in the path. Anyway – all good questions for the r-package-devel mailing list.
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Leonardo Collado Torres (11:32:30) (in thread): > thanks Hervé!
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Nur-Taz Rahman (15:50:49): > Hello! I am looking for any SoupX user or developer. Anyone familiar with this package?
Aaron Lun (15:52:44): > I tried it once and then gave up when I realized I didn’t have any prior knowledge about the genes thatshouldn’t be expressed.
Nur-Taz Rahman (15:55:13): > I am having trouble loading the cellranger outs folder from the core, therefore, it looks like I need to cluster the raw matrix to give it the cluster info, which I’m feeling too lazy to do . . . so I was wondering if anyone has had the same issue, any work-arounds etc.
Nur-Taz Rahman (15:58:00): > I’d also love to hear if anybody has any recommended package for doublet removal.
Aaron Lun (15:58:27): > @Pierre-Luc Germainand I have been working on integrating a variety of doublet detection functions intoscDblFinder
Aaron Lun (15:58:40): > the OSCA book also has an entire chapter devoted to doublet removal strategies.
Pierre-Luc Germain (16:03:38): > just to add: at the moment the methods from Aaron/OCSA are being integrated in the GitHub version of scDblFinder, and this hasn’t been pushed yet to bioC (so there there’s only the classical scDblFinder approach ATM)
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Leonardo Collado Torres (16:52:49): > https://twitter.com/hadleywickham/status/1289275316662202368?s=20 - Attachment (twitter): Attachment > Just two weeks to go to submit your talk proposals for rstudio::global() — https://blog.rstudio.com/2020/07/17/rstudio-global-call-for-talks/ . Please help us make this our most diverse, global conference yet! #rstats
Aedin Culhane (18:13:08): > post conference chat onbit.ly/bioc2020 .. is still going on if you want to join
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2020-08-01
FelixErnst (06:38:41) (in thread): > Hi@Mireia Ramos-Rodríguez. As far as I understood it the issue doesn’t occur, when you run it a docker container. Did you run the check automatically, by using the RStudio implemented check functionality viadevtools/R CMDor did you check it “manually” from the terminal or R session? > > The reason behind me asking, is that I had the a similar problem, in which covr behaved differently from an interactive session, than it did from a fresh non-interactive session. Maybe this is something you might want to test, if you think it is worth the effort and you are still interest in trying to getting to the bottom of this. > > Also, you are not alone:https://github.com/r-lib/covr/issues/435 . From this I guess there is maybe an underlying problem ofcurl
FelixErnst (07:15:40) (in thread): > Upon tracking down the dependencies, an argument could be made, that installing curl as a binary package and updatinglibcurl4-openssl-devin the docker image at different time points might lead to unexpected behaviour depending on how often the sides of the equation are updated. A quick check might a explicit (re-)install ofcurlfrom source in the GHA
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2020-08-02
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2020-08-03
Heather Turner (03:57:25): > No restriction now on answering the useR! 2020 survey:bit.ly/useR2020survey . If you watched/attended any useR! events, please take 5 min to let us know about it!
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2020-08-04
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Spencer Nystrom (13:48:09): > Does anybody have experience with a tool for database data entry which is user friendly and extensible by non-experts? Our group is looking to improve & better standardize sample tracking but we want a system that will be robust so that when people move on it can be maintained & updated simply. On the extreme end, we’ve looked at something like Air Table, but it just feels a little too Excel like for my liking on a first pass.
Simina Boca (13:51:25): > People in clinical research use RedCap
Simina Boca (13:51:32): > I think you need to pay for it though?
Simina Boca (13:51:56): > I’ve never used it myself but I know that folks at our med center (and many others) use it to make surveys, input data etc
Nicholas Knoblauch (14:03:32) (in thread): > As a former lab manager I would say: > 1. Most problems surrounding sample tracking (at the small and medium scale) are cultural/social problems and not technical problems. > 2. Don’t be so hasty to dismiss Excel.
Spencer Nystrom (14:05:26) (in thread): > I totally agree with you. We don’t need anything high tech. But we do need something with a little more structure than Excel, I think. For example, to conditionally allow specific metadata values based on sample type. In other words, error checking that doesn’t involve writing Excel macros.
Nicholas Knoblauch (14:07:35) (in thread): > I think Microsoft Access is designed more or less exactly for this purpose
Nicholas Knoblauch (14:09:02) (in thread): > The Ringo Starr of Microsoft Office
Spencer Nystrom (14:10:42) (in thread): > Yeah, we considered this, but ultimately, we have too many people using Linux. Kexi was something that also popped up in my searches (FOSS, cross platform Acess equivalent), but I haven’t tried it out.
Sean Davis (14:14:44) (in thread): > We built our own, in continuous use since 2008The Meltzer Lab SolexaDB
Sean Davis (14:16:12) (in thread): > I agree with comments above about Excel. The system noted above uses Excel templates and then imports them into a centrally-managed database. Web capabilities are built on top of that.
Spencer Nystrom (14:16:55) (in thread): > Thanks, Sean!
Spencer Nystrom (14:17:28) (in thread): > How do you check validity of the excel sheet?
Sean Davis (14:17:51) (in thread): > That all happens on import.
Spencer Nystrom (14:18:03) (in thread): > Gotcha, so it throws an error if something’s up.
Sean Davis (14:18:23) (in thread): > Yep.
Spencer Nystrom (14:18:35) (in thread): > :+1:
Sean Davis (14:18:48) (in thread): > And then we throw away the Excel sheet.
Spencer Nystrom (14:18:58) (in thread): > Music to my ears.
Sean Davis (14:18:58) (in thread): > Excel export is available if necessary.
Sean Davis (14:23:11) (in thread): > And the database schema…. It is more complicated than most need, but we use it as our LIMS as well as for simple sample tracking. - File (PNG): Meltzerlab_solexaDB_main_tables.png
Spencer Nystrom (14:25:34) (in thread): > Neat! Yeah, we’re just trying to regularize some disparate excel tables and standardize record keeping a little more. We definitely aren’t large scale, but we have a range of competencies across the group so need the structure to prevent Bad Things:tm:.
Sean Davis (14:27:50) (in thread): > Start with a discussion that includes your PI. Our system worked, not because it was technically great, but because the bosses got on board.
Nicholas Knoblauch (14:29:31) (in thread): > I swear I don’t work for Microsoft, but if your parent org is like mine and bought the super-duper-mega microsoft office enterprise package, it comes with a fancy google forms type thing that exports to Excel (or a database). That could be an easy way to at least get an MVP up and running
Nicholas Knoblauch (14:29:54) (in thread): > https://forms.office.com - Attachment (forms.office.com): Microsoft Forms - Easily create surveys, quizzes, and polls. > Easily create surveys and polls to collect customer feedback, measure employee satisfaction, and organize team events. Quickly create quizzes to measure student knowledge, evaluate class progress, and focus on subjects that need improvement. Microsoft Forms automatically provides charts to visualize your data as you collect responses in real time.
Spencer Nystrom (14:33:13) (in thread): > Oh, cool, just checked and we have the super-mega-pack so have Forms. At this point, we’re just trying to collect a few possible paths forward to discuss pros/cons as a group, so this is all really useful. Thanks!
Sean Davis (14:41:38) (in thread): > Shiny apps are a pretty good approach for this type of work, also. Then, interact with the data/metadata from R directly or via the Shiny app for non-programming users. You get plotting and analytical tooling “built in”. SQLite is a fine starting backend (though be sure to back up often).
Spencer Nystrom (19:43:26) (in thread): > Thanks, Kevin. At this point, I wouldn’t worry about sharing code, but I appreciate the offer!
2020-08-05
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2020-08-06
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2020-08-07
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2020-08-08
Dario Strbenac (20:15:22): > My coding has gotten worse recently. How do I best use a BSgenome inside a package function? > > if(!requireNamespace(genome, quietly = TRUE)) > stop("The package '", genome, "' could not be found. Please install it.") > > genome <- get(genome) > # Error in get(genome) : object 'BSgenome.Hsapiens.UCSC.hg38' not found >
Aaron Lun (20:35:05): > can’t you just ask people to pass in the object as a function argument?
Dario Strbenac (20:50:04): > That would be easiest. I was hoping to make their workspace clutter the minimal possible, but it’s not much difference in the end, so I’ll convert it to the object instead.
Aaron Lun (20:51:09): > I daresay that’s the best approach because it allows people to pass in custom objects that aren’t necessarily inside packages of the same name.
Spencer Nystrom (21:31:36): > Agree with Aaron. One possible exception could be if the function takes a granges object with a genome info entry that matched a BSgenome name.motifmatchrhas code that does this if you wanted an example. But generally for this task I think making the user be explicit is not a bad idea.
2020-08-09
Hervé Pagès (00:51:53): > @Dario StrbenacUseBSgenome::getBSgenome()for that. It will handle BSgenome objects or BSgenome data packages so is the most flexible option. SeeBSgenome::inferRefAndAltAlleles()’s code for an example of how to use it (very simple). Setload.only=TRUEif you don’t want the BSgenome data package to show up on the search path. See?getBSgenome.
2020-08-10
Wenxuan Fan (10:28:22): > @Wenxuan Fan has joined the channel
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Le Zhang (14:10:04): > Hi Bioc, we are building a package that imports a package on Github and it is a suggested pkg. If users have that package, the function will behave differently. It is totally fine if users don’t install that package. I noticed that bioc doesn’t allow Github packages. > 1. Is this apply on the suggested package too? > 2. If I remove this from suggest, there will be a warning on R CMD check. Then how do we solve the contradictory problem? On one hand you don’t want a Github package, on the other hand you don’t want to see warnings in check.
Dirk Eddelbuettel (14:15:19): > (At the CRAN side of things youare allowed to nameAdditional_repositories:in yourDESCRIPTIONand have suggested packages reside there. If you properly test for the package being present, you are all set. Brooke and I have a paper explaining all the nitty gritty in some detail for the case of a data package in a R Journal paper. Code packages work the same way… Seehttp://dx.doi.org/10.32614/RJ-2017-026 if interested)
Le Zhang (14:25:39): > Thanks@Dirk Eddelbuettel, I know about the CRAN options. I would like to ask about the Bioc regulations. IsAdditional_repositoriesallowed on Bioc package DESCRIPTION?
Hervé Pagès (18:53:54): > > Then how do we solve the contradictory problem? > No contradiction. Don’t make use of the GitHub package at all and the warning will go away:wink:At the same time start lobbying with the authors of the GitHub package to convince them to push their package to CRAN or Bioconductor, or ask them if it’s ok to copy/include the code you need into your package. This last solution is ugly and should be a last resort only (would be a temporary workaround until their package makes it to CRAN or Bioconductor).
Martin Morgan (20:04:02): > I don’t know your particular situation, but in some ways I think this is ‘feature creep’ where your package already does some things well, and you’ve decided to add some extra-special functionality. Even if the package enabling extra-special functionality were on CRAN / Bioconductor, maybe your own package would be more robust, easier for users to use, and easier for you to maintain if the extra stuff was delegate to some other resource, e.g., in a separate package on your own GitHub while the extra-special functionality matures. When the author of the extra-special package decides to make a radical change to their interface (hey, it makes much more sense:wink:) you don’t have to panic trying to update the release and devel versions of your already really great package, or to disappoint users of the no-longer-updated release-before-this that they have to go through elaborate contortions to use your already great package – it continues to work as before.
Henrik Bengtsson (21:17:29) (in thread): > In the spirit of what others have already said: > > > “If users have that package, the function will behave differently.” > > As a user, that scares me. If I run the same code again later I want it to produce the same results, regardless of I’ve installed or uninstalled another R package. > > My $0.02
Le Zhang (22:10:07): > Thanks for the explanation. I totally understand the concern here. I am building a shiny package and use some R API packages for JavaScript libraries. Most JS projects only need to reference the CDN or copy the entire code over. I guess the habit is carried over for shiny JS repos where you just download and use the code on backend. There is no need to push to CRAN, because shiny is more like a web product and users don’t need to or do not have access to source code. > I will try to ask them to push to CRAN or ask for permission to copy their code over.
Le Zhang (22:13:27) (in thread): > It’s shiny, not for results, just for some UI display. When you have the package, UI will be more beautiful.
2020-08-11
Krutika (12:36:20): > Hi Bioc! I’m usinghttps://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html to cluster some CNV data (gene as rows and Sample as columns) . The output is a similarity matrix Sample X Sample and cluster membership for each Sample. Does anyone have experience/can comment on ranking features (here it’s genes ) from the raw data which are ranked by importance for the generated clusters ? - Attachment (Bioconductor): ConsensusClusterPlus > algorithm for determining cluster count and membership by stability evidence in unsupervised analysis
2020-08-12
rohitsatyam102 (07:44:51): > Tried using #renkulab on CLI today withing ubuntu:rolling docker image. However, it keeps on throwing error
rohitsatyam102 (07:45:17): > Please select an action by typing its name (open, print, ignore) [ignore]:``Traceback (most recent call last):`` File "/root/miniconda3/envs/renku/bin/renku", line 8, in <module>`` sys.exit(cli())`` File "/root/miniconda3/envs/renku/lib/python3.6/site-packages/click/core.py", line 829, in *_call_*`` return self.main(*args, **kwargs)`` File "/root/miniconda3/envs/renku/lib/python3.6/site-packages/renku/cli/exception_handler.py", line 139, in main`` self._handle_github()`` File "/root/miniconda3/envs/renku/lib/python3.6/site-packages/renku/cli/exception_handler.py", line 186, in _handle_github`` getattr(self, '*process*' + value)()`` File "/root/miniconda3/envs/renku/lib/python3.6/site-packages/renku/cli/exception_handler.py", line 120, in main`` result = super().main(*args, **kwargs)`` File "/root/miniconda3/envs/renku/lib/python3.6/site-packages/renku/cli/exception_handler.py", line 91, in main`` return super().main(*args, **kwargs)`` File "/root/miniconda3/envs/renku/lib/python3.6/site-packages/click/core.py", line 760, in main`` _verify_python3_env()`` File "/root/miniconda3/envs/renku/lib/python3.6/site-packages/click/_unicodefun.py", line 130, in _verify_python3_env`` " mitigation steps.{}".format(extra)``RuntimeError: Click will abort further execution because Python 3 was configured to use ASCII as encoding for the environment. Consulthttps://click.palletsprojects.com/python3/ for mitigation steps.``This system supports the C.UTF-8 locale which is recommended. You might be able to resolve your issue by exporting the following environment variables:`` export LC_ALL=C.UTF-8`` export LANG=C.UTF-8``Click discovered that you exported a UTF-8 locale but the locale system could not pick up from it because it does not exist. The exported locale is 'en_US.utf-8' but it is not supported
rohitsatyam102 (07:46:13): > I don’t understand how to deal with it
Alan O’C (07:55:17): > Did you try changing your locale?
rohitsatyam102 (08:47:33): > Actually, it’s a multiuser machine (not partitioned for users) so as a caution I decided to go with the docker.
rohitsatyam102 (08:51:19): > I tried downloading the docker image of renku. But since I am new to the docker, it seems not to run usingdocker run -v "/home/iitm/rohit_satyam/temp-lib:/downloads" --name=renku -it renku/renkulab-py:3.7-0c91990
Alan O’C (08:54:06): > You can change the locale in the docker image tho. Anyway I have no idea what renku is but it doesn’t seem to be a bioc project, maybe you should raise the issue on their github?
rohitsatyam102 (08:55:06): > Oh!! Sorry. Actually we had a contributed talk about renku at BioC2020 so I thought to ask here. Never mind. Again my apologies
Ruth Schmidt (14:25:15): > Hi all, just wanted to share that I’m currently looking for jobs in datascience/dataviz:https://twitter.com/RuthLSchmidt/status/1293585269871054849?s=19 if you happen to know of anything pls feel free to reach out or RT. Thanks so much:heart: - Attachment (twitter): Attachment > Also, I am looking for jobs in #DataScience #dataviz/research/#scipol (open to academia & industry). Get in touch if you need s/o who knows how to handle large data sets, can build dashboards (#plotly), is creative & good in #scicomm!http://ruthschmidt.rbind.io/files/cv.pdf https://twitter.com/RuthLSchmidt/status/1293584344741744647 - Attachment (twitter): Attachment > Finally built my own completely free website with #hugo #academic & #blogdown (all from within #Rstudio). Check it out here: http://ruthschmidt.rbind.io > It took me only one day thanks to the amazing instructions by @apreshill https://alison.rbind.io/project/summer-of-blogdown/ #rladies
Leonardo Collado Torres (14:41:41) (in thread): > Check#jobs, maybe some of the ads there are of interest to you
Ruth Schmidt (14:54:47) (in thread): > Thank you!!
2020-08-13
Geet (16:22:24): > Hi everyone, I am trying to create a docker image for my one of the project . The project has several Rmds (R notebooks) and I have not seen any example using Rmds. Any help is greatly appreciated. Thank you!!
Sean Davis (16:29:02) (in thread): > A simple Dockerfile like this in the top level of your project should likely do it: > > FROM bioconductor/bioconductor_docker > > WORKDIR /home/rstudio > > COPY --chown=rstudio:rstudio . /home/rstudio/ > > Then,docker build .If you have large datafiles that you don’t want to include in the docker image, consider adding them to a.dockerignorefile. The resulting docker image will present you with an Rstudio instance with the contents of your project in the home directory.
Sean Davis (16:29:29) (in thread): > If you have more questions, consider moving the discussion over to#containers.
2020-08-14
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2020-08-16
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2020-08-17
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2020-08-18
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2020-08-24
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2020-08-25
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Lluís Revilla (14:12:00): > I will soon share a post about package submission to Bioconductor, I tracked how the bio-issue-bot helps users, how much involvement is on the issue (who posted, how many comments from reviewers…), and how long does it take. Is there anything you’d like to know when you submit a package?
Martin Morgan (14:25:39): > @Lluís RevillaI look forward to reading your post. I know that ‘automation’ is very helpful, but I believe it can be very useful to run checks (R CMD checkandBiocCheck::BiocCheck()) locally, especially when preparing a package for submission. Packages are often submitted with an incorrect version number (x.99.z is expected, typically 0.99.0 for a new package) or with some file sizes exceeding guidelines. All this does is delay the start of the review process. These problems are flagged manually before the repository is added togit.bioconductor.org and the review process starts. And the author has to respond, followed by an additional manual check. Here’s an example where the start of the review process was delayed by three dayshttps://github.com/Bioconductor/Contributions/issues/1599 , though often the delay is longer.
Modupeh Betts (21:30:46): > @Modupeh Betts has joined the channel
2020-08-26
saskia (03:57:04) (in thread): > Hi Lluís, I would also be interested to know whether people have updated their packages after initial submission and on average how many times? But maybe this falls outside your interest.
Lluís Revilla (13:31:46): > I’ll look into how long does a submission take to pass all the checks. Some of the issues you mention might be hard to track them.
Lluís Revilla (13:38:52) (in thread): > Actually it would be interesting but this information is not available through GitHub (the dataset I downloaded/created). Technically there is a new version every 6 months but some packages might not receive any update aside from a number version increase . It is hard for me to measure it (I would need to download all git repos of Bioconductor) . It might be easier for the Bioconductor core members to report back that information.
2020-08-27
saskia (19:35:13) (in thread): > Totally get that this is hard. I think the core also doesn’t record that information.
Vikki (21:02:48): > @Vikki has joined the channel
2020-08-29
stefano mangiola (21:06:04): > Hello, with online browsing is not really clear how to update an existing package. Could you point to a point form guide if existing? Thanks
Shian Su (21:23:51) (in thread): > Have you seenhttps://www.bioconductor.org/developers/how-to/git/ ?
Shian Su (21:24:50) (in thread): > The master branch of thegit.bioconductor.org repo corresponds to the devel branch on Biocondcutor.
stefano mangiola (21:28:58) (in thread): > Thanks. So basically we push to Dev branch in bioconductor (master) and it will be automatically become release. If we keep up-to-date the dev bioconductor branch, it’s enough?
Shian Su (21:30:26) (in thread): > If there’s major bugs that must be fixed, then you can push to a release branch labelledRELEASE_X_Yotherwise you should push to dev.
Shian Su (21:31:38) (in thread): > If possible, the push to release should only contain the bug fix, any other changes or new features should be deferred to the devel branch.
stefano mangiola (21:33:00) (in thread): > just to understand, RELEASE_X_Y is the past release, not the future
stefano mangiola (21:33:20) (in thread): > the future will be taken from DEVEL bioconductor branch, correct?
Shian Su (21:35:09) (in thread): > RELEASE_X_Y is either the past or a current release. The next release will be taken from DEVEL/master. RELEASE_X_Y is for changing what people receive usingbioc::installright now.
stefano mangiola (21:38:20) (in thread): > Amazing thanks! “The next release will be taken from DEVEL/master.” was the answer I was looking for.
Shian Su (21:51:18) (in thread): > Have a look athttps://bioconductor.org/developers/how-to/git/sync-existing-repositories/ on setting up the upstream if you maintain the package on both github and bioc.
stefano mangiola (21:52:02) (in thread): > Thanks guys. I keep my Bioconductor dev branch up-to-date already, so I guess I won’t have to do anything else:wink:
2020-08-30
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2020-09-01
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2020-09-02
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2020-09-03
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2020-09-06
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2020-09-08
Qian Liu (11:11:16): - Attachment: Attachment > BioCAsia is coming to a screen near you this October (15-18) . This will be the sixth Bioconductor Asia meeting that aims to bring together researchers with an interest in Bioconductor and R to exchange ideas and expertise. > We’re planning a fun and welcoming virtual meeting with talks and workshops to suit beginners through to more experienced users. > To learn about the amazing line-up of speakers, register for the event (it’s free!) or submit an abstract (short and lightning talk slots are available) please visit https://biocasia2020.bioconductor.org/ . Abstracts are due Friday September 25. > We hope to e-see you there!
Qian Liu (11:11:28): - Attachment (twitter): Attachment > Calling all Bioconductors in Asia! #BioCAsia is coming to a screen near you in 2020 (Oct 15-18). Amazing line-up of speakers, including #rstats #bioconductor co-founder Robert Gentleman. Abstract submission open until Sept 25. Learn more by visiting https://biocasia2020.bioconductor.org/ 1/2
Qian Liu (11:11:36): - Attachment (twitter): Attachment > #BioCAsia will have hands-on workshops in English and Mandarin and registration is free thanks to the support of our generous sponsors @CSL @F1000Research @RConsortium https://biocasia2020.bioconductor.org/ 2/2
Qian Liu (11:11:44): - Attachment: Attachment > Please feel free to RT and spread the word! :party_parrot:
Qian Liu (11:11:52): > Please join the#biocasia2020channel for more information! - Attachment: Attachment > Please also join the #biocasia2020 channel if you are interested!
Lori Shepherd (14:55:12): > The Bioconductor Release 3.12 Schedule has been posted and is tentatively scheduled for October 28th. Important deadlines can be found on the website and will be posted here and on the bioc-devel atr-project.org mailing list. As a quick summary: > > October 2: New package submission deadline (packages will still need to pass the formal review process to be included). Package submitted after this date are not guaranteed to be reviewed; they will be reviewed time pending. > > October 13 Current Release 3.11 Freeze. No changes will be accepted to the Bioconductor 3.11 branch after this date. > > October 21 No API changes to devel 3.12. Also, newly submitted packages need to be accepted by this date to be included in the release > > October 23 Deadline for packages to be passing R CMD install/build/check. > > October 27 Devel 3.12 branch is frozen to create release branch. > > October 28 Release Bioconductor 3.12
2020-09-09
frederick boehm (12:29:39): > @frederick boehm has joined the channel
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2020-09-11
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2020-09-14
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Alan O’C (06:10:45): > The email/password login panel onhttps://support.bioconductor.org/accounts/login/ hangs on load for me. It does eventually load but takes a few minutes
Lori Shepherd (08:06:14): > I suggest clearing your webbrowser cache. Also hang tight we plan on rolling out upgrades to the support site hopefully by the end of the month. That might also help speed things along
Alan O’C (08:36:55): > Happens to me across different browsers and in fresh instances (private window or with cleared cache). Sounds good though, upgrades may end up resolving it
NABISUBI PATRICIA (08:56:40): > Hey
NABISUBI PATRICIA (08:57:14): > Does anyone have any knowledge on how to do a PCA for snp data?
NABISUBI PATRICIA (08:58:19): > I have snippy results from mtb and I want to do a PCA
Vince Carey (09:47:43): > Have a look athttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0218306 … you can “just do it” but there are caveats. - Attachment (journals.plos.org): Consequences of PCA graphs, SNP codings, and PCA variants for elucidating population structure > SNP datasets are high-dimensional, often with thousands to millions of SNPs and hundreds to thousands of samples or individuals. Accordingly, PCA graphs are frequently used to provide a low-dimensional visualization in order to display and discover patterns in SNP data from humans, animals, plants, and microbes—especially to elucidate population structure. PCA is not a single method that is always done the same way, but rather requires three choices which we explore as a three-way factorial: two kinds of PCA graphs by three SNP codings by six PCA variants. Our main three recommendations are simple and easily implemented: Use PCA biplots, SNP coding 1 for the rare allele and 0 for the common allele, and double-centered PCA (or AMMI1 if main effects are also of interest). We also document contemporary practices by a literature survey of 125 representative articles that apply PCA to SNP data, find that virtually none implement our recommendations. The ultimate benefit from informed and optimal choices of PCA graph, SNP coding, and PCA variant, is expected to be discovery of more biology, and thereby acceleration of medical, agricultural, and other vital applications.
sanne.maas (09:50:22): > @sanne.maas has joined the channel
Will Townes (11:11:05) (in thread): > I recommend checking out the plink tool:https://www.cog-genomics.org/plink/1.9/
Will Townes (11:12:35) (in thread): > Also you might want to try terastructure as an alternative:https://github.com/StoreyLab/terastructure
2020-09-15
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Vince Carey (10:47:56): > i just noticed that R CMD INSTALL does not convey .bib files to the /doc folder of the installed package, so the Rmd copied there may not be compilable. Feature or bug?
Dirk Eddelbuettel (10:57:09): > IIRC the vignettes are presumed built from theR CMD buildstep. For my use among Rcpp* packages I have hadinst/Rcpp.bibfor years with theRcpppackage itself to ensure accessability by other packages already depending onRcpp.
2020-09-16
Mike Morgan (10:58:15): > @Mike Morgan has joined the channel
2020-09-17
Jared Andrews (11:56:43): > Is there a way to increase the output width of knit html from an Rmd when usingBiocStyle?
Martin Morgan (12:13:35) (in thread): > Including anoptions(width=...)command in an evaluated but not displayed block? Maybe I misunderstand your question. An actually I usually seem to find that the default is ~4 characters too wide…
Jared Andrews (12:18:10) (in thread): > Knit HTML file tend to have a lot of white space to the sides, presumably to try to replicate PDF output. I’d like to know how to increase the width of the content to actually utilize that space.
Jared Andrews (12:20:12) (in thread): > Not the output of run code, but the actual text content: - File (PNG): image.png
Jared Andrews (12:28:09) (in thread): > Nevermind, I was able to do this by adding a css block after the header like so: > > body { > max-width: 1800px !important; > } > div.main-container { > max-width: 1800px !important; > width: 1800px !important; > } > .toc-content { > padding-right: 0px; > padding-left: 0px; > } >
Jared Andrews (12:29:31) (in thread): > Reason behind this was just to make things easier to follow during a virtual walk-through.
Federico Marini (14:53:01) (in thread): > Had a similar issue some time ago, nice trick
Federico Marini (14:53:31) (in thread): > Wouldn’t mind having a fully fledged BiocStyle widescreen template though:stuck_out_tongue:
Jared Andrews (15:07:16) (in thread): > Same, wouldn’t mind that at all.
2020-09-18
Kasper D. Hansen (05:38:59) (in thread): > Im not too happy with the current setup either. I do think the solution is to take another view at the current setup on a variety of platforms including phone, laptop screen and various font magnifications.
Kasper D. Hansen (05:39:18) (in thread): > Ideally we want one layout which just works, so that all packages benefit from that.
Kasper D. Hansen (05:40:14) (in thread): > And that means not everyone is complete happy (which is ok), but the is a difference between settings which are very subjective and settings which are not great.
Kasper D. Hansen (05:40:48) (in thread): > For example, I occasionally view vignettes on my phone and I frequently feel that I can only see a fraction of the text, which is not great.
Chris Cheshire (05:41:02): > @Chris Cheshire has joined the channel
NABISUBI PATRICIA (09:12:29): > thanks@Vince Carey
2020-09-21
rohitsatyam102 (02:19:45): > Is there a way in R to make sashimi plot in real time as the user query a shiny application. I am asking this because I failed to find any package that runs in R.
Aaron Lun (02:40:08) (in thread): > I HATE THE TEXT WRAP.
Aaron Lun (02:40:40) (in thread): > BiocStyle’s default text wrap for code is insane.
Spencer Nystrom (06:33:13) (in thread): > There’s a Plos computational biology paper on a tool called ‘ggsashimi’ that wraps ggplot2, but it’s kind of a weird tool (it’s a python script that outputs an R script that plots a ggplot). Maybe the source code could be useful to you to use as an example to build your own?
Bob Policastro (07:52:45): > Gviz is what I use to make many of my genomic tracks, and it can make sashimi plots.
rohitsatyam102 (13:22:32) (in thread): > Oh Yeah@Spencer Nystrom. I saw that but I was experiencing difficulty in running in lately. Am on it. Will let you know the progress soon too. I was wishing something more functional in R such as a Bioconductor package
rohitsatyam102 (13:25:00) (in thread): > Thaks will check that out for sure
Nicholas Knoblauch (18:55:11): > Is there no concept ofNAforGRanges?
Aaron Lun (18:56:28): > Don’t think so. My two workarounds are either make amissingseqlevel or to make an empty entry in a GRangesList.
Michael Lawrence (18:57:09): > Not really. SeeHelloRanges:::NAGRanges()for one aproach.
Michael Lawrence (18:57:56): > That’s somewhat bedtools oriented, so it uses “.” for the missing seqname and an empty range [0,-1].
Nicholas Knoblauch (19:06:10): > got it. thanks!
2020-09-22
Mike Smith (11:22:53) (in thread): > @Kasper D. HansenI made some updates to BiocStyle regarding small screens before the last release (https://github.com/Bioconductor/BiocStyle/pull/67 ) Do you still see the issue in vignettes built for Bioc 3.11 ?
Aaron Lun (11:24:18) (in thread): > maybe you can solve 74 as well, by adding > > pre code { > white-space: pre; > } >
2020-09-23
Aaron Lun (01:00:58): > @Mike SmithLatestknitr BiocStyle
Aaron Lun (01:08:59): > https://github.com/Bioconductor/BiocStyle/issues/78
Al J Abadi (01:35:55) (in thread): > That explains why our GHA checks are failing
Hervé Pagès (01:36:10): > Thanks for the heads-up. That explains the hundreds ofR CMD buildfailures in the current builds. Expect a blood bath on tomorrow’s report!
Lori Shepherd (08:22:01): > FWIW: This will also affect any packages in the SPB as well. We are starting to see it in a few packages like TMExplorer.
Mike Smith (09:48:30): > Thanks for the heads up and the pull request. I’ll take a look ASAP. Andrzej is technically still in charge of the package, so I’ll message him to let him know too.
Dirk Eddelbuettel (09:51:38): > Our (i.e. tiledb) package is a reverse dependency whichcould have caught this but the (html-only) vignette is so simple (i.e. has no plots) that this didn’t bark or bite. Sorry!
Aaron Lun (13:10:07): > @Mike SmithKeep in mind we’re broken in both devel and release, so the sooner the better.
Mike Smith (13:37:07) (in thread): > Don’t worry, it’s gone to the top of my to-do list!
Mikhael Manurung (13:53:31): > Hi everyone, I am asking this question here just in case… Does any of you have doneVirScan before? I am looking for an estimate of cost per sample, but I could not find it anywhere. Thanks in advance! - Attachment (illumina.com): VirScan: beyond profiling the human virome | Illumina SciMon Video > null
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Aaron Lun (16:16:46) (in thread): > Go, no-go? Getting close to tomorrow’s build cut-off.
Aaron Lun (19:46:15) (in thread): > Well. I guess that never happened. Can we just merge in my fix and pick up the pieces later? This is a real blocker for a bunch of projects.
Leonardo Collado Torres (21:53:12) (in thread): > Thanks Mike for working on this and Aaron for the fix! I was just about to report it on bioc-devel when I saw these messages:smiley:I sent the email anyways, because others might not have seen the messages on Slack
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2020-09-24
Kanyerezi Stephen (08:12:25): > @Kanyerezi Stephen has joined the channel
Vince Carey (10:43:07): > https://datascience.nih.gov/news/cold-spring-harbor-laboratory-biological-data-science-codeathon
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Soroor (21:08:28): > Hi Channel. I have python calls in my vignette, which builds on macOS but not on windows and linux build systems (I am using virtual envs in reticulate package to call python from R). Does anyone have any similar experience and suggestions to resolve the build issue? many thanks!
Aaron Lun (22:05:45): > https://bioconductor.org/packages/devel/bioc/html/basilisk.html - Attachment (Bioconductor): basilisk (development version) > Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session.
Aaron Lun (22:06:50): > The guide is written for package developers, but you can use the same machinery to provision a conda instance anywhere.
2020-09-25
Soroor (03:28:19) (in thread): > thanks heaps, Aaron.
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2020-09-28
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2020-09-30
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2020-10-02
Sean Davis (07:15:18): > Just a reminder to those here interested in#education-and-trainingthat a dedicated channel exists.
Qian Liu (16:43:59): > Thank you to those who have submitted talks/workshops/posters to BiocAsia2020. NOTE that the poster submission is open until Oct. 10th. All are encouraged to submit directly to F1000Research following the instruction here:https://biocasia2020.bioconductor.org/call-for-abstracts - Attachment (biocasia2020.bioconductor.org): BioC Asia 2020 > Oct 15 - 18
Matt Stone (18:48:23): > Hi all, > > I’m trying to add a few vignettes to a submission in progress, and I’m wondering what the recommended approach for computationally intensive vignettes is. I’ve found this blog post on pre-compiling vignettes, but I’m finding that the cached figures exceed the package size limit. Is it okay to go over the limit for something like this, or is there a better approach for reducing the size that doesn’t require the vignettes to be fully computed on install? > > Thanks! - Attachment (ropensci.org): How to precompute package vignettes or pkgdown articles > As of earlier this year, we are now automatically building binaries and pkgdown documentation for all rOpenSci packages. One issue we encountered is that some packages include vignettes that require some special tools/data/credentials, which are unavailable on generic build servers. This post explains how to include such vignettes and articles in your package. On package vignettes By default, R automatically recreates vignettes during R CMD check or when generating pkgdown sites by running all R code.
Matt Stone (18:49:09) (in thread): > Also please let me know if this is better suited to another channel or to bioc-devel
Aaron Lun (18:49:30): > The OSCA book can be treated as a huge vignette that happens to take several hours to compile.
Matt Stone (18:59:06) (in thread): > Sorry, I’m a bit confused by this. I don’t think the OSCA book is a bioconductor package? The vignettes take several hours each to run, so it’s not feasible to expect the user to build them as a prereq for installing the package. However, the cached results, particularly the figures and rendered HTML vignettes, are above the 5 MB size limit on Bioconductor packages. Does Bioconductor generally permit exceeding this limit for vignettes/figures?
Matt Stone (18:59:14) (in thread): > Thanks!
Aaron Lun (18:59:31) (in thread): > Oh, but it is:https://github.com/LTLA/OSCA
Aaron Lun (19:00:01) (in thread): > But the biggest point here is that you want to separate your heavy documentation from your software.
Aaron Lun (19:01:06) (in thread): > Using prebuilt documentation is a big nono. I’ve been there, done that, stuff goes out of date in a flash. For example, the diffHic vignette hasn’t been updated in years - not because I don’t want to, but because I can’t, because I don’t have access to the files anymore!
Dirk Eddelbuettel (19:01:23) (in thread): > There is a very simple trick first described by Mark van der Loo here:http://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/ I am doing that for a few CRAN packages myself just to simplify builds. Works for me, keeps Suggests: and build time (i.e. on CI) shorter.
Aaron Lun (19:01:45) (in thread): > This would not have been a problem had I decided at the start to develop the vignettes in a more robust manner - see, for example, the csawUserGuide package that implements the user guide. For csaw.
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Matt Stone (20:05:26) (in thread): > I see! Ok, that makes sense. I have one “how to use the package” vignette, which hasn’t been an issue, and three vignettes which are additional examples of the package in use on various datasets, which are larger. I think I can remove the latter as vignettes from the package and just make them available through our pkgdown site
Matt Stone (20:05:36) (in thread): > Thank you!
Matt Stone (20:05:43) (in thread): > Thanks!
2020-10-03
Kasper D. Hansen (05:13:44) (in thread): > I think there are different approaches to this
Kasper D. Hansen (05:14:39) (in thread): > I agree with@Aaron Lunthat the fundamental experience of Bioconductor is that prebuilt vignettes should be avoided. However, this does not mean you can’t find packages with prebuilt vignettes like diffHiC that@Aaron Lunmentions or for that matter limma
Kasper D. Hansen (05:15:19) (in thread): > I think it is a bit different in your case where there is a basic vignette which is built and a more advanced / heavy vignette which could be pre-built.
Kasper D. Hansen (05:15:50) (in thread): > Where the purpose of the longer one is (perhaps?) to have a more realistic data processing example
Kasper D. Hansen (05:16:16) (in thread): > For the large figures, I think you need to figure out how to say use png()
Aaron Lun (05:16:55) (in thread): > My motto from now on is: if it doesn’t get run as part of the build system, then it doesn’t exist.
2020-10-04
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2020-10-05
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Sean Davis (08:29:16): > New job working with Bioconductor and Harvard. See#jobs.
Matt Stone (12:08:05) (in thread): > Thanks! Yes, the purpose of the longer vignettes is to 1) provide more realistic output and 2) to provide code to reproduce figures from the paper. > > I like the suggestion to build just the intro vignette. For now, I think I’ll move the heavier demos to a different branch with the pkgdown files and only include them on the website, rather than as package vignettes. If I have time I’ll follow the example in csawUsersGuide for making them available as online documentation through R.
Hervé Pagès (12:16:23) (in thread): > Our policy is to strongly discourage static vignettes as they defeat the QA process.
Dirk Eddelbuettel (12:18:01) (in thread): > Totally understood. This was in the context of “computationally intensive vignette”. There may be times when one does not want to build all, but that may only pertain to things outside of Bioc.
Federico Marini (12:24:18): > Hi everyone, just checking in whether someone of you have been already working with data from the BlueFuse Illumina system (https://www.illumina.com/clinical/clinical_informatics/bluefuse.html ), especiallyoutside the default software provided - I’m asking on behalf of a dear former colleague of mine who recently started some attempts for IVF. > Thankful as always for any input here (also on DM if preferred)! - Attachment (illumina.com): Bluefuse Multi Software > BlueFuse software provides molecular cytogenetic and in vitro fertilization (IVF) data analysis in a single framework.
Aaron Lun (12:25:36): > like, to study IVF? Or is she the subject?
Federico Marini (12:30:23): > She being the subject, in this case - her background is as classical biostatistician
Aaron Lun (12:31:03): > Wow, she got her hands on her own sequencing data?
Federico Marini (12:32:25): > She got the results for that, don’t think she really got the data itself. > Thing is, the results from the system are not so conclusive. So she was wondering whether there are better methods than the all-in-one thingo put together by illlumina
Aaron Lun (12:32:54): > yeah, I was wondering whether patients would regularly be requesting the FASTQs.
Federico Marini (12:36:04): > no clue there- I think she probably is asking because of the academic vicinity we shared:wink:
Matt Stone (12:52:44) (in thread): > Thanks Hervé for the clarification. I think the best solution for my case is to include a buildable vignette demo’ing the package functions, and move the computationally intensive vignettes to docs hosted on the package website. (See my comments in the thread below Aaron’s response for more detail) > > Martin flagged the pre-built vignettes in his review over the weekend as well, so I’ll be checking with him that this is acceptable, but please let me know if you have any additional suggestions. Thanks!
2020-10-06
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2020-10-07
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Vince Carey (13:58:02): > I’ve hit two occasions where lack of infrastructure for textshaping and ragg packages has slowed me down. Anyone else run into this?
Dirk Eddelbuettel (14:01:42) (in thread): > Please allow me to toot a common refrain here. What is happening is that an already installed package (pkgdown) now has added (recursive, via other packages) build-dependenciesoutside the view of the R package system so this fails. If we turned the screws one notch and made ourR packagessystem packages with system level dependsthen the added dependencies would have auto-installed on an upgrade . > > That is hard to pull off across all OSs. It is however feasible where it may matter most these days: Linux for cloud and CI deployments. I riffed on that before (w.r.t to BSPM and RSPM, and earlier for years on the upside of the PPAs for .deb packages under Ubuntu). Happy to do so again if I ever have an audience of more than one…
Nicholas Knoblauch (14:17:09) (in thread): > Dirk, what are your thoughts on going the other way around, i.e making R packages out of the system level dependencies? This isn’t always straightforward (e.g if the build system is anything other than autotools) but in cases where it is it seems like the easiest way to go in terms of user friendliness. On the other hand, I get the impression the CRAN folks wouldn’t be too keen on an R package that doesn’t “do” anything (i.e doesn’t have any R code)
Dirk Eddelbuettel (14:30:30) (in thread): > I don’t think one can well enough for all OSs. Or that one should simply because of the R needs. It’s complicated but on balance I am also against “vendoring” and multiple copies of the same stuff. > > But the tide seems to have turned the other way. Ditto with “fat” static binary builds.:confused:
Nicholas Knoblauch (14:50:03) (in thread): > Yeah I hear you
Ludwig Geistlinger (14:57:39) (in thread): > @Vince Careyyes ran into the same problem. In my case (GHA / Docker), textshaping and ragg couldn’t be installed due to missing libraries. I solved this via addingapt-get -y install libharfbuzz-dev libfribidi-devto the Dockerfile and the workflow yaml.
Vince Carey (15:00:48) (in thread): > Yes, the fix was easy. But the sense that this will recur … recurs.
Martin Morgan (15:31:50) (in thread): > Are textshaping and ragg somewhere in the dependencies (Depends, etc.) of pkgdown(?) ? Is pkgdown in the Depends: (etc) of a bioconductor package? I’m asking from the bioconductor/bioconductor_docker perspective, and whether this is an instance of a ‘bug’ in upstream software, or…
Dirk Eddelbuettel (15:34:11) (in thread): > “Depends of Depends”
Dirk Eddelbuettel (15:34:23) (in thread): - File (R): Untitled
Ludwig Geistlinger (15:48:57) (in thread): > Not sure about bioconductor packages, butpkgdownis inSuggestsof (all?) Bioc2020 workshops and associated workshop Docker containers built on top of bioconductor/bioconductor_docker …
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2020-10-08
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Flavia E (11:29:07): > Hello folks..I’m interesting in combine two different microarray with the same platform. How can I do it? Do I need to remove batcvh effect? I know that there is InSilico DB package to do this but it has been deprecated from Bioconductor… Any suggestion? Thanks in advance
Kasper D. Hansen (11:42:22): > You mean the array types are different but of the same kind, for example different kinds of Affy arrays?
Kasper D. Hansen (11:42:43): > Which arrays are we talking about
Levi Waldron (12:22:10) (in thread): > FYI this issue was fixed upstream yesterday (I had the same issue before realizing it was being discussed here!):https://github.com/rocker-org/rocker-versioned/issues/244
Dirk Eddelbuettel (12:23:42) (in thread): > That’s not really upstream (apart from the narrow sense of ’those basing their containers on Rocker containers, esp the versioned/versioned2 stack). That’s “just us” in Rocker. It doesn’t take away form what I said earlier that we all should really work towards full dependency resolution.
Levi Waldron (12:39:52) (in thread): > Yes it makes sense@Dirk Eddelbuettel. I think the system dependencies part of DESCRIPTION files is rarely used (I can’t even remember right now what the label is). I’m also interested in how to guarantee that a set of packages can be both installed and checked. on our Docker images. I guess it should be feasible to test whether a package defines external dependencies correctly in its DESCRIPTION so that a Docker container can be programmatically built from a basic container specifically for it, that can install and check it.
Hervé Pagès (13:14:37) (in thread): > FWIW the change was in CRAN packageragg pkgdown EnhancedVolcano EnhancedVolcano ragg textshapping libfribidi-devon the Linux builders 2 days ago to allow the newragg
Hervé Pagès (13:16:05) (in thread): > Here is the full list of Ubuntu/deb packages required for the builds:https://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-Ubuntu-20.04-HOWTO.md#packages-needed-by-some-cran-andor-bioc-packages
Dirk Eddelbuettel (13:16:44) (in thread): > There were two, ragg and textshaping. The main point, as discussed, is that a CRAN or BioC package has no depends. A binary package such as the 4600 in Michael Rutter’s PPA (for Ubuntu, with some BioC) or the 15k (!!) in Inaki Ucar’s Copr repo (no BioC AFAIK) do. I riffed on that earlier in a thread and have eg some demos on my blog under code/r4.
Dirk Eddelbuettel (13:18:03) (in thread): > Yes, and “manually” curating lists works approximately well enough. I kinda do the same on the box on which I run reverse depends for Rcpp and related packages. We could do better though.
rohitsatyam102 (18:23:02): > Hi@James MacDonaldfound this Genomewide annotation of Oryza Sativa to be really instrumental lately in one of my collaboration study. It would be a wonderful addition to theOrgDb packages :https://github.com/xuzhougeng/org.Osativa.eg.db
rohitsatyam102 (18:23:59): > I would also like to ask if there are plans to extend such packages to other organisms as well in the near future
James MacDonald (18:43:19): > @rohitsatyam102the OrgDb packages are pretty static these days. Instead most of the new annotation packages are hosted onAnnotationHub. For example, there are three riceOrgDbpackages there: > > > query(hub, c("orgdb","oryza")) > AnnotationHub with 8 records > # snapshotDate(): 2020-04-27 > # $dataprovider:[ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/](ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/)# $species: Sitophilus oryzae, Pyricularia oryzae_70-15, Oryza sativa_subsp.... > # $rdataclass: OrgDb > # additional mcols(): taxonomyid, genome, description, > # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, > # rdatapath, sourceurl, sourcetype > # retrieve records with, e.g., 'object[["AH80658"]]' > > title > AH80658 | org.Oryza_sativa_(japonica_cultivar-group).eg.sqlite > AH80659 | org.Oryza_sativa_Japonica_Group.eg.sqlite > AH80660 | org.Oryza_sativa_subsp._japonica.eg.sqlite > > They don’t appear to have the specific mapping of the package you mention, but instead of generating installable packages, we would rather host that sort of package onAnnotationHub. If you think that would be a good addition, you might contact the person who made the package you like and see if they are willing to contribute it toAnnotationHub. I am not sure about the details of contribution, but I assume there is something in the vignette, or for sure@Lori Shepherdwill know.
2020-10-09
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rohitsatyam102 (04:59:31) (in thread): > Actually, the reason I mentioned this is most of the studies that I have come across uses rice genome from this database:http://rice.plantbiology.msu.edu/ . However, the database gives you MSU LOC-ID(gene ids) and when I use GID key in GSEA it throws the following error:preparing geneSet collections...–> Expected input gene ID: 4326124,9266343,4327093,4331490,4343002,107276559Error in check_gene_id(geneList, geneSets) : –> No gene can be mapped….``
rohitsatyam102 (05:04:14) (in thread): > > hub <- AnnotationHub() > query(hub, "oryza sativa") > rice <- hub[['AH75917']] > gse <- gseGO(geneList=gene_list, > ont ="ALL", > keyType = "GID", > nPerm = 10000, > minGSSize = 3, > maxGSSize = 800, > pvalueCutoff = 0.05, > verbose = TRUE, > OrgDb = rice, > pAdjustMethod = "none") >
rohitsatyam102 (05:04:21) (in thread): > This was my code
rohitsatyam102 (05:06:09) (in thread): > > gene_list<-c("LOC_Os01g24920","LOC_Os01g24940","LOC_Os01g24950","LOC_Os01g25060","LOC_Os07g12780","LOC_Os01g25240","LOC_Os07g47510") >
rohitsatyam102 (05:08:38) (in thread): > The biggest challenge for me was how to convert these LOC_ID to numbered GID such as (4326124)
rohitsatyam102 (05:15:14): > Any suggestion on packages for intron-retention study using RNASeq with a proper vignette
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Robert Castelo (06:42:25) (in thread): > ASpli should allow you to analyze alternative splicing events from RNAseq, including intron retention. I believe the maintainer is not in Slack, so if you have questions you should make a post at the Bioconductor supportsite addingASplias a tag to ensure the maintainer gets notified or contact her directly. - Attachment (Bioconductor): ASpli > Integrative pipeline for the analysis of alternative splicing using RNAseq.
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James MacDonald (10:40:48) (in thread): > I guess I don’t see what the problem is. You have an annotation package that will do the mapping, right? In that case why does it matter if another, different package won’t do the mapping?
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rohitsatyam102 (15:49:19) (in thread): > Yes I haveorg.Osative.eg .db but before knowing that it exists, I was trying it with Annotation hub and was failing previously. That’s why I suggested including it as R package among other 20 orgdb packages.
rohitsatyam102 (15:49:57) (in thread): > Thanks@Robert Castelowill check this out.
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James MacDonald (17:23:45) (in thread): > That’s why I suggested that you talk to whomever built that package, and see if they want to contribute it to the AnnotationHub.
saskia (20:34:57): > <!channel>The Bioconductor project now has acode of conduct . This code of conduct applies to all Bioconductor events as well as all communication channels, such as slack. We are committed to keep building an open, welcoming and kind community for everyone.
Bharati Mehani (20:52:30): > Hey I am looking for any package available to integrate the 450k methylation data with the EPIC array data, which can take care of all sorts of batch corrections. Any lead will be helpful. Thanks in advance.
brian capaldo (21:13:31): > Check out CPACOR, not a package though, but a very thorough batch of limma scripts
brian capaldo (21:14:06): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365767/ - Attachment (PubMed Central (PMC)): A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies > DNA methylation plays a fundamental role in the regulation of the genome, but the optimal strategy for analysis of genome-wide DNA methylation data remains to be determined. We developed a comprehensive analysis pipeline for epigenome-wide association …
brian capaldo (21:14:26): > If the control probes overlap, it should work
Bharati Mehani (21:36:50): > Thanks brian, will check it
2020-10-10
Flavia E (02:32:30) (in thread): > Same arrays (platform fro example hg133plus2a) different samples gsm###.
rohitsatyam102 (03:58:56) (in thread): > Sure
rohitsatyam102 (15:48:34): > Hi everyone. > I have theseSj.out.tabfiles obtained from STAR and am aware that these files contain high confidence collapsed splice junctions. However, I failed to find tools/R packages that take these files as input and help you do some meaningful analysis like differential splicing. Can you point me to some papers that have used these files for similar kind of analysis or can suggest packages that use these files? Read Aspli but seems like it has it’s own way of extracting the splicing information using inbuilt functions rather than taking some external count file.
2020-10-11
Hervé Pagès (18:15:02): > @rohitsatyam102 GenomicAlignments::readSTARJunctions()should be able to import these files. Have you considered asking this type of questions on the support site? This is a much better place for that. If you tag your question properly you’ll get better chances to receive useful answers than here. Also your questions and their answers will be indexed and searchable making the resource permanently available to the broad community.
rohitsatyam102 (18:23:41): > @Hervé PagèsThanks for the suggestion. I haven’t raised it on STAR’s support site but posted it on Biostars. Because I didn’t got a reply there, I tried asking it here. Thanks for your response. Will try looking around this function and downstream analysis that follows
Hervé Pagès (18:25:55): > I meant the Bioconductor support site:https://support.bioconductor.org
rohitsatyam102 (18:33:22): > My apologies, but I have seen cross posting of questions both on Bioconductor and Biostars have seen infuriated responses from the community members. But will start using it more often from now onwards over biostars and will share the link here for your valuable inputs.
Jared Andrews (18:36:36): > To be clear, you are still free to post general analysis/bioinformatics questions on Biostars (I am a mod there), but if it’s something Bioconductor-specific (how to use a given package, errors, etc) then the Bioconductor site is likely the better choice. The package authors will actually be notified of such posts on the Bioconductor site, while many may not frequent or even know Biostars exists. Generally though, yes, cross-posting should be avoided.
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2020-10-12
Welcome Bot (02:31:51): > @Charlotte Sonesonadded a workflow to this channel:Welcome Bot
Stevie Pederson (12:00:25) (in thread): > Hi@rohitsatyam102. This sounded like a feature request forngsReportsso I’ve added an import functionimportSJ()to that package. Currently it’s only athttps://github.com/steveped/ngsReports , but will be pushed to Bioc in time for the next release. Would love it if you gave it a road-test.
rohitsatyam102 (12:20:47) (in thread): > Wow!! This is cool@Stevie Pederson. It was only yesterday that I had to write a shel script to parse STAR log file and then make a table and import it using read.csv in R. I plan to use this more often now given it’s additional functionality to process STAR and trimmomatic files. Thanks for developing it.
rohitsatyam102 (13:03:35) (in thread): > Oh!. So you have included this feature in R version 4 or above. Will update my R and let you know
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2020-10-13
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2020-10-14
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rohitsatyam102 (06:52:12): > Hi! everyone. Just wanna understand what’s advisable and what’s not. Let’s say for same RNAseq dataset, I wish to do DE, DTU (Differential Transcript Usage) and DEU (Differential Exon Usage). Is it advisable to use two different aligners STAR for DE, DEU and Salmon for DTU on same dataset, because I read ithere that STAR is too conservative for DTU estimation and might underestimate genes having multimapping reads. Kinda curious if it will be objected while we submit our manuscript. - Attachment (Introduction to RNA-Seq using high-performance computing): Quantification of transcript abundance using Salmon > This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
rohitsatyam102 (06:52:43): > PS: my data has lot of mutimapping reads too.
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Federico Marini (09:46:49): > I’d have a general question which seems hard to google in a targeted way (and it can be I am just using the wrong keywords to describe it, in that case sorry if it sounds too naive). > Many of us are familiar with Ontologies like GO or Cell ontology. My question would be, whether there is an ontology for describing bioinformatics/computational biologyApplications
Federico Marini (09:47:33): > I said hard to google mostly because of how dominant GO and cell ontology can be if I input these as search strings…
Federico Marini (09:51:30): > Possible values for different degree of granularity can include for example “transcriptome analysis”, “ATAC-seq”, “cell type deconvolution”, “gene fusion”, “data visualization”.
Federico Marini (09:53:29): > As I am writing these examples, I am realizing this could go in the direction of what BiocViews do - but still: wondering if there is any other formalism we can use. > The aim for this “tagging” would be to deploy a website for a joint initiative where we are collecting different expertises from different fields, under the large umbrella of “quantitative biomedical and life sciences”
Lluís Revilla (10:00:26): > @Federico MariniThere is the BioSchemas that powershttps://bio.tools/ . There is a pending pull request to integrate it on Bioconductor:https://github.com/Bioconductor/bioconductor.org/pull/25 - Attachment (bio.tools): bio.tools · Bioinformatics Tools and Services Discovery Portal > A registry of bioinformatics software resources including biological databases, analytical tools and data services
Rob Patro (10:02:10): > @rohitsatyam102 : you can use salmon for DTE, DGE (at the gene level via tximport) and DTU (I’d take a look athttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178912/ for recommended approaches to all 3 of these types of analysis). For differential exon usage, STAR seems appropriate. - Attachment (PubMed Central (PMC)): Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification > Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Here we present a simple workflow using a set of existing R/Bioconductor packages for analysis …
Ludwig Geistlinger (10:02:33): > @Federico MariniCouple of ontologies come to mind here: check eg EDAM ontologyBioinformatics operations, data types, formats, identifiers and topics (eghttps://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Ftopic_3308 ), and SWO ontology. Also EFO, OBCS, and of course NCIT feature this to some extent.
Kasper D. Hansen (10:03:12): > @Federico MariniIm not sure what to say here, because it is a matter of opinion, but I consider it very unucontroversial that you use different tools / pipelines / methods on the same dataset for a different end goal.
Kasper D. Hansen (10:04:19): > But I can also easily imagine people being uncomfortable by this because of this notion that there is a best way to process the data
rohitsatyam102 (10:06:53) (in thread): > Thanks for sharing this paper. Will give it a read.
rohitsatyam102 (10:08:22) (in thread): > Oh! I realised I have been reading the same paper.
Federico Marini (10:20:29): > Fantastic, thanks a lot to all of you@Lluís Revilla@Ludwig Geistlingerand@Kasper D. Hansen! > It will be more than enough to start the discussion and use nicely rolling wheels instead of having to reinvent them!
Rob Patro (10:26:46) (in thread): > :+1::slightly_smiling_face:
rohitsatyam102 (10:44:52): > @Michael Loveregarding the salmon documentation, I faced a problem as reportedhere as i was using the transcript fasta obtained from ensemble (cdna.fa file). It would be really helpful for new users like us if you mention it either in the documentation or in the github md. Producing transcript.fa from gffread must be included as an essential step in the document, I believe. Please pardon me if it’s already in the docs because I couldn’t find it.
Michael Love (14:42:45): > Hi@rohitsatyam102maybe this would be best added as a new Issue on Salmon GitHub? My lab is closely associated obviously but Patro group is lead developer, and they can address your issue as needed
rohitsatyam102 (15:10:12) (in thread): > Hi@Michael Love. The issue got sorted by the solution posted on the same thread and thanks to you and other who worked that out. All I was saying was to include it as an essential step in the document so that it’s there in black and white and new users can be saved some trouble. Though I found the issue listed on github, It took me a while to figure out what to search to reach to this post. Perhaps, it will save time for them.:smiley:
Michael Love (15:23:10) (in thread): > Sounds good but I still think the docs suggestion should go over on the GH
Michael Love (15:23:50) (in thread): > Salmon is closely related to Bioc via tximport / tximeta but it’s not Bioc … has its on repo elsewhere and own channel
Rob Patro (16:03:30) (in thread): > @rohitsatyam102 : just saw this. I agree adding the relevant info to the howto / FAQ makes sense. Also, hi@Michael Love:wave:.
Michael Love (16:38:01) (in thread): > Thanks@rohitsatyam102for pointing out the docs fix
Kozo Nishida (17:45:42) (in thread): > @saskiaWhere can we send a request to the code of conduct? The BioPackathon community has ideas for mentioning languages and timezones.
Laurent Gatto (17:51:54) (in thread): > Either by emailing the CoC committe atcode-of-conduct@bioconductor.orgor contacting individual members directly on slack.
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Zepeng QU (20:06:10): > @Zepeng QU has joined the channel
saskia (20:08:21) (in thread): > We are super interested in getting the CoC translated into other languages and very open to suggestions about all things.
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2020-10-15
rohitsatyam102 (02:17:15) (in thread): > I am glad you considered:slightly_smiling_face:
Federico Marini (03:50:02) (in thread): > to follow up on this point (sorry for not picking it up right away): in this case, the aim would “just” to annotate and define applications, expertises, use cases - without going into the detail of what software or tool or pipeline was/would be used
Kasper D. Hansen (05:11:40) (in thread): > sorry, I tagged the wrong person in my reply
Kasper D. Hansen (05:12:16) (in thread): > @rohitsatyam102This (and my next message) was meant for you.
Federico Marini (05:52:49) (in thread): > Whoopsie:slightly_smiling_face:I could indeed not really relate the 2 aspects, thanks for clarifying
rohitsatyam102 (06:51:35) (in thread): > That’s like someone else getting someone else’s halloween treat:face_with_hand_over_mouth:
Gwen (08:16:37): > @Gwen has joined the channel
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Jianhai Zhang (16:53:05): > Hello, > > I received this email a few days ago, but I cannot find my package spatialHeatmap at the devel branch. Anyone has the same issue? > > Your package will be included in the next nigthly ‘devel’ build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) athttps://bioconductor.org/checkResults/
Hervé Pagès (17:10:51): > There was a problem with the builds and we don’t have a new report today. Was announced on#bioc-buildsearlier today.
Jianhai Zhang (17:29:23): > My new package was accepted one week ago. If I add new functionalities to this package before this release date. Will the new functionalities be reviewed again like the first submission?
Hervé Pagès (17:45:33): > No, the new functionalities are not going to be reviewed. However, adding new functionalities to your package this close to the release is a risky game. Please make sure to runR CMD build+R CMD checkon your package before pushing the new functionalities togit.bioconductor.org , and keep a close look on the daily report after you push. Thanks!
Jianhai Zhang (17:52:50): > If there are errors derived from new functions and cannot be fixed, can I revert my package to the previous version for release?
Hervé Pagès (18:01:36): > You can revert your changes but you can’t decrease versions. So whatever you do, the version must go up. But if your are careful to runR CMD build+R CMD checkbefore pushing your changes, you should be OK. Although you should make sure that you use the same settings as the build system when you do so. Seehttps://bioconductor.org/checkResults/3.12/bioc-LATEST/Renviron.bioc I don’t know about your package but if it contains code that was carefully written to be platform-agnostic, then chances are good that if it passesR CMD build+R CMD checkon your machine it will also pass build/check on the build system.
Jianhai Zhang (18:06:21): > Thanks for the explanation! The new functions already passedR CMD build+R CMD checkon my computer.
Hervé Pagès (18:33:44): > Sounds good! I still want to suggest that you refrain from embarking on any new serious developments on your package at this point. You’ll be able to do this right after the BioC 3.12 release, when we start the new 6-month devel cycle for BioC 3.13.
Jianhai Zhang (20:28:38): > Got it. Thanks!
wenqiang he (22:11:23): > @wenqiang he has joined the channel
2020-10-16
Jared Andrews (12:40:23): > Who is the proper person to complain to regarding the Bioconductor logo header on the support site leading to the main Bioconductor landing page rather than the support site landing page? Because I gotta say, I click it every time expecting to go back to the main support page.
Kayla Interdonato (14:25:50) (in thread): > We are working on a support site upgrade. Feel free to open an issue on the Githubhttps://github.com/Bioconductor/SupportUpgrade/issues .
Jared Andrews (14:26:28) (in thread): > Will do.
Jianhai Zhang (15:13:00): > On the PDF manual published on Bioc, I have many overflow lines, should I manually break the line? or there is an auto way to do that?
Jianhai Zhang (15:14:12): - File (PNG): Screenshot from 2020-10-16 12-13-46.png
Jianhai Zhang (15:14:42): - File (PNG): Screenshot from 2020-10-16 12-11-02.png
Alan O’C (16:52:56): > Code comments should have 80 char limit (as should the rest of the code ideally)
Alan O’C (16:53:20): > If the references are inserted manually, two spaces at the end of a markdown line inserts a line break
Jianhai Zhang (17:39:00): > Is there an auto-way to meet the 80 char limit?
Jianhai Zhang (17:40:20): > If I have 160 char on code comment, does it mean I have to reduce it to 80? or I can break it to 2 lines, 80 each?
Marcel Ramos Pérez (18:23:51): > If you’re usingvi/vim, it’sgqq
Marcel Ramos Pérez (18:27:26): > for code you may want to tryhttps://github.com/r-lib/styler I’ve heard good things about it. I haven’t tried it myself.
Hervé Pagès (18:44:07): > best way to meet the 80 char limit is to write your code in a 80-char wide terminal:wink:
Tusharkanti Ghosh (18:48:31): > @Tusharkanti Ghosh has joined the channel
Dirk Eddelbuettel (18:50:23) (in thread): > Similar to what@Marcel Ramos Pérezsaid aboutvim, I always thought thethe killer feature of Emacs was to be able to do that for just every file type or language source. I.e. the recommendation to use it for code style is even in the manual (R Internals, Chapter 9,https://cran.r-project.org/doc/manuals/r-release/R-ints.html#R-coding-standards ). I useM-qall the time, same for Markdown. But I think you are also in an odd spot:usually markdown gets rendered bysomething . Either latex for pdf, or some css for html that would take care of this. It seems that you have an usual verbatim setter here. - Attachment (cran.r-project.org): R Internals > R Internals
Jianhai Zhang (21:02:21): > Thank you for advice!
Jianhai Zhang (21:03:15): > There is no error/warnings when I trigger a version bump, but there are errors/warnings in the nightly built. Should I fix the nightly built errors?
Hervé Pagès (21:22:08): > The error on nebbiolo1 (av not available) is because nebbiolo1 didn’t have the libavfilter-dev system dep (required by av). I just installed it but it will only be effective for tomorrow’s builds i.e. spatialHeatmap’s error won’t clear out before Sunday’s report. The error on Windows (invalid character in attribute value [9]) seems like a problem in the package itself. Maybe something you introduced with your most recent commits, since the package didn’t have that error on tokay1 during the submission process.
Jianhai Zhang (21:25:26): > Got it. Thank you!
Hervé Pagès (21:28:32): > No problem. Please use#bioc-buildsfor further specific build questions. Thanks!
koki (23:38:30) (in thread): > Thanks,@Laurent Gatto@saskiaHow about including “language” and “culture” in the “identity:” item of the CoC? > > Also, I don’t think the following should be written in CoC, but for multilingual support I think there are many things that can be solved by technology like below: > > - Audio live captions-based meeting (e.g. Google Meet) > - Communication in writing rather than speaking (e.g., Slack, Chat) > - Translation of the websites related to BioC into multiple languages (e.g. outsourcing to translation company, auto translation like DeepL/Google translator, or community-driven translation) > > I also think that we can do to be creative about different time zones. > > At the last BioC 2020, I wasn’t able to attend some interesting talks because they were in the middle of the night in Japan (I saw the Youtube videos later, and I’m grateful for that), If the duration of the day were shorten and instead the number of days and parallel sessions were increased, I think it would allow more people from more countries to participate. > > These are something I’ll try to experiment with the next time I plan an event.
2020-10-17
Laurent Gatto (03:24:29) (in thread): > * Thank you very much for your suggestions! I think these are useful and I will add them on the agenda for an upcoming CoC meeting. (Note that we already have a packed agenda, so we might not get around immediately). > * As for you suggestions that don’t directly apply to the CoC policies, maybe it would be useful to bring them up with the CAB in#community-advisory-board. They are the right people to formulate recommendation for an increased inclusivity in the community.
Kevin Blighe (08:23:40): > @Kevin Blighe has joined the channel
Leo Lahti (16:33:31) (in thread): > Would need to check Gitter licenses but lately saw good feedback about Zulip which should be fully open source, and it also seems to be rather widely adopted by now.
2020-10-18
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rohitsatyam102 (15:39:30): > Hi everyone!! I posted a query on Bioconductor regarding Differential Transcript Usage. Your inputs will be highly appreciated:https://support.bioconductor.org/p/134820/
saskia (18:57:53) (in thread): > Thanks Laurent. Will discuss these in the CoC meeting this week.
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2020-10-19
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2020-10-20
rohitsatyam102 (02:46:54): > Hi<!channel>@Aaron Lun@Michael Love. Inputs from all of you would be appreciated. Hope you could help me withthis query tht I posted on bioconductor (tried adding some results too). I just want to understand that in condition wherein you don’t have control case situation but have stage specific rnaseq data or say data from different layers of an organism (ground state is not known), how do you choose which sample to act as an intercept? Or even choosing intercept make sense in such situation. I am baffled on this point so much because when I ran DRIMSeq with an intercept I get more genes exhibiting differential transcript usage rather than when I don’t use intercept. Would you suggest using intersection of both (intersection of both with and without intercept results) as true positives (conservative approach)? Or I am just overthinking about the intercept and DRIMSeq smartly takes care of it for naive users like me?
Soroor (03:12:29) (in thread): > see edgeR::catchKallisto or edgeR::catchSalmon. If you don’t want to compare to control, you can use contrasts (see page 31 of edgeR users guide)
rohitsatyam102 (03:30:47) (in thread): > Hi@Soroor. Yes I got my counts generated from Salmon and imported them using tximport as per@Michael Lovef1000research paper . I read the edgeR manual too since DRIMSeq pointed at several places about its function being similar with edgeR. On page 31 of edgeR (under heading GLM approach), the functionmodel.matrixwill generate an identity matrix which will not have intercept term in itdesign <- model.matrix(~0+group, data=y$samples). I am getting less number of genes by not keeping the intercept and I wish to know whether it’s really necessary to have it or not in a case where you do not have control case situation. - Attachment (f1000research.com): F1000Research Article: Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification. > Read the latest article version by Michael I. Love, Charlotte Soneson, Rob Patro, at F1000Research.
Peter Hickey (04:37:12) (in thread): > notifying > 1000 people by @-ing the entire channel probably isn’t going to incline people towards helping you anymore than they otherwise would (and possibly less). please be considerate of people’s time; i’m sure if Aaron or Mike (or others) have the time/inclination to offer advice on the support forum to your question that they will
rohitsatyam102 (04:44:08) (in thread): > Thanks@Peter Hickey. Sorry for the inconvenience caused if any. I thought @-ing channel meant asking people in#generalgroup. However, I will try to keep my queries low profile by tagging the relevant individuals so that the other folks are not disturbed. Sorry again. Still in learning phase:grimacing:
Peter Hickey (04:48:56) (in thread): > all good:slightly_smiling_face:FYI when you post to the support forum and include tags (e.g.DRIMseq) then the developers of the tagged packages will already receive a notification that there is a question on the support forum, so you don’t need to re-tag them here on Slack. also, as far as i can tell, neither aaron nor mike have anything to do with DRIMseq, so I don’t think you should expect them to offer support for a package they are not involved in
rohitsatyam102 (04:53:37) (in thread): > Actually, Mike have writtenthis p rotocol which uses DRIMSeq for DTU analysis and Aaron replied to some queries on intercept and design matrix on Bioconductor. So I thought they might be able to help.
Alan O’C (06:13:08) (in thread): > It might be useful for you to simulate data from 4 groups with and without a significant intercept, and fit linear models to the simulated data to see what happens. Also yeah tagging general is… somewhat of a faux pas in most slack workspaces
Mahmoud Ahmed (07:39:58): > @Mahmoud Ahmed has joined the channel
Sean Davis (08:03:19): > Just a note to everyone that there is a new channel#bioc_africato discuss all things Bioconductor related to users and work in Africa.
Michael Love (08:18:01) (in thread): > i’ll defer to the DRIMSeq authors re: the bioc post. Yeah, I do prefer to have all support related Qs on the support site. And the question really should be looked at by the pkg authors – while i wrote thernaseqDTUworkflow (and reply to posts on support site with that tag), I’m not 100% certain on what’s possible within their package
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2020-10-21
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Aaron Lun (23:00:12): > To my great surprise, this does not work: > > library(S4Vectors) > x <- List(1,2,3) > for (i in x) { > print(i) > } > ## Error in for (i in x) { : invalid for() loop sequence >
Aaron Lun (23:00:16): > I could have sworn that I did this routinely, but apparently I just loop over the names or indices.
Aaron Lun (23:00:46): > I’m guessing that this is a limitation with base R’s ability to recognize loopable objects. Perhaps we could ask forforto try to convert its right argument into an ordinarylistbefore throwing an error.
Hervé Pagès (23:40:16): > I first ran into this when I was trying to dofor (a in assays(SE)) {...}a few years ago. At the time I consulted with@Michael Lawrenceand we worked on a patch for R to makeforloops work on S4 objects with a list-like semantic. The idea was to use[[internally to extract the list elements. The patch worked but IIRC unfortunately it was introducing a performance regression whenxis an atomic vector or ordinary list. So we gave up. Can’t remember the details. Note that systematic conversion of the right argument to an ordinary list could be hugely inefficient in some situations. Think DNAStringSet object with millions of strings. Especially when there is a chance to break out of the loop early e.g. when you’re hoping that you’ll find what you’re looking for inxonly after a few iterations. There is no reason to pay upfront the cost of a full expansion to ordinary list in that case. Another approach maybe would be to make it possible to turnforinto a generic function with dispatch on its 2nd arg. Then we could do what we want. Even though this would also probably slow down things a little.
Hervé Pagès (23:43:22): > When we tested the patch on CRAN packages I think we also ran into some exotic objects wherelength(x)and[[don’t behave consistently. With our patch, doing aforloop on these objects would do very strange things.
Hervé Pagès (23:51:04): > So yes, as you said, the problem is how to recognize “loopable objects” i.e. objects for whichlength(x)andx[[i]]behave consistently. Even thoughforwouldn’t use it, you’d also want “loopable objects” to have anas.list()method that behaves consistently withlength(x)andx[[i]]. No easy way to check that AFAIK.
2020-10-22
Aaron Lun (01:14:50): > Mm. That’s a shame.
Aaron Lun (01:17:27): > Seems that, to preserve existing behavior, a hypothetical solution would need to intercept the code flow insideforjust before it emits the error, and then just “do something sensible” - for some definition of sensible, be it a generic or[[-based access. Then all existing code would behave as expected without performance penalties or breaking weirdo edge cases, while new code would be able to use the new sensible approach, whatever that might be.
Amarinder Singh Thind (01:22:05): > any recommendation of best tools/pipelines for isoform and alternative splicing events study?
Kasper D. Hansen (03:11:01): > perhaps it is time forFor()
Kasper D. Hansen (03:11:19): > or with a little pun in the nameSFor()
Christa Toenhake (06:00:35): > @Christa Toenhake has joined the channel
Lori Shepherd (09:40:34): > <!channel>The support site update will be happening today in roughtly 30 min. The support site will be temporarily unavailable until the update is complete. We will make an announcement on the support site and on the bioc-devel mailing list when it is okay to start posting. Thank you for your patience and understanding.
ImranF (11:38:57): > @ImranF has joined the channel
Lori Shepherd (13:10:05): > support site is back up and able to post. Please post issues, bugs, concerns togithub.com/Bioconductor/support.bioconductor.org/issues
Aaron Lun (13:27:50): > oh my god, the search finally works!
Lori Shepherd (13:28:37): > and is case insensitive
Aaron Lun (13:29:20): > i can finally update my profile!
Hervé Pagès (13:35:23): > The search works? No kidding! Wow, today isreally a day to celebrate (https://github.com/Bioconductor/MatrixGenerics/issues/19#issuecomment-714591642 ):fireworks::tada::+1::wine_glass::champagne:
Hervé Pagès (13:54:27): > Hopefully people will finally be able to search and find answers from 8 years ago and upvote them:sunglasses:
Aaron Lun (13:55:28): > What’s the dfiference between the green and blue boxes? I thought blue was for “answered”.
Kayla Interdonato (13:58:07): > Lori opened an issue about colorshttps://github.com/Bioconductor/support.bioconductor.org/issues/19 , should be addressed soon
Aaron Lun (13:58:10): > k
Lluís Revilla (15:03:41): > Also now the logo links back to the main page of support:star-struck:🥳🥳
Jared Andrews (15:18:16) (in thread): > My greatest contribution to the Bioconductor ecosystem, without a doubt.
Hervé Pagès (15:28:37): > How are tags generated? I don’t seem to be able to find the BSgenome tag. No BiocManager tag either. > > Edit: ok, the tags actually exist but for some reason I can’t add them to my “My Tags” list in my profile > > SOLVED: Now it seemed to work. Sorry for the noise
MEHADI HASAN (15:33:12): > @MEHADI HASAN has joined the channel
Jianhai Zhang (16:32:58): > Does the support site update still affect the R CMD BiocCheck? I am receiving this warning: Checking for support site registration… > Warning in if (suppressMessages(content(response))) { : > the condition has length > 1 and only the first element will be used > Error in if (suppressMessages(content(response))) { : > argument is not interpretable as logical > Calls: -> BiocCheck -> checkForSupportSiteRegistration
Lori Shepherd (16:33:50): > Yes sorry – we are working on a fix – it has to do with the support site upgrade@Natay Aberraand I did this afternoon – please ignore for now
Peter Hickey (17:07:52) (in thread): > Looks great, Lori! Thank you
Lori Shepherd (17:09:36) (in thread): > Thank@Natay Aberrahe really spear headed the heavy coding
Peter Hickey (19:03:12) (in thread): > Thank you@Natay Aberra!
Natay Aberra (19:04:55) (in thread): > No problem! Glad to help.
2020-10-23
Rebecca Howard (08:15:15): > @Rebecca Howard has joined the channel
Federico Marini (08:36:52): > Hi@Lori Shepherd, a quick feedback on the new support site (which looks so much better, well done!): > When checking from the Bioc homepage, the post type information generate “extra clutter”
Federico Marini (08:36:55): - File (PNG): image.png
Federico Marini (08:39:12): > i.e. I probably would not need to seeComment: Comment:orAnswer: Answer:, but rather “the most” of each post title. > Is this unexpected or desired to be this way? Just thinking out loud, as maybe some changes are unwanted side effects after switching. > Or well, at least, I thought it was easier to digest the preview info from the mini box. Just me being nitpicking?
Lori Shepherd (08:41:52): > Thanks. Can you open an issue atbioconductor.org so I don’t forget to look at it – I think this actually is more to do with how the main site gets the recent posts but will have to look further into it – (not intended and I think we did truncating for the old support site to make sure this didn’t happen that probably just needs a tweak)
Lori Shepherd (08:42:25): > But more an issue forhttps://github.com/Bioconductor/bioconductor.org/issues
Federico Marini (08:59:49): > Sure, will do. > Thanks for pointing me to the right place to file it:wink:
Federico Marini (09:03:09) (in thread): > Done
Falola Dare (10:18:16): > @Falola Dare has joined the channel
Ludwig Geistlinger (10:41:24): > Maybe I missed that but why did theplatformstag recently started to say:somefor packages that support all three major platforms (linux, windows, mac)? - File (PNG): Screen Shot 2020-10-23 at 10.38.59 AM.png
Lori Shepherd (10:46:08): > thank you for bringing this to my attention – I will investigate
Ludwig Geistlinger (10:46:31) (in thread): > Thanks, Lori
Alan O’C (10:46:50): > Possibly because of warnings on one platform?
Ludwig Geistlinger (10:47:54): > It affects also packages that build fine, virtually every package I checked actually - File (PNG): Screen Shot 2020-10-23 at 10.47.07 AM.png
Lori Shepherd (11:05:51): > it should only appear if there is an ERROR on a platform – i’ll debug
Federico Marini (11:40:37) (in thread): > Same here, looks like it shows up on pretty much all of them
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Bob Policastro (14:20:37): > Hi all, is there an expectation that the standard deviations returned fromBiocSingular::runPCAshould be similar to those returned byprcompfor each PC? Just trying out a basic examplerunPCA(t(mtcars), center=FALSE, scale=TRUE, rank=6)$sdevversussummary(prcomp(mtcars, center=FALSE, scale=TRUE))seems to yield fairly different results.
Aaron Lun (14:23:23): > Why do you have thetin the former?
Bob Policastro (14:25:17): > Oh wow, for some reason I had thought they wanted variables as rows. Taking that out does indeed yield the same results. Time to slink back into a corner in shame.
Aaron Lun (14:26:26): > The confusion may be because of a deeply unfortunate name clash withscater::runPCA, which does expect variables as rows.
Bob Policastro (14:27:53): > ~I must have looked at that on accident~, I did in fact look at runPCA from scater. My apologies!
Alexander Toenges (15:18:01): > Is anyone aware of documentation towardsedgeR::catchSalmonfor tx-level DE beyond what the help() offers (which is not much)? The manual only mentions the function but does not really go into details. Does it really come down to just dividing the counts by the estimated overdispersion values and the rest of the pipeline stays the same as we would do it in gene-level DE?
Aaron Lun (15:32:30): > probably a question to ask on the support site.
Alexander Toenges (15:34:27): > True, wanted to be sure I am not missing anything obvious.https://support.bioconductor.org/p/p132381/
Rob Patro (16:47:45): > Don’t worry@Alexander Toenges, I’m sure Gordon will let you know if you’re missing anything obvious:stuck_out_tongue_winking_eye:.
Alexander Toenges (17:01:32): > No doubt he will:stuck_out_tongue:
2020-10-24
Vince Carey (11:47:35): > I have been looking at load times for packages.https://github.com/vjcitn/stackweight shows some naively generated figures plotting time to load (sys.time for a fresh R session library() call) against number of packages loaded for that call to succeed. For interactivity, specifically apps that use bioc packages, long load times can be discouraging. Are others concerned about this phenomenon, or is it just the cost of doing business?
Dirk Eddelbuettel (12:15:41) (in thread): > I had a related use case where I had to (repeatedly, while debugging) load code undervalgrindwhere the package dependency tail of one test runner setup was so much worse (i.e. you could “see” the resulting delay) than another that I switched test runner packages. Now, Brian Ripley has a good quote in thefortunespackage (IIRC) that it is in fact not quite clear (paraphrasing) “what one will do with the few microseconds saved”. But it can accumulate though, hence “lightweight is the right weight” (c.f. https://tinyverse.org )
Vince Carey (13:22:18) (in thread): > I like the “lightweight” concept. I wonder whether a finer-grained approach to “imports” could pay off. Import-on-need?
Dirk Eddelbuettel (13:28:30) (in thread): > It’s complicated. You can argue that it matters for everything.I.e. every CI run can be a minute faster or slower depending on what one depends on. And while many packages offer genuinely useful features (which is why we use them), sometimes others can do the same (or almost) at a lower (run-time, load-time, breakage-risk) “cost” (where the cost function is to be defined / may vary by user). So my aim would not be on a new and untested “import-on-need” mechanism but on the implementations I control in my package.
2020-10-25
Martin Morgan (05:37:53) (in thread): > The proximate concern (‘takes a long time to load’) seems like something developers and ‘production’ workflows are concerned about, but for many users perhaps this is a one-time cost at the beginning of the day paid over a sip of coffee? > > What are the packaging issues that contribute to this cost? > > I guess most of the cost reflects code complexity implied by extensive dependencies (and hence the discussion of reuse [good], too-ambitious feature implementation, extreme fragility of code from exposure to the maintenance practices of so many developers, refactoring ‘core’ packages for modular reuse, etc.). > > Some cost might be associated with data in packages that might better be hosted in Annotation- or ExperimentHub. > > Visualization might be an interesting candidate to explore – perhaps packages primarily focusing on analysis should avoid implementing ‘plot’-like functions in their favorite paradigm, but should instead provide functions that transform the data into a form that can be used for visualization, with examples in vignettes. A side effect of this is that the computations leading to visualization can be exposed to unit tests, which is very difficult for plotting functions generally. > > I would very much discourage any kind of strategy that increases package complexity, like ‘import-on-need’ (e.g., moving an Imports: package to Suggests:, and only loading the package when used) because of the lousy user experience [‘hey, I’ve already had my coffee earlier today, and now you want me to install and load more software?’] and the costs to the developer of maintaining and adequately testing the conditional infrastructure. > > It might be interesting to reflect on ‘case studies’. > > One example I found quite illuminating was in theNewWave package submission, where the authors want to use parallel evaluation for some heavy but ‘purely’ numerical work using a SNOW-like cluster (independent processes). If the optimization code is implemented as functions in the package, then the entire package is loaded on each node. But the package Depends: on SummarizedExperiment for user-facing standardization and interoperability, so each node pays the time and space costs of loading SummarizedExperiment. The authors originally used functions defined in inst/scrpt for use on nodes, avoiding the cost of loading SummarizedExperiment but then also escaping the helpful eye of R CMD check and other tools. The review process iterated on different approaches to this, including a package containing only the numerical optimization code or including the optimization code in the R/ directory of the package but defined in a local environment with parent not equal to the package namespace. Both of these add complexity to the package, including, as evidenced by the extended back-and-forth, considerable specialized knowledge. The solution adopted (a local environment) doesn’t seem ideal, but an improvement over the original situation but not as complicated as maintaining a separate package. > > Another case study might be the artMS package discussion on thebioc-devel mailing list (it starts in the middle of an unrelated thread, unfortunately). The maintainer wanted to know how to avoid a conflict arising from the import of the same function,pheatmap, from two separate packages. The practical solution is to use selective imports (importFrom()orimport(..., except=)) from one or both of the packages introducing the conflict. But it is useful to ask why artMS needs to import two packages supporting heatmaps (pheatmapis from the pheatmp package, and also from ComplexHeatmap, where the pheatmap function is a wrapper, you guessed it, forpheatmap::pheatmap). This would seem to be the case where the author would be better to choose a poison, and implement visualizations using one but not both packages. Or perhaps even better separate the visualization from the proteomics analysis that the package views as its primary strength, with simple code illustrating visualization in a vignette and perhaps supporting numerical functionality in the package.
Alexander Toenges (08:12:11): > @Natay AberraAny idea what happened to this post here (found via google)https://support.bioconductor.org/p/58135/
Alexander Toenges (08:12:33): > Looks completely messed up and OPs actual question seems to be missing.
Natay Aberra (08:35:25): > The formatting issue comes from the post coming in mailing list form ( which added extra stuff ), there is an issue open and we are looking into it :https://github.com/Bioconductor/support.bioconductor.org/issues/28 . > As for OPs actual question missing, this post was created in the mailing list days and perhaps back then this reply was entered as a new question. Looking into the old database ( pre upgrade ), that seems to be the case.
Vince Carey (19:01:36) (in thread): > Thanks to both@Dirk Eddelbuetteland@Martin Morgan. There is a lot to ponder. My thought after Dirk’s comment on what to do with the saved milliseconds is that slow loads and heavy dependency lists may be symptoms of opportunities to improve and streamline packages for other reasons. Certainly that is the case for a number of my packages. The case studies are very clear and will merit further discussion. It would be nice for SummarizedExperiment to be very light weight.
Dario Strbenac (20:00:23): > When typing a question, there is text SeePosting Guide for guidance on creating a post. But, it goes to a question about IlluminaHumanMethylation450k.db Reference Versions rather than a posing guide.
Dario Strbenac (20:10:13): > Also, copying and pasting error messages from R into the question writing area such as “function ‘assay<-’ for signature” produces an error because the apostrophes are not ASCII characters but the curly style ones.
Lori Shepherd (20:26:44): > @Dario Strbenacplease open issues on GitHub so we can keep track of them….https://github.com/Bioconductor/support.bioconductor.org/issues/
Dario Strbenac (20:30:27): > I shall.
Lori Shepherd (20:57:04): > Thank you!!
2020-10-26
Dvir Aran (05:40:10): > Hi, I’m trying to install a package called IMVIGOR210CoreBiologies that was published by Genentech a couple of years ago. The package is dependent on many BioC packages, one of them is DESeq (1 not 2). However, DESeq is not supported in Rv4 (I can’t even find the github repo anymore). I am only interested in the data, but can’t load it because of the dependency. Any suggestions how to solve this?
Dario Strbenac (06:00:26): > Well, it’s just an R package. So, you can decompress the archive and simply load the RData file from the data directory which you want to work with. Something such asload("IMvigor210CoreBiologies/data/cds.RData").
Federico Marini (06:07:13) (in thread): > FYI, DESeq has been deprecated for a couple of cycles now, and it is upon request of the developers retired
Dvir Aran (06:33:24): > Thanks@Dario Strbenac. I tried that, and as I said, the data itself is dependent on DESeq. I can’t load it.
Federico Marini (06:56:03) (in thread): > Probably not the most “kosher” variant in terms of mixing versions of Bioc, but if this is the only option: > try installing “manually” a version from older releases, just to read in the data, and export it e.g. to a SummarizedExperiment object (which is more likely to be there to stay in the next years)?
Dvir Aran (10:24:57) (in thread): > That worked! Thanks@Federico Marini
Jeffrey O’Brien (13:36:00): > @Jeffrey O’Brien has joined the channel
Brenda Pardo (14:45:29): > @Brenda Pardo has joined the channel
2020-10-28
Al J Abadi (01:08:47) (in thread): > Thanks. I’ll have a look:slightly_smiling_face:
Kevin Rue-Albrecht (05:24:05): > here’s a second if you want/need to compare :https://github.com/kevinrue/velociraptor/blob/master/.github/workflows/build_check_deploy.yml
David Zhang (07:15:53) (in thread): > Just to mention, I did run into a GHA-specificpkgdowndeployment error (https://github.com/dzhang32/dasper/runs/1277685149?check_suite_focus=true ) after switching tobasilisk. I haven’t got round to fixing it (was planning to come back to it after the 3.12 release), but know it’s GHA-specific aspkgdown::deploy_to_branch(new_process = FALSE)runs okay locally. Everything else in the workflow works fine though.
Lori Shepherd (15:03:51): > Bioconductor 3.12 is Released! Thank you to all developers and community members for contributing to the project! Please see the full release announcement:Bioc 3.12
Nitesh Turaga (15:04:37): - Attachment: Attachment > Bioconductor 3.12 is Released! Thank you to all developers and community members for contributing to the project! Please see the full release announcement: Bioc 3.12
Lori Shepherd (15:09:51): > I’m still investigating theplatformsbadge showingsomewhen it should beallfor certain packages– I hope to have it resolved soon
2020-10-29
Pinki Dey (01:38:33): > @Pinki Dey has joined the channel
Lori Shepherd (11:38:20) (in thread): > Found the issue. I believe I have a fix implemented. I’ll rerun the badges for platforms now.
Lori Shepherd (11:43:55) (in thread): > Please allow a few hours to display on the landing page but this should be resolved. Let me know if it is not
2020-10-30
rohitsatyam102 (07:32:57): > I was trying submitting a query@Lori Shepherdbut it’s prompting me to add package names from the list. I already have added 3 packages from that list. What else should I do - File (PNG): image.png
Kevin Rue-Albrecht (07:35:10): > ah ! i just posted the same issue in#support-site:laughing:
Kevin Rue-Albrecht (07:35:30): > though in your case, i would just drop the ‘#’
Kevin Rue-Albrecht (07:35:58): > in my case, the post is not about any package, but rather posting a conference-related announcement
Lori Shepherd (07:36:32): > Yes please don’t use a # in front of the package names
rohitsatyam102 (07:39:40): > Wow this functionality is really useful for tagging the right packages. Thanks@Kevin Rue-Albrecht@Lori Shepherd
Lori Shepherd (07:43:14): > That was the plan! Hopefully no more random spelling mistakes and caps errors!
Kevin Rue-Albrecht (08:13:35): > Hello community! > > The#eurobioc2020submission deadline is extended toMonday, November 16th EuroBioC 2020 Conference > Welcome to the OpenReview homepage for EuroBioC 2020 Conference
Hervé Pagès (11:54:10) (in thread): > Thanks Lori. Theplatformsbadges look good on the release landing pages. It looks like the devel landing pages reuse the same badges as in release, whatever the availability in devel is. For example:https://bioconductor.org/packages/3.13/bioc/html/zlibbioc.html Is that intended? - Attachment (Bioconductor): zlibbioc (development version) > This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use.
Lori Shepherd (11:58:15) (in thread): > we redid how this badge was done – it doesn’t take into account if it hasn’t built on a platform – it only reflects if a package was marked as unsupported for a particular platform –
Lori Shepherd (11:58:45) (in thread): > we could probably change the behavior to check to make sure there is a build product as well – if we think that is appropriate
Hervé Pagès (12:11:52) (in thread): > Ah I see, I was wondering about that. Thanks for clarifying. The current behavior is fine. If a build product is missing, it’s generally temporary. If it’s permanent, then we should probably mark the package as unsupported on the missing platform if it’s not already.
2020-10-31
Kevin Rue-Albrecht (06:05:30) (in thread): > https://community-bioc.slack.com/archives/C35G93GJH/p1603183448174800?thread_ts=1603176414.173600&cid=C35G93GJH By the way, please note that tagging individual people on the#generalchannel does not reduce the noise; this still notifies and “disturb” - as you wrote in the linked message - all 1,142+ community members around the globe. > You can see from the channel description that#generalis about “team-wide communication and announcements. All team members are in this channel.”. That means that everyone on the channel is notified when messages are posted here. > What you should do is browse the list of smaller and more targeted channels, identify the one most relevant to your issue (as I said, I chose#support-sitein this case), and post your message there. You’ll reach fewer people, but those are the ones who are most likely interested/expert on the topic. If not, they’ll often redirect you to another more appropriate channel if they know one.#generalis often misused for relatively targeted queries, I found it best used for major events like Bioconductor releases and conferences. > I hope that helps! - Attachment: Attachment > Thanks @Peter Hickey. Sorry for the inconvenience caused if any. I thought @-ing channel meant asking people in #general group. However, I will try to keep my queries low profile by tagging the relevant individuals so that the other folks are not disturbed. Sorry again. Still in learning phase:grimacing:
2020-11-02
Leonardo Collado Torres (08:06:25) (in thread): > Can you send an email toevents@bioconductor.org ? I don’t see it athttps://bioconductor.org/help/events/
Kevin Rue-Albrecht (08:13:12) (in thread): > You mean the deadline should also appear in the Google calendar? Because I can see the conference on 14-18 December
Leonardo Collado Torres (09:55:14) (in thread): > the conf, I don’t see it under “upcoming”
Leonardo Collado Torres (09:55:27) (in thread): > though I do see it on the Google calendar
Leonardo Collado Torres (09:55:29) (in thread): > hm…
2020-11-03
Antonio Federico (05:58:59): > @Antonio Federico has joined the channel
Qian Liu (12:41:13): > I have been struggling with my Bioconductor package (Rcwl) logo design for a long time… I wonder if anyone could give any suggestions on commercial logo design website or private designers? Really appreciate!!!:pray:
rohitsatyam102 (13:55:57): - File (PNG): image.png
rohitsatyam102 (13:56:19): > A random attempt
Qian Liu (14:47:43): > @rohitsatyam102wow , like your idea! Did you generate the pipeline image yourself?
2020-11-04
rohitsatyam102 (02:18:41): > No. I took it from the Google
rohitsatyam102 (02:18:48): > But it can be generated
rohitsatyam102 (02:20:54): > Did some editing in PowerPoint
rohitsatyam102 (09:57:51): > Hi Everyone! I have this gtf file obtained from ensemble that contains exactly one transcript per gene (no isoforms). In such case does running DEXSeq makes sense. I did my alignments using star (in a single pass only) and I am aware that DEXSeq uses gene Flattening model as described below: > I wonder, if the absence of say isoform B and C (novel transcripts) from gtf will give me false estimate across different treatment condition because it relies on gtf for generation of flattened model and binning and simply counts reads falling in those bins. Say there are three treatment condition; and in second treatment Isoform B (which is absent from gtf file) is used over the canonical transcript A. We might see differential exon usage in bin n3 and n4 but we will not be sure from if the reads are coming from canonical isoform A or the other isoforms (B or C). Also, does studying Intron Retention events (using tools such as ASpli that employ binning approach or others that uses gtf) make sense? - File (PNG): image.png
Kevin Rue-Albrecht (11:57:15) (in thread): > Hi@rohitsatyam102. > Did you see my previous message to you in this thread?https://community-bioc.slack.com/archives/C35G93GJH/p1604138730293900?thread_ts=1604057577.288800&cid=C35G93GJH Please consider posting this kind of question in a more specific channel (or create one, I can’t find an existing relevant channel right now), or in this case, it probably even belongs better on the support sitehttps://support.bioconductor.org/ - Attachment: Attachment > https://community-bioc.slack.com/archives/C35G93GJH/p1603183448174800?thread_ts=1603176414.173600&cid=C35G93GJH > By the way, please note that tagging individual people on the #general channel does not reduce the noise; this still notifies and “disturb” - as you wrote in the linked message - all 1,142+ community members around the globe. > You can see from the channel description that #general is about “team-wide communication and announcements. All team members are in this channel.”. That means that everyone on the channel is notified when messages are posted here. > What you should do is browse the list of smaller and more targeted channels, identify the one most relevant to your issue (as I said, I chose #support-site in this case), and post your message there. You’ll reach fewer people, but those are the ones who are most likely interested/expert on the topic. If not, they’ll often redirect you to another more appropriate channel if they know one. > #general is often misused for relatively targeted queries, I found it best used for major events like Bioconductor releases and conferences. > I hope that helps!
rohitsatyam102 (12:08:29) (in thread): > Hi@Kevin Rue-Albrecht. I didn’t tag the channel this time. I just wanted to know if what I was thinking was valid or not and if it is advisable to perform such analysis. Simple consensus kinda question. I think bioconductor support is more for resolving package related issue (here in my case I don’t have that) rather than discussing on what are best practices or if doing certain analysis make sense or not. I never meant any trouble. I just got into this unique situation wherein my gtf contained all genes with single transcript (no isoform). So wanted to ask if the aforementioned analysis made sense or not.
Kevin Rue-Albrecht (12:25:37) (in thread): > Right. I hope someone has an answer for you on this particular question. That said, it’s just a type of question that would be more useful to have on a forum-type website (e.g. the Bioconductor support site or BioStars) than a Slack workspace. > On a forum, your question and its answer would end up being indexed and more easily searchable whenever other people Google the same question.
Sridhar N (13:15:43): > 1. Dexseq will not give you any false estimate, it will give you reads mapping to x isoform/exon based on the reference that you provided > 2. If you feel there are novel isoform/exon then i would use stringtie to generate a gtf with novel isoform and use that with dexseq
Sridhar N (13:18:21): > Intron retention can be done using different methods what is the question that your are trying to ask?
Hervé Pagès (13:36:34) (in thread): > The support site (support.bioconductor.org ) is a better place to ask this kind of question. It’s not just a place for resolving package related issues but also a place to discuss all aspects of an analysis. With proper tagging if the analysis has anything to do with particular packages like it seems to be the case here (DEXSeq, ASpli). Thanks!
Kishore A (14:17:10): > @Kishore A has joined the channel
rohitsatyam102 (14:33:34) (in thread): > I wanted to ask tools such as ASpli highly depends on gtf for to define bins for IR, ES and other AS types. This comes from the discussion with the author of ASplihere . As rightly put by you, I need to first assemble novel transcripts, generate new GTF that contains information of these new transcript and then proceed further. I was unaware about transcript assembly approach. Thanks for that. I shall be using HISAT, Stringtie as describedhere . It’s just this little suggestion that I wanted. Thanks@Sridhar N.
Sridhar N (14:36:22) (in thread): > HTH, as suggested earlier try posting these questions on bioconductor website or biostars. It may have been already answered and or some one will help you there.
Sridhar N (14:37:36) (in thread): > by posting a question in the forum it stays there for others to access this would help any one who crosses the same path again
rohitsatyam102 (14:42:31) (in thread): > I will summarize this in biostars forum too and will keep this. I had this notion that bioconductor forum is specifically for package related queries (mine was ensembl gtf related query)
Regina Reynolds (15:51:22): > @Regina Reynolds has joined the channel
Dario Strbenac (19:30:39): > Say I have aDataFramewith 20 rows and I really want to see all 20, can I print them without usingas.data.frame?
Jared Andrews (20:12:09): > Doesheadnot work?
Sridhar N (20:15:18) (in thread): > sure thing, stuff like hey guys this package is broke etc… could be asked in here
Dario Strbenac (20:15:23): > No, it shows the first 5 rows and last 5 rows. I’m thinking there’s an obscure print method somewhere, with an option.
Sridhar N (20:15:34) (in thread): > by posting it you are contributing/helping others too
Martin Morgan (20:21:23): > You can use the optionoptoins(showHeadLines = 20), but it seems like it’s almost easier to coerce to a data.frameprint(as.data.frame(df), max = nrow(df))(or tibble,df %>% as_tibble() %>% print(n=nrow(df)))
2020-11-05
Qi (09:33:36): > @Qi has joined the channel
Jeff Gentry (10:08:41) (in thread): > Why not use the CWL in there?
Qian Liu (10:17:47) (in thread): > @Jeff GentryRcwl is a bioconductor package that works as an R interface for CWL. So we are hoping the logo will reflect some of this ideas.
Jeff Gentry (10:19:08) (in thread): > Right, I’d imagine havingRcwlin a hexagon w/ the CWL logo would convey that?
Jeff Gentry (10:19:41) (in thread): > Although I could see Crusoe maybe not wanting the logo to be used that way, not sure precisely how it is licensed for use
Aaron Lun (12:09:54): > where was the channel about multimodal stuff?
Aaron Lun (12:10:23): > I have a few functions that I want to get out ofscran scater
Marcel Ramos Pérez (12:21:51): > I don’t think we have a channel for SCMM stuff. SingleCellMultiModalhttps://bioconductor.org/packages/devel/data/experiment/html/SingleCellMultiModal.html serves up data. What kind of functions do you want to offload?
Aaron Lun (12:22:46): > scater::runMultiUMAPwants to live somewhere else, and I have another function to rescale matrices for different modes for standard downstream analyses.
Marcel Ramos Pérez (12:24:56): > I think it would be better to add those to a SCMM d/s analysis package
Aaron Lun (12:25:21): > Do we have one?
Marcel Ramos Pérez (12:26:11): > ¯*(ツ)*/¯
Dan Bunis (12:30:16): > My lab is planning on putting together some tooling for multi-modal data, but with a pretty narrow focus (at least if I have my way…). These sounds like they’d be useful there. But also 1) ideally they’d be in some other package that ours could pull from, like scater lol, and 2) it’s in pretty early stages so maybe why am I even saying any of this rn.
Marcel Ramos Pérez (12:30:59): > we could create one that uses data fromSingleCellMultiModal
Aaron Lun (12:34:31): > sounds like someone should start a repo.
Aaron Lun (12:41:51): > the name should obviously be eminem.
Ludwig Geistlinger (12:44:33) (in thread): > https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002568 - Attachment (journals.plos.org): MC EMiNEM Maps the Interaction Landscape of the Mediator > Author Summary Phenotypic diversity and environmental adaptation in genetically identical cells is achieved by an exact tuning of their transcriptional program. It is a challenging task to unravel parts of the complex network of involved gene regulatory components and their interactions. Here, we shed light on the role of the Mediator complex in transcription regulation in yeast. The Mediator is highly conserved in all eukaryotes and acts as an interface between gene-specific transcription factors and the general mRNA transcription machinery. Even though most of the involved proteins and numerous structural features are already known, details on its functional contribution on basal as well as on activated transcription remain obscure. We use gene expression data, measured upon perturbations of various Mediator subunits, to relate the Mediator structure to the way it processes regulatory information. Moreover, we relate specific subunits to interacting transcription factors.
Ludwig Geistlinger (12:45:36) (in thread): > not that it should stop you from naming the package accordingly:wink:
Aaron Lun (12:45:43) (in thread): > ah damn
Marcel Ramos Pérez (12:46:40) (in thread): > marshall mathers
Hervé Pagès (13:00:23) (in thread): > personally I prefer M&Ms
Kevin Rue-Albrecht (13:51:20) (in thread): > How about Marvel (multiverse and all) ? > Looks available on CRAN and BioC
Kevin Rue-Albrecht (14:01:46) (in thread): > “Multimodal Analysis in R - a Very Extensive Library”:stuck_out_tongue:
2020-11-06
FelixErnst (07:21:25) (in thread): > Godzilla? (Which would it bring it back to eminem) I mean if it is that extensive, Godzilla is also quite massive:grin:But haven’t cracked the acronym part of the equation
Kevin Rue-Albrecht (07:39:32) (in thread): > “Mockingbird” starts with an M, though it’s challenge, acronym-wise …
FelixErnst (07:42:26) (in thread): > @Aaron Lunwhat would have been the full name?
Aaron Lun (19:04:43) (in thread): > mumosa probably.
Aaron Lun (19:04:55) (in thread): > multi modal single-cell analysis
2020-11-07
Kevin Rue-Albrecht (13:46:05) (in thread): > mimosa perhaps? a cocktail could nicely illustrate the mix:slightly_smiling_face:
Aaron Lun (19:12:42) (in thread): > where’s the I come from
2020-11-08
Kevin Rue-Albrecht (04:59:03) (in thread): > so many questions !:stuck_out_tongue:MultIMOdal Single-cell Analysis ?
Levi Waldron (11:27:32): > I want to invite Bioconductor users and contributors to take part in organizing the BioC2021 conference. It will be a hybrid conference online and, pandemic permitting, in Seattle next August 4-6. The conference organizing committee meets monthly until next spring, when the frequency of meetings increases with the approaching conference. If you’re interested in getting more involved with the project and in expanding your Bioconductor network, it is a good way to contribute. There is work to be done on sponsorship, communication, program development, technical development of various platforms, Code of Conduct enforcement, and local organizing in Seattle. If you are interested in getting involved, fill out this short survey with your contact information and interests:https://forms.gle/Hb6WYxBzUJfqkq2D6 - Attachment (Google Docs): BioC2021 Committee Application > The organizing committee for BioC2021, to be held in Seattle on August 4-6, needs organizers to help in planning the event. Participation involves attending approximately monthly remote meetings plus taking on responsibilities in one or more of the areas listed below.
2020-11-10
Aaron Lun (02:54:00) (in thread): > Here’s the current state.https://github.com/LTLA/mumosa
Federico Marini (03:10:44) (in thread): > Oh damn
Federico Marini (03:11:35) (in thread): > Lightning struck here: the mimosa has this pointy-style - take a picture of the flower and color it like tSNE/UMAP?:art:
Kevin Rue-Albrecht (03:13:01) (in thread): > I don’t think you’ll convince Aaron with a flower at this point, cocktail was my last shot:yum:
Kevin Rue-Albrecht (03:18:19) (in thread): > It brings me back more than a few years, but the power rangers “Megazord” just seemed to me a fun illustrations of multiple pieces coming together:rolling_on_the_floor_laughing: - File (JPEG): Image from iOS
Kevin Rue-Albrecht (03:20:35) (in thread): > Multimodal Ensemble Genomics Analysis… zord
Federico Marini (03:22:42) (in thread): - File (PNG): image.png
Federico Marini (03:23:06) (in thread): > @Aaron Lun:hugging_face::hugging_face:
Kevin Rue-Albrecht (04:00:51) (in thread): > On a sticker, the Megazord could be wielding the bioc note instead of the sword
Dan Bunis (12:10:28) (in thread): > Also no idea on the ‘zord’ part but I love this sticker idea so much, and I would love to see it.
Kevin Rue-Albrecht (12:12:40) (in thread): > I’d want the old school design, to be clear:smile:https://www.youtube.com/watch?v=xj-DDWoywQg&ab_channel=LegendaryPowerRangers - Attachment (YouTube): Dino Megazord vs Goldar First Fight | Mighty Morphin Power Rangers | 25th Anniversary
Kevin Rue-Albrecht (12:13:55) (in thread): > plus it’s free advertising for Power .. I mean Cell Ranger:stuck_out_tongue:
rohitsatyam102 (12:38:02): > Hey! Has anyone here used JunctionSeq R package for DEU and DJU analysis?
Federico Marini (14:36:05) (in thread): > From now on I will have to think of something for Differential Abundance where at the end it will readDaitarn 3
2020-11-11
watanabe_st (05:05:37): > @watanabe_st has joined the channel
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Kozo Nishida (23:28:14): > @Aaron LunI think you are the only author of the “Online Books” package (except OSCA).https://bioconductor.org/news/bioc_3_12_release/#new-online-books I’m also interested in creating “Online Books” package, but I don’t know if there are any guideline for that. > Please let me know if we need to consider anything particular (unlike software packages) to create “Online Books” package.
Aaron Lun (23:43:18): > Easiest way to start is to just take one of the book packages and replace the book’s contents with your own. For examplehttps://github.com/LTLA/csawUsersGuide
Aaron Lun (23:44:28): > The magic sauce is thevignettes/Makefileto trickR CMD buildinto runningbookdown::render_book. Other than that, it’s mostly the standard package build process (minus the actual R code, because you won’t have any functions in a book package).
2020-11-12
Kozo Nishida (00:19:24) (in thread): > Thank you for the information!
Kasper D. Hansen (04:05:13): > The best part of working from a copy ofcsawUsersGuideis that you can just leave the maintainer field as is. That will save you a lot of trouble going forward.
Robert Ivánek (10:22:41): > Hi, I tried to submit a job ad on the support site but it does not allow me to do it without selecting one of the packages as tag, is this a feature or a bug?
Lori Shepherd (10:37:03) (in thread): > feature and a bug – there are acceptable tags like Bioconductor but I just added in “Job Posting” for an acceptable option as well –
Robert Ivánek (10:42:10) (in thread): > Thank you.
Abby Spangler (11:40:31): > @Abby Spangler has joined the channel
Martin Morgan (11:52:23): > For those who have written / want to write a book, It would be great to have a pull request, maybe underhttps://github.com/Bioconductor/bioconductor.org/tree/master/content/developers as ‘book-guidelines.md’ that provided some guidance, maybe with a link after line 16 of content/developers.md (how do I get this page to render in github without markdown processing?)
Marcel Ramos Pérez (11:54:06): > https://raw.githubusercontent.com/Bioconductor/bioconductor.org/master/content/developers.md ?
Leonardo Collado Torres (12:12:49): > Hi! These awards might be of interest to you or people you knowhttps://twitter.com/lcolladotor/status/1326935687321489411?s=20 - Attachment (twitter): Attachment > Do you know someone or work on making it easier for others to re-use public data in science? > > If so, please nominate them for these awards!! > > :spiral_calendar_pad:Deadline December 5th > :globe_with_meridians:https://researchsymbionts.org/ > :trophy: Up to $2,500 USD for conference registration or society memberships > > #OpenScience https://twitter.com/TheSymbionts/status/1322345555419406337 - Attachment (twitter): Attachment > 4th Annual Research Symbiont Awards: 2020 call for nominations! > > https://youtu.be/41UC7jPZm38
Aaron Lun (19:54:31) (in thread): > crap, forgot the converted book is actually athttps://github.com/LTLA/csawBook
Aaron Lun (19:54:45) (in thread): > FYI the correct URL is actually athttps://github.com/LTLA/csawBook
2020-11-13
NABISUBI PATRICIA (05:05:48): > You’re reminded that today at 1:00 pm EAT, the Artificial Intelligence team will be presenting their work and your presence will be much appreciated. Find below the details for the zoom session. > > Join Zoom Meetinghttps://niaid-discovery.zoom.us/j/99368946962?pwd=SkN6Qk01Ym5SS3dJK2ZPTmw2SEZqdz09 Meeting ID: 993 6894 6962 > Passcode: 652748
Welliton de Souza (06:44:27): > @Welliton de Souza has joined the channel
2020-11-14
rohitsatyam102 (04:24:50) (in thread): > Hi@Stevie Pederson. I was using your package ngsreport. I am raising a feature request on a github. Please have a look.
2020-11-15
Aaron Lun (19:57:24) (in thread): > Come on, surely someone has more thoughts for multi-modal functions.
2020-11-16
Kevin Rue-Albrecht (05:52:37) (in thread): > “Avenger”? > Y’know… because avenger…. assembles
Kevin Rue-Albrecht (05:55:35) (in thread): > There’d be Captain ATAC, The Bulk, and the big villain Th…enex
Kevin Rue-Albrecht (05:55:55) (in thread): > You could even have the hero “Aaron Man”
Kevin Rue-Albrecht (05:56:30) (in thread): > (That last one works best with a French accent)
Kevin Rue-Albrecht (05:57:20) (in thread): > if that’s not multimodal I don’t know what is
Carmen Abaurre (05:57:54): > @Carmen Abaurre has joined the channel
Federico Marini (06:27:38) (in thread): > I want the Aaron Man suit:smile:
Federico Marini (06:28:16) (in thread): > BULK smash:grimacing:
Kevin Rue-Albrecht (06:29:37) (in thread): > ohhh and the sticker could use the infinity stones to represent the modalities
Kevin Rue-Albrecht (06:30:27) (in thread): > then there’s Vision… or is it Visium?:stuck_out_tongue_winking_eye:
Kevin Rue-Albrecht (09:37:01) (in thread): > :grimacing: - File (PNG): avenger.png
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Kevin Rue-Albrecht (11:26:42) (in thread): > or with a few more droplets … - File (PNG): avenger4.png
Stephanie Hicks (13:25:11) (in thread): > thanks@Aaron Lun! Just to confirm, for people wanting to make their own book, we should start with thecsawBookrepo (notcsawUsersGuide) and replace with our own contents?
Stephanie Hicks (13:27:18) (in thread): > and then for deployment, is it still the same instructions as what’s in theSingleRBook-basereadme?
Kevin Rue-Albrecht (14:15:28) (in thread): > actually.. might as well reference the human cell atlas:smile: - File (PNG): avenger5.png
Aaron Lun (14:16:16) (in thread): > dammit Albrecht, stop making stickers and start writing functions!
Kevin Rue-Albrecht (14:17:39) (in thread): > lol - i’m just taking breaks from preparing lectures. New logo = swapping the background image = 2s whenever i get a new idea:wink:
Kevin Rue-Albrecht (14:25:02) (in thread): > last one just for everyone’s fun (I hope:sweat_smile:) - File (PNG): avenger6.png
Aaron Lun (14:29:53) (in thread): > deployment is simplified to “submit to BioC and let@Hervé Pagèshandle the rest”
Stephanie Hicks (14:51:48) (in thread): > Ok thanks
Stephanie Hicks (16:10:05) (in thread): > I noticed there is no longer aMakefilethat precompiles the workflows and caches data. How is that handled now?
Aaron Lun (16:10:42) (in thread): > oh,vignettes/books/Makefilenever did anything anyway. THe more important one isvignettes/Makefile.
Stephanie Hicks (16:15:32) (in thread): > oh I meant this file:https://github.com/Bioconductor/OrchestratingSingleCellAnalysis/blob/master/Makefile . I’m assuming if a new book depends on the existence of workflows used throughout the book, that thisMakefilestill needs to be included?
Aaron Lun (16:16:02) (in thread): > That Makefile doesn’t do anything.
Aaron Lun (16:16:14) (in thread): > It’s not necessary for the build.
Aaron Lun (16:16:27) (in thread): > It was just something I was trying out to get parallel execution.
Stephanie Hicks (16:20:08) (in thread): > oh interesting. ok so when you wrap the book in an R package, if I want to see what the book looks like locally, can I still usebookdown::render_book('index.Rmd')inside thevignettes/folder? Or do I just install the package like I normally would?
Aaron Lun (16:20:58) (in thread): > yes. or at least, inside thevignettes/book.
Stephanie Hicks (16:21:41) (in thread): > ah yes, right
2020-11-17
Kevin Rue-Albrecht (04:33:11) (in thread): > AVENGER: > Amalgamate Variegated Epigenomics and Next-Gen Expression data in R:grimacing:
Kasper D. Hansen (08:54:59): > whats up with the redirection “error” onosca.bioconductor.org . I like the “short” URL for something like this
Stephanie Hicks (10:19:07): > not exactly sure, but I’m guessing it has something to do with now that books are officially being built on the bioc build system as packages and the new linkhttp://bioconductor.org/books/release/OSCA/ reflects how books will be named moving forward (i.e. with usual package urls/release/<name>vs/devel/<name>) as opposed to custom urls for each book. - Attachment (bioconductor.org): Orchestrating Single-Cell Analysis with Bioconductor > Or: how I learned to stop worrying and love the t-SNEs.
Lori Shepherd (10:30:58): > We haven’t activated short links for books yet but I’ll try and look at it over the next few days
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2020-11-18
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Lori Shepherd (07:48:22) (in thread): > Also as far as the redirect there was some discussion here:https://community-bioc.slack.com/archives/CEQ04GKEC/p1600024685025600?thread_ts=1599602495.011500&cid=CEQ04GKEC to leave a redirection message to give people time to change links if they had it bookmarked/linked somewhere else… - Attachment: Attachment > How about displaying a simple page at osca-dev.bioconductor.org that tell people where the new location is instead of using an automatic redirect? That way they get a chance to update their bookmarks and maybe one day we can get rid of osca-dev.bioconductor.org .
Lori Shepherd (07:49:42) (in thread): > Following up a little on this. Yes the idea is that as more books get added to Bioconductor we would standardize the links like we do for other packages for consistency. This would not only include the short urls and release/devel links but also a location in the biocViews page or a standard location listing etc …
Stephanie Hicks (09:22:29) (in thread): > Thank you@Lori Shepherd!
Bharati Mehani (21:11:43): > Hello all, i have an query “is it ok to merge Affymetrix and Agilent244Kdata?”
Bharati Mehani (21:12:14): > This is about tcga data
Bharati Mehani (21:13:09): > Anybody has any experience with this or can share any workflow how to integrate the two?
Henrik Bengtsson (22:59:00) (in thread): > Ha, it’s nice to see that good old copy-number analysis is brought up here. The short story and the good news is that, yes, you can combine such CN-ratios as-is, pass them to a CN-segmentation method, and get valid results. … and, no, there aren’t really any bad news. > > Details below …
Henrik Bengtsson (22:59:58) (in thread): > First, yes, you can combineCN-ratio estimates from different platforms as long as they measure the same thing (e.g. tumor/reference ratios where the same tumor is used and a comparable reference is used in all cases). Obviously, you need to makes sure the estimates are (ii) on the same scale (e.g. all log-scale or all non-log scale), and (iii) they are aligned to the same genome reference (i.e. not shifted along the genome). > > If you make sure the above is in place, you can combine such CN-ratios as-is, pass them to a CN-segmentation method, and get valid results. I think() you’re also guaranteed to get greater signal-to-noise ratios this way, which means you will find more copy-number changes at the same false-positive rate when combining two or more platforms than using any of them by themselves. > > ( ) I’m making this particular claim from memory so can’t recall if we actually studied this, but I’m quite sure this is true as long as (i)-(iii) is true.
Henrik Bengtsson (23:01:40) (in thread): > Now to the fun part. You can improve your signal-to-noice ratio of the combined set of CN-ratios but normalizing them to be one the same scale. (Disclaimer, I’m the author) Have a look at the multi-source copy-number (MSCN) normalization method that we developed for combining CN estimates from four different platforms (and labs). It works without any hocus pocus. You can read about it inhttps://doi.org/10.1093/bioinformatics/btp074 . You’ll find an overview on Slides 21-30 inhttps://www.aroma-project.org/share/presentations/BengtssonH_20091013-Improved_copy_number_analysis.pdf - File (PNG): mscn-before.png - File (PNG): mscn-after.png
Henrik Bengtsson (23:03:05) (in thread): > The method is implemented in CRAN packagearoma.cn . You can find a “vignette” athttps://www.aroma-project.org/vignettes/MSCN/ . It takes a bit to setup the input data, but afterward it should work out of the box without having tune parameters, and so on. - Attachment (cran.r-project.org): aroma.cn: Copy-Number Analysis of Large Microarray Data Sets > Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.
Henrik Bengtsson (23:06:43) (in thread): > … and yes, we developed this method because TCGA produced CNs from four different platform at the time but there’s nothing specific to TCGA in this method.
Henrik Bengtsson (23:10:49) (in thread): > Also, before some look at those full-resolution CN plots and tells you that Affymetrix is much noisier than, say, Agilent 244K, that is not correct. We’re looking at raw data at different resolutions. When binned to the same resolution the differences are much smaller. People kept asking us/me which platform is the best. We refused to answer that because it cannot be concluded from this small data set and we never did a full study to answer that question.
2020-11-19
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Mike Morgan (12:15:52): > Is there a specific email to contact about adding a data package to ExperimentHub? I can’t find anything in the guidelines:https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html
Lori Shepherd (12:19:53): > hubs@bioconductor.org
Lori Shepherd (12:20:23): > which is listed in several places of that documentation
Mike Morgan (12:22:20): > Thanks
Vahid (16:39:27): > <!here>We recently studied the change in citation per-year pattern of publications whose respective software is available from Bioconda, Bioconductor, BioTools, and Galaxy ToolShed. The results of the study shows that a common norm in the Bioconductor community is to publish code and manuscript at about the same year, and packages receive a significant boost in their citation count after they were added to package management systems (e.g., Bioconductor). I think we already knew it, but good to see in numbers! Congratulations to the community and the maintainers.https://www.biorxiv.org/content/10.1101/2020.11.16.385211v1 > > The figure plots the normalized per year citation count of publications before (negative date offset), and after (positive date offset), their respective software was added to package management systems. The publications are grouped in low, mid, and highly-cited clusters. The difference between two consecutive citation counts is plotted asCitation Count Change. - File (PNG): clustered_citation_change.png
Vahid (16:40:12): > (Of course this is a pre-print and work-in-progress, so any comments and suggestions are welcome!:slightly_smiling_face:)
Leonardo Collado Torres (16:43:44) (in thread): > Hi@Vahid. Please avoid using@hereon such a massive channel as this one. Only major announcements such ashttps://community-bioc.slack.com/archives/C35G93GJH/p1602290097050400 use@hereor@channel. Thank you! - Attachment: Attachment > <!channel> The Bioconductor project now has a code of conduct . This code of conduct applies to all Bioconductor events as well as all communication channels, such as slack. We are committed to keep building an open, welcoming and kind community for everyone.
Vahid (16:45:05) (in thread): > Sounds good, thanks!
Leonardo Collado Torres (16:45:51) (in thread): > Thanks! ^^
Bharati Mehani (21:52:38) (in thread): > Thanks much@Henrik Bengtssonfor explaining it nicely. Looking forward to integrate these.
2020-11-20
Levi Waldron (06:17:56): > I have a developer or post-doc position available in the areas of multi’omic data analysis, human microbiome research, and/or Cloud computing - seehttps://waldronlab.io/positions/ . In NYC but obviously with flexible remote working arrangements possible!
Qian Liu (12:41:28) (in thread): > It might help to also post in the #job channel.:slightly_smiling_face:
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2020-11-21
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2020-11-22
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2020-11-23
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2020-11-24
Dario Strbenac (21:00:07): > Is there an annotation package that stores the locations of LIN1, SVA, Alu repeats in genomic coordinates of hg38? I wonder if it’s possible to avoid downloading the BED file from UCSC Genome Browser.
2020-11-25
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Vince Carey (11:31:30) (in thread): > I don’t think so. Creating an AnnotationHub resource with these locations sounds worthwhile.
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2020-11-26
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Mikhail Dozmorov (20:36:05): > Is there a recipe for liftOver of Paired BED data?rtracklayer::liftOver()fails onPairsobject, althoughshowMethods("liftOver")suggests it should work. Cannot find source code forliftOverto check. Some data and code to reproduce:https://gist.github.com/mdozmorov/edc359ea0ed6ec44d484899363a601fc
2020-11-27
Dominique Paul (04:28:54): > Are there any books that you guys would recommend or personally found useful to learn more about all the biological details behind gene data analysis?:slightly_smiling_face:
Federico Marini (04:51:20): > I found an older collection of papers suggested by Jeff Leek quite nice. > Might be that now there are better/more up-to-date resources. > Anyway, here it is:https://github.com/jtleek/genomicspapers - I’d love to hear what other’s favorites are.
rohitsatyam102 (04:55:51) (in thread): > Maybe this could help sir:mcols(GR.read1.hg38)$name <- read1$name
rohitsatyam102 (04:56:45) (in thread): > The metadata col was not populated
rohitsatyam102 (04:56:57) (in thread): > DataFrame with 9021 rows and 0 columns
rohitsatyam102 (05:00:04) (in thread): > It doesn’t show up when we print the GRangesList, but it is still stored and accessible with mcols now
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Mikhail Dozmorov (08:20:26) (in thread): > liftOver may be lossy, some regions may fail to be remapped, some may map to multiple places. So, reassigning metadata won’t be reliable. And yes,mcols(GR.read1.hg38)givesDataFrame with 124830 rows and 0 columns, but it has zero columns, so no metadata that is cleanly mapped to the relevant entries. Thank you, I thought it would be simple, but apparently it is not.
rohitsatyam102 (08:21:11) (in thread): > Yes sir. Indeed it isn’t:sweat_smile:
Vince Carey (08:45:40) (in thread): > @Mikhail Dozmorovthis query might go to support site or to Mike Lawrence specifically. It seems like a good use case to solve.
Mikhail Dozmorov (08:58:35) (in thread): > Will post on the support site. Indeed, it seems like a good case scenario that remains unsolved.
Levi Waldron (10:06:45) (in thread): > Just FYI there’s an#education-and-trainingchannel where this question might get more attention
2020-11-28
Aaron Lun (01:41:47): > Looking through the removed packages in 3.12, I saw BayesPeak… one of the first packages I looked at when I used to do ChIP-seq data analyses. Never got it to run, but gee, that was a long time ago.
Aaron Lun (01:42:17): > Oh wow, biosvd. Both maintainers have left the company, those addresses probably don’t work anymore!
Aaron Lun (01:44:34): > Hm. 3.12 was a bit of a bloodbath with respect to removed packages. Quite a few compared to other releases.
Rory Stark (12:30:04): > @Rory Stark has joined the channel
Lori Shepherd (16:13:17): > It was the larger changes in R 4.0 that really lead to the increased package breakage, That with outdated emails did a toll.
2020-11-29
FelixErnst (06:38:28): > Hi. Does anyone know of a package, which acts like a wrapper for running lm/glm/whatever on aSummarizedExperiment? What I want is to test associations per feature/sample taking into account other covariates, e.g.outcome ~ assay + age + sex + medication + ...orassay ~ variable + age + sex + medication + .... A list of models per feature would be the ideal return value.DESeq2is to specific for the purpose I have in mind
Kasper D. Hansen (12:03:08): > limma::lmFit
Aaron Lun (14:55:33): > scran testLinearModel()function for DA-aware fitting.
2020-11-30
Dominique Paul (05:36:24) (in thread): > Very cool, thanks
Michael Lawrence (16:29:18) (in thread): > How would you expect this to work? It would lift over left and right separately and return a Pairs? Within each element, any combination of left/right would need to be considered.
Mikhail Dozmorov (16:40:06) (in thread): > Yes, lift over each part separately, and keeping track of pairing. Also, considering that some coordinates may fail to map. So, if each part of a pair can be successfully lifted over, return it (keeping metadata). If any or both parts fail to lift, save them into a ‘Failure’ slot, or output on screen.
Gabriel J. Odom (16:54:51): > Hi all, > Is there a channel I should use to ask for help specifically related to fixing bugs in an already accepted package? (I’m not asking for code help, but Git help.) I’ve been able to get an update committed and pushed to devel /master, but I am having trouble pushing the changes to RELEASE_3_12.
Aaron Lun (16:57:41): > sounds like#bioc_git.
Michael Lawrence (17:03:27) (in thread): > The way liftOver currently works is to return a GRangesList with the possible destinations (empty if none). So I think it’s as simple as just returning the two parallel GRangesLists.
Gabriel J. Odom (17:15:24) (in thread): > Thank you!
Michael Lawrence (17:24:10) (in thread): > Also, to clarify,liftOver()just returns the ranges; there is no attempt to carry over any metadata, because who knows if it is still relevant. The typical workflow is to perform the lift over, decide which ranges to keep, then just carry over the metadata as it makes sense.
Mikhail Dozmorov (18:37:35) (in thread): > Yes,GRangesListkeeps emptyGRangeswhen a region cannot be converted. However, these regions are dropped when unlisting theGRangesList. This: > > > GR.read1.hg38 > GRangesList object of length 10: > [[1]] > GRanges object with 0 ranges and 0 metadata columns: > seqnames ranges strand > <Rle> <IRanges> <Rle> > ------- > seqinfo: 1 sequence from an unspecified genome; no seqlengths > > [[2]] > GRanges object with 1 range and 0 metadata columns: > seqnames ranges strand > <Rle> <IRanges> <Rle> > [1] chr9 75026704-75029880 * > > becomes this: > > > GR.read1.hg38 %>% unlist() # Metadata missing, can't merge > GRanges object with 9 ranges and 0 metadata columns: > seqnames ranges strand > <Rle> <IRanges> <Rle> > [1] chr9 75026704-75029880 * > > Googling how to merge two GRangesLists gives the answerpc(GR.read1.hg38,GR.read1.hg38). But unlisting it still drops the empty GRange. One can write another checker of empty GRanges to exclude the associated metadata, but it already feels too complex.
Michael Lawrence (19:06:27) (in thread): > I guess you are looking for some sort of “NA” value, but there is no such convention for GRanges. Feel free to come up with your own.
Hervé Pagès (19:26:00) (in thread): > Yes, we’ve decided to be a little bit more proactive with respect to unmaintained/broken packages. Thx to Lori@Lori Shepherdfor leading that effort. What’s the point in building/checking/hosting useless stuff especially considering there’s a cost to it? Getting rid of it is the easiest and most effective way to improve the overall quality of the project.
2020-12-01
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2020-12-02
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rohitsatyam102 (06:05:08): > Bioconductor forum webpage is down, isn’t it??
rohitsatyam102 (06:09:46): > working now
Michael Lawrence (10:37:23) (in thread): > I checked in a method for liftOver on Pairs
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Mikhail Dozmorov (15:58:54) (in thread): > Found thiscommit . After updating to latest R and Bioconductor, rtracklayer still won’t install from GitHub. What to do about this error? > > Warning: undefined slot classes in definition of "RTLFileList": elementMetadata(class "DataTable_OR_NULL") > Warning: undefined slot classes in definition of "BrowserViewList": elementMetadata(class "DataTable_OR_NULL") > Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE, : > class "UCSCSchema" cannot extend class "SimpleList": slot in class "UCSCSchema" must extend corresponding slot in class "SimpleList": fails for elementMetadata > Error in setClass("UCSCSchema", representation(genome = "character", tableName = "character", : > error in contained classes ("DFrame") for class "UCSCSchema"; class definition removed from 'rtracklayer' >
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2020-12-03
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2020-12-04
Martin Morgan (04:47:48): > R-devel (SVN revision r79553) now has native ‘pipes’|>(functioning like%>%) > > > mtcars |> subset(cyl == 4, c("mpg", "cyl")) > mpg cyl > Datsun 710 22.8 4 > Merc 240D 24.4 4 > Merc 230 22.8 4 > Fiat 128 32.4 4 > Honda Civic 30.4 4 > Toyota Corolla 33.9 4 > Toyota Corona 21.5 4 > Fiat X1-9 27.3 4 > Porsche 914-2 26.0 4 > Lotus Europa 30.4 4 > Volvo 142E 21.4 4 > > and anonymous functions\(x) x + 1(same asfunction(x) x + 1) > > > mtcars |> > + subset(cyl == 4) |> > + sapply(\(x) diff(range(x))) > mpg cyl disp hp drat wt qsec vs am gear carb > 12.500 0.000 75.600 61.000 1.240 1.677 6.200 1.000 1.000 2.000 1.000 >
Pablo Rodriguez (07:58:36): > Regarding that, if anyone is interested, packagepoorman also imitates pipes using base R and dependency free, including also other dplyr functions such asselect(),filter(),summarise(), etc
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Aaron Lun (11:19:23): > ugh!
Aaron Lun (11:19:52): > I’m putting those into the same bucket asTandF.
Martin Morgan (11:24:27) (in thread): > There are definitely opinions about this; personally I find the logic offoo |> bar() |> baz()more consistent with my thought process than the inside-out reasoning implied bybar(baz(foo))(and recognize that unintelligible code can be written in both paradigms).
Aaron Lun (11:33:13) (in thread): > As you might expect, I would disagree. The intuition granted by the pipes only works if one also uses->so that the final step precedes the assignment; otherwise I have to read it back to front anyway to figure out what the value is going to be. (Withx <- bar(baz(foo)), I know the output is going to be the return value ofbar()immediately.) And if you’re using->, you’re in the realm ofWTH? constructs that confuse readers. > > In practice, pipes promote these monstrous 20-step one-liners that are impossible to read and debug. If you’re writing code the proper way, it becomes pretty clear that this is an anti-pattern and you would break it up into separate steps instead.
Jeff Gentry (12:53:13) (in thread): > Disagree that they’re analogous in that way. The assignment operator is terminal - one is saying “take the value of this expression and assign it to this variable”. Regardless of directionality of<-vs->that logic is the same. > > Piping, chaining combinators, etc provides one to express the logic of the expression itself in more of a dataflow style. “Take this value, then do this, then to that, apply this transformation, add 42 to it …. and then assign it to the specified variable”
Aaron Lun (12:57:36) (in thread): > Sure, but if you want to talk like that, then you should really be doingfoo |> bar() |> baz() -> my_output_var, bash-style. What I’m saying is that if you domy_output_var <- foo |> bar() | baz(), you have to read it back to front anyway to figure out what the final return value is. In contrast, withmy_output_var <- baz(...), I know immediately that I’m getting an output of the type returned bybaz(). Sounds like a small difference but the pipe encourages people to chain together many, many steps - now I have to remember the variable nameand read all the way to the end of the pipeline to figure out what happened? No thanks, my mind can’t hold that much in memory at the same time.
Jeff Gentry (13:06:07) (in thread): > The type is a fair point. I do most of my development in statically typed environments
Hervé Pagès (13:10:12) (in thread): > Not a big fan of the pipe either. To me it’s just a convenience when working interactively but that doesn’t translate into clean/readable package code. Can we officially declare the use of pipes and\(unwelcome in package internal code? Possibly enforced by BiocCheck?:grin:
Sridhar N (13:19:53): > gotta use another key mapper to include this!?
Martin Morgan (13:30:43) (in thread): > I think it would be better to just declare unwelcome code that is unreadable. > > This includes long piped expressions, but also nested calls likeif (!any(sapply(x[i], function(x) x != f(y))) { ... }but with function and variable names each a dozen characters long. > > I’ve found the one line per pipe approach readable, with chained expressions restricted in length to some sort of coherent ‘concept’. I also think of the initial assignment as ‘to calculatefit, I will start withmtcarsand …’ > > fit <- > mtcars |> > filter(cyl == 4) |> > lm(formula = mpg ~ disp) > > I’ll admit to struggling with the\(x) x + 1notation (some have suggested that the\is an ascii lambda…)
Alan O’C (13:42:45) (in thread): > lambdas look great to me as just a contraction of the ubiquitousfunction(x), but I largely agree with the comments on pipes. IME tidyverse code in general is great for interactive but is really poor in packages. God knows I’ve had fun working with ggplot2 and dplyr programmatically…
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Federico Marini (16:30:33) (in thread): > My point about readability is that it you can really “read it out loud”. > I think that can be quite a nice perk to have when you teach, for example
Federico Marini (16:31:38) (in thread): > when made into different lines, it easy to say > To obtainthe_left_hand_side_thingyyou do: > * this > * then that > * then that…
Aaron Lun (16:34:02) (in thread): > That’s not really an advantage if you’re skipping over the regular syntax of function calls.
Aaron Lun (16:35:01) (in thread): > as soon as they need to do anything that doesn’t involve shuttling one argument to another function, they’re screwed.
Aaron Lun (16:38:10) (in thread): > If you really want to read it out loud, then split each one to a separate line: > > x <- bar(foo) > output <- baz(x) > > Then at least people can have a look at whatxactually is before they proceed to the next step. If you have 10 expressions chained together in a pipe, how confident are you that you really know what’s happening at the 7th step?
Aaron Lun (16:39:05) (in thread): > This just seems like a very convoluted style of programming, without the streaming benefits offered by real (sh) pipes.
Hervé Pagès (17:13:25) (in thread): > > If you really want to read it out loud, then split each one to a separate line > Exactly. Amen
Hervé Pagès (17:21:28) (in thread): > > This just seems like a very convoluted style of programming, without the streaming benefits offered by real (sh) pipes. > I wouldn’t be surprised if a fraction of the R pipe users somehow had this idea that their code is more efficient because the data is magically streaming thru the pipe, or because they don’t use intermediate variables like in the “one function call per line” style, or some other misconception like that. Because there’s no way to justify the use of the pipe in package code based on improved readability only.
Hervé Pagès (17:30:31) (in thread): > BTW if you want your data to stream from one disk representation to another, useas(x, "TileDBArray")where, say,xis an HDF5Array object. If, in addition, you want to perform some on-the-fly transformation on the stream, you’ll do something likeas(log(x + 1), "TileDBArray")or maybe something a little bit more complicated (documented in?DelayedArray::write_block). You’ll be implementing a pipe, a real one, but you’ll never need|>for that.:wink:
James MacDonald (18:03:10) (in thread): > This sort of nonsense reminds me of ‘the bad old days’ when_and<-were synonymous. But probably worse. It’s one thing to have the tidyverse as a Borg sitting over yonder, gobbling up all the youngs that are learning R, but this looks like the barbarians are at the gate.
Hervé Pagès (19:03:14) (in thread): > Yes=instead of<-,T/Finstead ofTRUE/FALSE, partial argument matching, pipes, and more generally any shortcut that allows one to pack as much operations as possible per line of code, is not a new trend, unfortunately. They always seem neat at first and it always takes a few years and hundreds of thousands of lines of messy package code with zillions of hard-to-debug problems, before people start to realize that maybe it was not such a great idea after all. When I see this in package code, I can’t help but think that this is lazy, rather than an attempt at being concise. But also I’m not on Twitter and I don’t send code snippets over my cell phone so yeah I’m biased:wink:
Aaron Lun (19:14:17) (in thread): > tidyverse code looks like perl.
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2020-12-05
Aaron Lun (03:49:08) (in thread): > https://github.com/Bioconductor/Contributions/issues/1801 . The offer still stands, if anyone has interesting ideas for analysis functions for multi-modal data, I’m happy to try to implement them.
Sridhar N (12:00:18): > did not look at the source code but are you planning to add Dirichlet-multinomial framework by any chance?
FelixErnst (12:46:11): > I think@Martin Morgantook care of that a few years agohttps://bioconductor.org/packages/release/bioc/html/DirichletMultinomial.html - Attachment (Bioconductor): DirichletMultinomial > Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.
Sridhar N (12:52:43): > right is that going to be part of the repo@Aaron Lunis working on?
Sridhar N (13:04:43): > https://twitter.com/tomkXY/status/1335275638932918272?s=19 - Attachment (twitter): Attachment > Evolution of the R language > #Rstats #Rlang https://pbs.twimg.com/media/EofaFUnU8AIS5RX.png
Sridhar N (13:04:51): > Lol…
Nicholas Knoblauch (13:10:39) (in thread): > The new pipe is more efficient because of copy elision
Nicholas Knoblauch (13:20:39) (in thread): > The pipe is a huge win for readability and code quality for (at least) two reasons > 1. Code with fewer assignments means fewer objects for me to keep track of when rereading code. Every time<-or=is used, you’re adding to the namespace. > 2. It encourages developers to write functions and/or create classes that compose nicely. (for a little more on this, check outhttps://win-vector.com/2016/08/06/the-magrittr-monad/ ) - Attachment (Win Vector LLC): The magrittr monad > Monads are a formal theory of composition where programmers get to invoke some very abstract mathematics (category theory) to argue the minutia of annotating, scheduling, sequencing operations, and side effects. On the positive side the monad axioms are a guarantee that related ways of writing code are in fact substitutable and equivalent; so you want your supplied libraries to obey such axioms to make your life easy. On the negative side, the theory is complicated. > In this article we will consider the latest entry of our mad “programming theory in R series” (see Some programming language theory in R, You don’t need to understand pointers to program using R, Using closures as objects in R, and How and why to return functions in R): category theory! > > In practice the programming language Haskell improved greatly when non-monadic I/O libraries were replaced by better monad inspired I/O libraries. But this also created the unfortunate false impression you had to understand monads to use Haskell (when in fact you only have to understand them to implement Haskell). > The fun side of Monads is flexibility in using them and occasionally saying (either formally or informally) “hey, x turns out to be a monad!” > This can vary from meaning: > “x is nice (and not in fact a monad).” > “x is cryptomorphic to a monad (a term favored by mathematician Gian-Carlo Rota).” > “I went to graduate school!” > “Or x really obeys the monad laws.” > Saying “x is a monad” is like singing in the shower, it is always more fun to say than to hear. I know I am certainly guilty of this in writing this article. > It turns out the magrittr pipe package in R obeys the monad axioms. So if you are a data scientist who has tried magrittr you have already benefited from monadic design. > Obviously I am nowhere near the first to notice this, but it is something I wish to comment on here. It doesn’t matter if this is core intent or a side-effect of good design, but it does give yet another reason to trust the package. > Let’s load the magrittr package and spot-check the monad laws. > library(‘magrittr’) > > # Identity function, > ret > First we check that magrittr’s %>% operator obeys the Monad laws when using %>% as “bind” and ret as “return”. For simplicity we would like to think of magrittr as a category over single argument functions (though obviously magrittr works over more values than these, and the big part of the the magrittr service is Currying code fragments into single argument functions). > a > Axiom 1 Left identity: ret(a) %>% f == f(a): > ret(a) %>% f > ## [1] 0.8414710 0.9092974 0.1411200 -0.7568025 -0.9589243 > f(a) > ## [1] 0.8414710 0.9092974 0.1411200 -0.7568025 -0.9589243 > Axiom 2 Right identity: m %>% ret == m: > # > m %>% ret > ## [1] 1 2 3 4 5 > m > ## [1] 1 2 3 4 5 > Axiom 3 Left Associativity: (m %>% f) %>% g == m %>% (function(x) {f(x) %>% g}): > (m %>% f) %>% g > ## [1] 0.6663667 0.6143003 0.9900591 0.7270351 0.5744009 > m %>% (function(x) {f(x) %>% g}) > ## [1] 0.6663667 0.6143003 0.9900591 0.7270351 0.5744009 > Let’s go through those rather abstract axioms again and specialize them using our knowledge that “ret” is the identity. > Axiom 1’ Left identity: a %>% f == f(a). Says: “piping a value into a function is the same as applying the function to the value.” In general the original says ret has to be faithful in the sense that %>% can recover enough information to compute f(a). > Axiom 2 Right identity: m %>% ret == m. Now implied by Axiom 1’. But in the cases where we don’t have ret is the identity this would tell us that %>% is faithful in the sense it is retaining enough information about m that ret can re-build m. > Axiom 3 Associativity: (m %>% f) %>% g == m %>% (function(x) {f(x) %>% g}). There is a notational convention hidden in this statement: we assume m %>% f %>% g is to be read as (m %>% f) %>% g. Mathematicians like left-association as Curried functions are left-associative (and not necessarily right associative, consider Curry(f) ○ g ○ h where f is originally a two argument function that ignores its first argument). The axiom plus the convention tell us we can consider piping as moving the value m through f and then through g. This is where we are really checking %>% is behaving like a pipe. > As a user we would like to be able to write “a %>% (f %>% g)” or “h % g; a %>% h”. That is: we would like to be able to save complex magrittr pipe sequences for re-use (without introducing more notation, such as “. %>%”). We would like to have right-associativity (reified composition of operators) in addition to the left association we expect from magrittr being described a “forward-pipe operator” (from magrittr’s description). > It turns out that isn’t one of the monad axions, and we can’t immediately do that: > h % g > ## Error in g(.): non-numeric argument to mathematical function > We can fix this one of two ways: by introducing a function or using a built-in “dot notation” (thank you to Professor Jenny Bryan for pointing this out to me.) > h % f %>% g } > a %>% h > ## [1] 0.6663667 0.6143003 0.9900591 0.7270351 0.5744009 > h % f %>% g > a %>% h > ## [1] 0.6663667 0.6143003 0.9900591 0.7270351 0.5744009 > It turns out category theorists anticipated this problem and fix. The function wrapping trick is essentially building the Kleisli category derived from our monad (see “Monads Made Difficult”). > In principle we could implement a Kleisli arrow %>=>% operator in addition to the magrittr bind operator (%>%) which would allow code like the following (all four statements below would be equivalent): > %>=>% % (sin %>=>% cos %>=>% abs) > ## [1] 0.6663667 0.6143003 0.9900591 0.7270351 0.5744009 > a %>% ((sin %>=>% cos) %>=>% abs) > ## [1] 0.6663667 0.6143003 0.9900591 0.7270351 0.5744009 > a %>% (sin %>=>% (cos %>=>% abs)) > ## [1] 0.6663667 0.6143003 0.9900591 0.7270351 0.5744009 > abs(cos(sin(a))) > ## [1] 0.6663667 0.6143003 0.9900591 0.7270351 0.5744009 > Note that the above %>=>% operator is not in fact the desired general Kleisli operator as we haven’t implemented the critical Currying services that the magrittr %>% operator supplies (these services would be what category theorist call the “endofunctor” which would map R functions to specialized savable R functions; definitions such as function(f,g) { . %>% f %>% g } won’t work either as we would need to capture unevaluated arguments inside the %>=>% function and can not delegate that to interior %>% calls). > In the Kleisli category we would no longer need special monad axioms, they are replaced by the more common associativity and category axioms in the Kleisli category. One still has to prove you have a category, but it is a more standard task. > You can say standard imperative styles of analysis that see operations as sequenced transient steps that mutate data are “strict left to right associative” ways of thinking (the “((a %>% sin) %>% cos) %>% abs” form). Databases, and standard data analyses in R are usually so organized. > The “general associativity” way of thinking (the “h =>% cos %>=>% abs; a %>% h” form) emphasizes the processing pipeline as a reusable entity and data a transient quantities that flow through the pipeline. Systems like Weka, LingPipe, and graphical data science tools such as Alpine Data workflow notebooks essentially represented processes in this manner. > > Analysis steps as a durable graph: Alpine Data workflow notebooks > > The guarantee of full associativity is just a mathematical way of saying: you can mix these styles (data oriente…
Henrik Bengtsson (13:44:21) (in thread): > Note that|>operator issyntactical sugar and is handled by the parser. After parsing, there is no difference between usinga(b(x))andx |> b() |> a(), i.e. the abstract syntax tree (AST) is identical. Except fromsrcrefattribute, it is not possible to tell the difference. In other words, run-time behavior, performance, stability, and so on is identical. > > For example, > > > expr_0 <- quote(head(subset(mtcars, cyl == 4))) > > expr_1 <- quote(mtcars |> subset(cyl == 4) |> head()) > > identical(expr_0, expr_1) > [1] TRUE > > or, similarly, > > > lobstr::ast(head(subset(mtcars, cyl == 4))) > █─head > └─█─subset > ├─mtcars > └─█─`==` > ├─cyl > └─4 > > > lobstr::ast(mtcars |> subset(cyl == 4) |> head()) > █─head > └─█─subset > ├─mtcars > └─█─`==` > ├─cyl > └─4 > > AFAIU, this is very much intentional because this means that the introducing of|>does not introduce unknowns and is 100% backward compatible with the existing R ecosystem. There is no need to worry about surprising corner cases and side effects showing next week, in a year, or ten years from now. > > Note thatmagrittr %>%pipe operator didn’t have the luxury of this approach, because it could not inject itself into the parse but everything had to be done at runtime. Following it from the outside, the original author and the following maintainers, have really tried their best to have%>%emulate as far as possible what|>is now achieving. They made another big leap toward harmonize this further inmagrittr https://www.tidyverse.org/blog/2020/08/magrittr-2-0/ . I can only guess, but I see this move to not just improving things they wanted to fix over time but also making it easier (mentally and technically) to migrate existing%>%code to|>. Because of backward compatible reasons, it will be a few generations before we’ll such a migration, which means everyone has time to adjust.
Aaron Lun (13:45:30) (in thread): > 1. You can just assign back into the same variable if you’re so concerned about it. Me, I want to have new variable names, because that’s self-documenting code. > 2. I don’t see how any of that is relevant. But I’m guessing you’re saying that the pipes will force me to write my functions in a particular way. Well, good luck with that.
Nicholas Knoblauch (13:56:20) (in thread): > Assigning back into the same variable is even worse, because now when I seexsomewhere in the code, I no longer have a single source of truth for whatxis.
Aaron Lun (13:59:38) (in thread): > Then just make a new variable. You’re paying the cost of keeping track of unnamed variables anyway when you try to figure out what the entire pipe is doing. And how are you meant to communicate about it? “Oh, the bug is in the fourth, no, the fifth step of the pipe? It doesn’t have a name so you’ll just have to, I dunno, assign the intermediate output to a new variable to see what it actually contains.”
Aaron Lun (14:01:11) (in thread): > Me, if a single executable of code contains more than 3 operations, that’s already too many. Break it up.
Nicholas Knoblauch (14:01:41) (in thread): > This is like exactly why we write functions though? You don’t refer to the bug being in the fourth step, the name of the function in the fourth step is where the bug is
Nicholas Knoblauch (14:02:16) (in thread): > debugonce(name_of_fourth_step_function)
Aaron Lun (14:02:47) (in thread): > Or I could just doname_of_fourth_step_variablein mydebug().
Aaron Lun (14:03:12) (in thread): > Which is way more convenient.
Nicholas Knoblauch (14:03:32) (in thread): > why would you break at a level above where you know the bug is?
Henrik Bengtsson (14:03:42) (in thread): > Because of this, the whole discussion around|>is only on coding style. To me, that is a matter of personal and team taste, context (at the R prompt, in an R script, in a vignette, in package code), and the ability to reflect what is performed. > > For the latter, there are procedures/algorithms that are better thought of in mathematical/functional terms whena(b(x))is a better choice. In other cases, what is performed is more straightforward to describe in a procedural style whenx |> b() |> a()is more descriptive. I can see how the procedural style is better suited when function calls have side effects wheretime andmemory-of-the-past is a factor, e.g. saving to file, working toward a database. > > Then there are cases where one style is not clearly better than the other. > > To conclude, as a heavy user ofz <- a(b(x))ory <- b(x); z <- a(y), I think it’s important to have an open mind here and try to consider why one style is prefer over another beyond personal preference.
Aaron Lun (14:04:33) (in thread): > Because I want to see the input into the offending step,and the output from the offending step. The problem isn’t necessarily in the fourth function, it’s the logic of the stuff that’s flowing in and out of it.
Nicholas Knoblauch (14:05:02) (in thread): > then you need to write another function
Aaron Lun (14:05:13) (in thread): > no, I need to assign the output into a variable and then look at it.
Nicholas Knoblauch (14:05:48) (in thread): > If you can’t reason aboutfoofrom withinfoo, that’s a major code smell
Aaron Lun (14:07:16) (in thread): > Your functions sound pretty trivial if you can debug by just looking at the code without inspecting the output.
Aaron Lun (14:08:21) (in thread): > to me, every step is potentially wrong. Each line does as little as it can, so I can always inspect the output individually.
Nicholas Knoblauch (14:10:23) (in thread): > If you can’t debug your function by just looking at it, it needs to be (at least) two functions
Aaron Lun (14:11:33) (in thread): > I can only assume that you exclusively write one-line functions.
Nicholas Knoblauch (14:19:39) (in thread): > when I break in my functionfoo(x,y,z)I get to seex,yandz. I can inspect each of them as much as I like to make sure that they satisfy the requirements I have for them. I can then see the functions called infooand debug those to make sure they work properly. Unless there’s non-local state being manipulated somewhere, that’s it
Nicholas Knoblauch (14:21:42) (in thread): > By introducing lots of variables and assignment to “document” the code, it’s like naming a characters in a story and never referring to them again.
Aaron Lun (14:22:01) (in thread): > And iffoocontains a line that doesaa <- x |> blah() |> whee() |> stuff() ... 10 steps later ... |> more_blah(), how do you debug that line? You probably can’t.
Nicholas Knoblauch (14:30:24) (in thread): > So if I know that line is where the problem is, and none of those functions gave me any kinds of warnings or errors, I’m still in a way better place because each of those only get input fromxand the step immediately before
Aaron Lun (14:36:22) (in thread): > Oh, if only. Because in any non-trivial function, you’ve probably got all sorts of stuff going on. Like the 8th step has something likewhee2(other=y)or something like that. Or maybe the 5th step has to use that silly.notation becausezneeds to be passed as the first argument. Linearity? Forget about it, you’ll be taking inputs all over the place. > > But that’s beside the point, because you wouldn’t be able to debug that line anyway. Without, well, I dunno, splitting it up into smaller chunks? Assigned to intermediate variables, so you can look at the output of each step?
Nicholas Knoblauch (14:36:23) (in thread): > If I have > > a_variable_name <- blah(x) > some_var <- whee(a_variable_name,y) > some_other_variable_name <- stuff(some_var) > ...more assignments > more_blah(who_is_this_guy...,three_other_variables_you_dont_recognize) > > you for sure have to go one step at a time, because there’s no way of knowing what came from where. The fact that you have to “stop” the pipe when you need intermediate output is a feature not a bug. it documents branch points in the code
Aaron Lun (14:37:16) (in thread): > So in other words, you’re saying that: to do any sensible debugging, I will break up my pipe into individual lines anyway.
Nicholas Knoblauch (14:38:09) (in thread): > debug mode has step over and step in for this very reason
Nicholas Knoblauch (14:38:24) (in thread): > S4 does make this painful
Nicholas Knoblauch (14:40:57) (in thread): > Yeah if your code isn’t linear, then you can’t express it with pipes. I don’t see how that’s a problem with pipes though
Aaron Lun (14:41:03) (in thread): > I want to print my intermediate variables. I want todigestmy intermediate variables. I want to apply operations to my intermediate variables. And I don’t want to have to realize, “oh crap, the intermediate variable is in the middle of this 10-step pipeline. Better break it up.” Any pipeline would naturally devolve into a sequence of stepwise calls.
Nicholas Knoblauch (14:41:22) (in thread): > you can do all of that with a debugger
Nicholas Knoblauch (14:41:39) (in thread): > none of the intermediate variables go away
Aaron Lun (14:42:32) (in thread): > in an non-interactive session (or one that is effectively so)? fat chance.
Nicholas Knoblauch (14:42:33) (in thread): > if you have a function that takesxandy, you can break at that function and do whatever you want to those variables. If not, you can step over or in
Aaron Lun (14:45:32) (in thread): > and the last I heard,debug()steps over the entire line. So your 10-line pipe is really just a single step todebug(). Unless they’re inserting debug breakpoints for each invocation of|>… good luck trying to figure out where your problem is!
Nicholas Knoblauch (14:45:33) (in thread): > If you aren’t at a REPL, then enforce checks on the function inputs. If that doesn’t work then add logging.
Nicholas Knoblauch (14:46:21) (in thread): > no you havenextandstep
Aaron Lun (14:46:24) (in thread): > No, the only way is to inspect intermediate objects, because you cannot trust any step that you called in the function.
Nicholas Knoblauch (14:58:15) (in thread): > The function is broken and needs debugging if the return of the function is not what you expect given the inputs. If my function internally is linear, if it’s just one thing passed to the next, then I debug it in a linear fashion by debugging each component in sequence, and that’s great. If my function is nonlinear, and there are multiple complex intermediate objects I can’t reason about in isolation, it would likely benefit from refactoring, but it would be nice if it at least looked different than the other parts of my code (i.e had lots more<-)
Aaron Lun (15:00:20) (in thread): > And I would say that, even if your function is internally linear, it would benefit from being broken up into many smaller steps with explicit assignments to intermediate variables, rather than just being a one-line 20-step pipe-infested mess.
Martin Morgan (15:01:47) (in thread): > The translation from piped code to ‘idiomatic’ code is essentially line-for-line, e.g., > > mtcars |> > subset(cyl == 4) |> > lm(formula = mpg ~ disp) > > becomes > > x <- mtcars > four_cyl <- subset(x, cyl == 4) > lm(four_cyl, formula = mpg ~ disp) > > which I think is part of the appeal compared to the unpacking and re-arrangement required for understanding a nested style. > > Complicated compositions of more than three or four lines of piped code are likely as unintelligible as expressions of more than three or four nested calls. And debugging intermediate values inas(log(x + 1), "TileDBArray")would be as cumbersome as debugging intermediate values in > > log(x + 1) |> > as("TileDBArray") > > (actually in either case one might, say debugonce("as") and arrive at the same place quickly). Effectively writing and debugging in either style requires a level of experience and understanding that I find challenging and fun to aspire toward – my pipes have become shorter as I’ve gained experience with them, just as my functions have become more modular. > > The tidyverse style guide for use of pipeshttps://style.tidyverse.org/pipes.html provides guidance that seems relevant here, including to avoid using pipes when there are intermediate objects that could be given meaningful names, expressing short (one-verb) pipes as regular function calls, and refactoring complicated pipes into a series of statements creating explicit intermediate variables with evocative names. > > I use pipes in my package code – the development of a short series of transformations as a pipe fits well with my thought process during the creative part of solving a (well-circumscribed) problem. Maybe if I were more formal and rigorous I would translate the result of the creative phase into more idiomatic code, but I know the most likely outcome would be introduction of bugs during the translation. And the collection of operations into a pipe helps to structure my code, augmenting use of white space and, at a more granular level, function calls to group related thoughts together into coherent expression. The one-line 20-step pipe is not something to aspire toward. > > Henrik mentioned how magrittr has worked to obey how R behaves, but the native implementation gets that ‘for free’. A fun example is > > stop("foo") |> \(...) "bar" > sample(1e30) |> \(...) "ok" > > where evaluation is lazy (the LHS is only evaluated when needed), just as inf = function(...) "bar"; f(stop("oops")) - Attachment (style.tidyverse.org): 4 Pipes | The tidyverse style guide > 4 Pipes | The tidyverse style guide
Aaron Lun (15:03:58) (in thread): > In the log case, I would just do: > > lx <- log(x + 1) > as(lx, "TileDBArray") >
Aaron Lun (15:05:37) (in thread): > not that I don’t trust herve’s implementation oflog()for DA’s, but just in case.
Aaron Lun (15:07:42) (in thread): > And insofar as we’re talking syntax, good luck to those people who accidentally miss a|or>when they’re trying to type the new pipe, because it seems the resulting incorrect expression could be entirely valid.
Nicholas Knoblauch (15:08:29) (in thread): > You don’t use a keyboard shortcut for the assignment operator?
Aaron Lun (15:08:52) (in thread): > hell no. why would I need to?
Martin Morgan (15:09:10) (in thread): > Yes, R has several traps like that, e.g.,x < -2instead ofx <- 2(we should just use=like any normal language and have done!:smiley:)
Aaron Lun (15:10:01) (in thread): > I have more than enough APM to handle a few extra keys
Nicholas Knoblauch (15:10:27) (in thread): > the keyboard shortcut for pipe and assignment means I don’t make that whitespace mistake
Nicholas Knoblauch (15:10:47) (in thread): > with my mere mortal APM I don’t have that kind of time
Aaron Lun (15:20:56) (in thread): > @Martin Morganbut then how could R core write their convoluted assignments within function calls? e.g., fromp.adjust: > > if (all(nna <- !is.na(p))) > nna <- TRUE > > Which, on an unrelated note, is buggy:p.adjust(numeric(0), n=0)throws an error instead of returningnumeric(0).
Martin Morgan (15:22:05) (in thread): > Yeah, I was looking at those paradigms in SingleR just now! > > SingleR master$ grep "if (.**<-" R/** | wc -l > 5 >
Aaron Lun (18:15:44) (in thread): > what’s the applicaton?
Sridhar N (19:00:56) (in thread): > > multi-modal analyses > > ?!?
Sridhar N (19:01:06) (in thread): > no?
Aaron Lun (19:02:49) (in thread): > yeah, but what exactly do you have in mind? Dirichlet-multinomial is just a distribution, what do you want to use it for? E.g., I use the Dirichlet-multinomial inemptyDrops().
Sridhar N (19:04:06) (in thread): > https://pubmed.ncbi.nlm.nih.gov/29928470/ - Attachment (PubMed): Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data - PubMed > We introduce an iterative normalization and clustering method for single-cell gene expression data. The emerging technology of single-cell RNA-seq gives access to gene expression measurements for thousands of cells, allowing discovery and characterization of cell types. However, the data is confound …
Sridhar N (19:04:12) (in thread): > aah ok
Sridhar N (19:05:19) (in thread): > i cannot think of specific use case top of my head but like i said i did not read the source code. If you have it hereemptyDrops()then good on ya will look at it
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2020-12-06
Aaron Lun (04:38:32) (in thread): > Yes! I finally have a R-bugzilla account. Time to dig through my backlist of weird things.
Hervé Pagès (16:10:24) (in thread): > @Nicholas KnoblauchThanks for the pointer toThe magrittr monad article. Interestingly most of the article discusses how the magrittr pipe fails to cleanly pass the Associativity axiom and the possible workarounds. That is, it would be nice if: > > (m %>% f) %>% g > > was semantically equivalent to: > > m %>% (f %>% g) > > Unfortunately the latter doesn’t work, unless you replace it with something ugly likem %>% (function(x) {f(x) %>% g})or introduce another operator (the author introduces his own%>=>%). Note that the Unix pipe does pass the Associativity axiom i.e.: > > (cmd1 | cmd2) | cmd3 > > is semantically equivalent to: > > cmd1 | (cmd2 | cmd3) > > So yes, another weakness and important difference of the magrittr pipe vs the Unix pipe.
2020-12-07
Nicholas Knoblauch (12:45:32) (in thread): > Yeah you know what they say: “you never go full monad”. Given the reaction to the pipe as it is, I can’t imagine people would be more enthusiastic if associativity got added to the mix…
Ying Chen (20:08:33): > @Ying Chen has joined the channel
Jenny Drnevich (20:10:56): > I just saw that a new mouse reference genome assembly, GRCm39, came out a few months ago.http://genomeref.blogspot.com/ . It’s on NCBI as the default mouse reference (https://www.ncbi.nlm.nih.gov/genome/?term=mus+musculus ) but it is not on Ensembl yet, and they just released 102 on 30 Nov. Anyone started using it yet? It seems like it is mostly reducing gaps and not a major upheaval of gene models (only 1473 / 46318 ENTREZIDs are not inorg.Mm.eg .db v3.12). It also doesn’t contain any patches or haplotypes, which I remove anyway. There always seems to be a lag between a new assembly release and widespread use of it - I’d be interested in hearing how long people might wait to start using it. Right away? 6 months? A year or more?! - Attachment (ncbi.nlm.nih.gov): Mus musculus (ID 52) - Genome - NCBI > This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.
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2020-12-08
Shubham Gupta (09:25:33): > Is there any function in bio-conductor to convert RefSeq Protein IDs to UniProt IDs?
Sridhar N (11:34:45): > that would be a good question to ask on the forum
Sridhar N (11:34:57): > but anything that you could not scavenge from ` > > library('org.Hs.eg') >
Sridhar N (11:35:20): > looking at the available keys is where i would start
Sridhar N (11:36:18): > and then there is also thishttps://www.uniprot.org/uploadlists/
Sridhar N (11:38:47): > and thishttps://bioconductor.org/packages/release/bioc/html/UniProt.ws.html - Attachment (Bioconductor): UniProt.ws > A collection of functions for retrieving, processing and repackaging the UniProt web services.
Shubham Gupta (11:56:55): > Thanks. I should have posted on Bioconductor forum
James MacDonald (12:11:07) (in thread): > Based on the fact that theTxDbpackage is 964 out of 971?https://bioconductor.org/packages/release/data/annotation/html/TxDb.Mmusculus.UCSC.mm39.refGene.html I’d guess nobody is using it yet.:face_with_monocle: - Attachment (Bioconductor): TxDb.Mmusculus.UCSC.mm39.refGene > Exposes an annotation databases generated from UCSC by exposing these as TxDb objects
Jenny Drnevich (12:48:06) (in thread): > Ah, I missed that BioC had a TxDb package for it already. Why does UCSC insist on using non-standard names like mm39? And why does BioC make their TxDb packages from UCSC?!
Alan O’C (13:35:12) (in thread): > org.Hs.eg .dbpresumably
Sridhar N (13:37:10) (in thread): > aah yes, i blame crappy instant coffee thanks
James MacDonald (14:46:03) (in thread): > I think the rationale for getting the data from UCSC is that they have the data in a database that’s easily queryable. (<- why slack thinks that’s not a word is beyond me, btw). > > In the past this always meant that the data were based on NCBI gene IDs, which to me presented a clear difference between the ‘stock’TxDbsthat Bioconductor generated and the Ensembl based ones that@Johannes Rainermakes. Which is important, given the clear differences between the two annotation services, particularly at the transcript level. > > But now UCSC has gone completely off-script, basing their knownGene table for GRCh38 on Ensembl IDs rather than NCBI. So if you know thatTxDb.Hsapiens.UCSC.hg19.knownGeneis comprised of NCBI genes/transcripts, then you could be forgiven for thinking thatTxDb.Hsapiens.UCSC.knownGenewould be NCBI as well. But it’s not!
James MacDonald (14:47:07) (in thread): > But long story short, I think it’s way easier to get the data for aTxDbfrom UCSC than it would be to get it directly from NCBI.
Dario Strbenac (18:00:07): > Riddle me this.validfunction shows all packages are up-to-date. But the subsetting fails with an error. It works on another server with CentOS 8 and a personal computer with Windows 10 but not on the server I need to use, which happens to operate Debian 10. > > library(VariantAnnotation) > example(readVcf) > subset(vcf, FILTER == "PASS") # Error in eval(expr, as.env(envir, enclos)) : object 'FILTER' not found > > BiocManager::valid() > [1] TRUE > > sessionInfo() > R version 4.0.1 (2020-06-06) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Debian GNU/Linux 10 (buster) > > What happens on your operating system?
Martin Morgan (18:09:29): > The ideas that come to mind are (a) different versions ofBioconductor::version()(to explain the different behavior, but not why only one works) (b) additional packages on the search path, providing their own version ofsubset()(tryBiocGenerics::subset()) (c) a ‘locale’ encoding, though that seems very weird [it would likely result in a complaint about the RHS string, and only if e.g., it had non-alphanumeric characters)
Dario Strbenac (18:30:23): > Thanks. None of those seem to be involved. It seems to be using a relevant subsetting, although that function appears to be undocumented. > > 1: subset(vcf, FILTER == "PASS") > 2: subset(vcf, FILTER == "PASS") > 3: .local(x, ...) > 4: S4Vectors:::evalqForSubset(subset, rowData, ...) > 5: evalArg(substitute(expr), envir, ..., where = parent.frame()) > 6: safeEval(expr, envir, enclos, ...) > 7: eval(expr, envir, enclos) > 8: eval(expr, envir, enclos) > 9: eval(expr, as.env(envir, enclos)) > 10: eval(expr, as.env(envir, enclos)) > > ?evalqForSubset > No documentation for 'evalqForSubset' in specified packages and libraries > > Anyone got Debian and can try it?
James MacDonald (19:29:43): > What doesrowData(vcf)return?
Dario Strbenac (19:30:54): > > DataFrame with 5 rows and 1 column > paramRangeID > <factor> > rs6054257 geneA > 20:17330_T/A geneA > rs6040355 geneB > 20:1230237_T/. geneB > microsat1 geneB >
James MacDonald (19:31:28): > That’s weird. It should be > > > rowData(vcf) > DataFrame with 5 rows and 5 columns > paramRangeID REF ALT QUAL > <factor> <DNAStringSet> <DNAStringSetList> <numeric> > rs6054257 geneA G A 29 > 20:17330_T/A geneA T A 3 > rs6040355 geneB A G,T 67 > 20:1230237_T/. geneB T 47 > microsat1 geneB GTC G,GTCT 50 > FILTER > <character> > rs6054257 PASS > 20:17330_T/A q10 > rs6040355 PASS > 20:1230237_T/. PASS > microsat1 PASS >
James MacDonald (19:32:06): > Which explains why it can’t find the FILTER column
Alan O’C (19:35:18): > Works for me on Ubuntu, VariantAnnotation 1.36.0
Dario Strbenac (19:40:02): > Seems likereadVcfis dropping the columns somehow, although the file is good: > > > fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") > > vcf <- readVcf(fl, "hg19") > > rowData(vcf) # Should be 5 columns. > DataFrame with 5 rows and 1 column > paramRangeID > <factor> > ... ... > > system(paste("grep FILTER", fl)) > ##FILTER=<ID=q10,Description="Quality below 10"> > ##FILTER=<ID=s50,Description="Less than 50% of samples have data"> > #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 >
James MacDonald (19:43:58): > And you are using VariantAnnotation_1.36.0?
Dario Strbenac (19:45:44): > Sure am. > > > BiocManager::version() > [1] '3.12' > > BiocManager::valid() > [1] TRUE > > Might have to step throughreadVcfline-by-line to see when the columns are lost.
James MacDonald (19:47:46): > There’s like a gazillionreadVcffunctions out there:http://search.bioconductor.jp/codes?utf8=%E2%9C%93&query=readVcf You might check for masking.
James MacDonald (19:48:13): > Since they all (presumably) will read in a VCF file…
Dario Strbenac (21:30:12): > It looks like the columns are lost in the last step ofVariantAnnotation::VCFfunction. > > Browse[3]> fixed > DataFrame with 5 rows and 4 columns > REF ALT QUAL FILTER > <DNAStringSet> <DNAStringSetList> <numeric> <character> > 1 G A 29 PASS > 2 T A 3 q10 > 3 A G,T 67 PASS > 4 T 47 PASS > 5 GTC G,GTCT 50 PASS > Browse[3]> X=new(class, SummarizedExperiment(assays = geno, rowRanges = rowRanges, > + colData = colData, metadata = as.list(exptData)), fixed = fixed, > + info = info, ...) > Browse[3]> rowData(X) > DataFrame with 5 rows and 1 column > paramRangeID > <factor> > rs6054257 NA > 20:17330_T/A NA > rs6040355 NA > 20:1230237_T/. NA > microsat1 NA >
2020-12-09
Phil Xie (05:59:13): > @Phil Xie has joined the channel
Jenny Drnevich (09:22:12) (in thread): > I completely understand about the practicality of data acquisition! I wish NCBI would finally standardize with Ensembl/Havana/Gencode, at least for human and mouse.
Vince Carey (10:53:30): > https://www.itprotoday.com/compute-engines/amazon-amex-fund-software-developers-new-github-program - Attachment (IT Pro): Amazon, Amex to Fund Software Developers in New GitHub Program > The additions help expand GitHub’s Sponsors program, which previously let individuals support software projects and the millions of developers who use the digital platform to collaborate on, share and store code
James MacDonald (11:06:16) (in thread): > Are they not?https://www.ncbi.nlm.nih.gov/refseq/MANE/
James MacDonald (11:10:08) (in thread): > In that contextrowDatais just a stand-in formcols. What do you get frommcols(vcf)andfixed(vcf)?
James MacDonald (11:10:57) (in thread): > I get > > > fixed(vcf) > DataFrame with 5 rows and 4 columns > REF ALT QUAL FILTER > <DNAStringSet> <DNAStringSetList> <numeric> <character> > 1 G A 29 PASS > 2 T A 3 q10 > 3 A G,T 67 PASS > 4 T 47 PASS > 5 GTC G,GTCT 50 PASS > > and > > > mcols(vcf) > DataFrame with 5 rows and 5 columns > paramRangeID REF ALT QUAL > <factor> <DNAStringSet> <DNAStringSetList> <numeric> > rs6054257 geneA G A 29 > 20:17330_T/A geneA T A 3 > rs6040355 geneB A G,T 67 > 20:1230237_T/. geneB T 47 > microsat1 geneB GTC G,GTCT 50 > FILTER > <character> > rs6054257 PASS > 20:17330_T/A q10 > rs6040355 PASS > 20:1230237_T/. PASS > microsat1 PASS >
Jenny Drnevich (13:49:18) (in thread): > Unfortunately, that is not super useful for RNA-Seq / Salmon: > 1. “MANE Select:One
Dario Strbenac (18:00:22) (in thread): > Thanks for all your help. I solved it by running a personal version of R 4.0.3 instead of the system’s version 4.0.1 with--no-environ``--no-site-fileand--no-init-file. There must be some obscure dependency in a system-wide library that is outdated.
2020-12-10
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James MacDonald (12:14:31) (in thread): > Ah, I see what you are getting at. I am not sure that’s ever going to be a thing, given the differences in how the two annotation services define what is and isn’t a transcript. And I am not sure there is anything to gain by doing so. At some point in time we may have coalesced into a consensus set of transcripts, but right now I am not so sure either NCBI nor EBI/EMBL (or Havana or GENCODE) have a monopoly on the correct set of transcripts.
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Hervé Pagès (18:05:28): > Sorry in advance if there’s a more appropriate channel to discuss this. > > Many many packages in the methylation business (methylation array or MethylSeq) define dozens of data structures (S4 classes) for the purpose of representing methylation data. Some of the most outstanding data structures seem to be RnBeadSet in RnBeads, MethylSet in minfi, MethyLumiSet in methylumi, BSdataSet in methylPipe, BSrel and BSraw in BiSeq, etc… Some are SummarizedExperiment derivatives, some are eSet derivatives, others don’t extend anything and reimplement a lot of things from scratch. I wonder if some kind of unification/standardization effort has been considered. Would be great to achieve some sort of consensus like has been done with SingleCellExperiment for single cell data. Having the consensual classes implemented in their own package, and separated from any particular application like in the case of SCE, would help with exposure and reusability. > > For the context: I’m currently looking at a new submission (MAGAR) that implements yet another set of S4 classes (methQTLInput and methQTLResult) almost from scratch:https://github.com/MPIIComputationalEpigenetics/MAGAR/blob/a5281222426441ed48581cd5b45d1d81d6537ed4/R/methQTLResult-class.R#L38-L57 andhttps://github.com/MPIIComputationalEpigenetics/MAGAR/blob/a5281222426441ed48581cd5b45d1d81d6537ed4/R/methQTLResult-class.R#L38-L57 . I’m hoping that they can avoid that by reusing (either directly or by extending) something that’s already available in the ecosystem but it’s not clear to me what to recommend:confused:
2020-12-11
Kevin Rue-Albrecht (04:02:30) (in thread): > Really good point. How about adding this as a BiocChallenges?https://kevinrue.github.io/BiocChallenges/ ? > Each challenge is a vignette undervignettes/challenges. > I’m about to give a presentation introducing this at EuroBioc2020:slightly_smiling_face: - Attachment (kevinrue.github.io): Challenges for the Bioconductor community > This package hosts challenges contributed by and for the Bioconductor community. It provides functionality to manage, filter, and display challenges as articles of a pkgdown website. Challenges are bite-sized projects led by volunteers, encouraging collaboration and sharing of expertise between contributors.
Malte Thodberg (05:25:16) (in thread): > Another case of this is packages dealing with TFBSs (most are under BiocViews) which implements many different versions of PFMs and PWMs. > A small but easy step on the way to encourage more standardization and interoperability could to update (and make more visible) the guidelines here:https://bioconductor.org/developers/how-to/commonMethodsAndClasses/
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rohitsatyam102 (09:44:41): > Hi everyone if you are trying to download anything from ensemble follow the following advice. The FTP links will not work anymore. Here is what ensembl Team have to say: > > Are you using Google Chrome? Unfortunately, Google have decided to disable FTP > protocol. We are hurriedly trying to change all the links from our pages to > http:// instead of ftp://, but have not managed it all yet. You should be able > to access these files by changing to http://. >
Spencer Nystrom (09:48:49) (in thread): > You should be able to use firefox for ftp links.
rohitsatyam102 (10:01:09) (in thread): > I thought sharing this since maximum of us use Google Chrome, I guess:sweat_smile:. Yes you can use other browsers like operamini and firefox. It works on microsoft edge too.
2020-12-12
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2020-12-14
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Kozo Nishida (12:38:52): > I sent an email tohubs@bioconductor.org andmaintainer@bioconductor.org (to request access to S3 bucket [for creating an AnnotationHub package) , but I received replies from the email daemon. > Are you able to send emails to these email addresses without any problems?
Jonathan Griffiths (12:40:05) (in thread): > I had this recently toohttps://community-bioc.slack.com/archives/CDSG30G66/p1607173107031700 I sent again the next morning and it was fine - weird behaviour - Attachment: Attachment > I’ve recieved an email delivery error for something I sent to the hubs@bioc email address - this seems unusual. Is it a known issue at the moment? Might be something on the @roswellpark.org end of things? > > Diagnostic-Code: smtp; 550 #5.7.1 Your access to submit messages to this e-mail system has been rejected.
FelixErnst (13:12:00) (in thread): > I had to get in touch with the hubs-team as well. I sent the mail 15 min ago and haven’t received a deamon, yet. So I think it went through
Kozo Nishida (13:15:30) (in thread): > Thank you for the information. > I will sendhubs@bioconductor.org an email again.
Lori Shepherd (13:26:35) (in thread): > You might consider joining the#biochubschannel for hub related questions. If you still have issues sending tohubs@bioconductor.org you can reach out to myself and@Kayla Interdonatofor access –
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Bharati Mehani (19:22:12): > Hi all, i am using Cibersotx to deconvove TCGA gene expression data and getting my the expression values in fractions. I am not sure whether these should be considered as normalized count to perform differential expression among samples or we require any normalization as TMM in EdgeR. Anybody has any experience with this? Not sure whether it os a suitable channel to post this question. Thanks in advance.
Alan O’C (19:33:21): > I don’t imagine you’d need to normalise estimates of cell type proportions as they are by nature confined to [0, 1]. However they’re not normalised counts
Aaron Lun (19:33:40): > Probably should be better suited to the support site.
Bharati Mehani (19:57:13): > @Alan O’CMy question is about the deconvolved gene expression values, not the cell proportions. These are not confined to [0,1].
Bharati Mehani (19:58:45): > Hi@Aaron Lunalso posted there but didn’t get any response.
Alan O’C (19:58:53): > Fair, I’ve not used Cibersort in any great detail as it’s proprietary
Dario Strbenac (20:30:06): > It is an interesting question, though. Effectively, it’s something like “which genes are differentially expressed specifically in cancer cells or another cell type of interest?” It might be useful for an analysis such as primary tumour versus metastasis, where many of the genes which initially appear to be differentially expressed between the two conditions are simply only expressed in one tissue but not the other and unrelated to cancer.
Bharati Mehani (20:37:15): > @Dario StrbenacYes, i am trying to address something similar
Bharati Mehani (20:37:30): > But not sure how to process these values
Bharati Mehani (20:38:04): > Thinking of just taking their log to compare the two groups of cell. Also looking for any of yours suggestion.
2020-12-15
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Kasper D. Hansen (06:54:54): > I would expect you want to estimate cell type proportions (summing to 1) and include them as covariates. But since cibersort is only semi-open, why don’t you file a help request with them?
2020-12-16
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2020-12-17
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2020-12-18
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2020-12-19
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2020-12-20
Dario Strbenac (05:00:11): > Does anyone have, for any of the Bioconductor RNA-seq differential expression packages, a flowchart showing the varieties of options at each stage of analysis (e.g.x choices for compositional adjustment,y choices for dispersion estimation,z choices for hypothesis testing) to illustrate to a biologist that there are a lot of combinations of parameters before they see a final summary table of results with the gene symbol and p-values they recognise and love? I am hoping that someone who does teaching would have a slide such as this already made and willing to share it (and it would be a bonus to have the minimum and maximum of the number of genes identified at an F.D.R. of 0.05 as well).
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2020-12-21
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2020-12-22
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2020-12-23
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2020-12-24
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2020-12-30
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2021-01-01
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2021-01-05
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2021-01-07
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2021-01-11
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2021-01-12
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2021-01-13
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2021-01-14
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Koen Van den Berge (08:59:42): > It’s not exactly that but Fig6 in ourreview paper attempts to give somewhat of an overview of analysis options in a DE analysis. Credits to@Michael Lovefor making the figure. - File (PNG): image.png
Darren (09:04:33): > @Darren has joined the channel
Jenny Drnevich (09:44:38): > Anyone know of a virtual, interactive exercise to demonstrate alignment and assembly? We teach a yearly workshop on Intro to Bioinformatics to a nearby liberal arts college. In the past, we’ve usedshotgunator to chop up a short sentence into reads, printed them on thin sheet magnets and have the students do both alignment and assembly with them. It works really well to demonstrate the main concepts to 2nd year biology students but this year we have to go remote. Thanks!
Mikhail Dozmorov (13:09:31): > TeachEnG is a great resource for interactive demo of alignment algorithms,https://teacheng.illinois.edu/index.html
Dario Strbenac (17:00:15) (in thread): > It would look a lot more cluttered if all the possible choices at each stage were shown. It shows the right amount of detail.
Leonardo Collado Torres (17:43:23): > RStudio Global 2021 is free and the registration form is open in case you are interestedhttps://rstudio.com/conference/ . The event will be on Jan 21st - Attachment (rstudio.com): rstudio::global(2021) > A virtual conference about all things R and RStudio
Aaron Lun (23:38:34): > Y’know what would be really nice? being able to callon.exitand link that to another function environment.
Aaron Lun (23:38:38): > Just going to throw that out there.
2021-01-15
Milan Malfait (04:30:59) (in thread): > Not sure if it’s exactly what you’re looking for, but this might be of interest:https://withr.r-lib.org/reference/defer.html - Attachment (withr.r-lib.org): Defer Evaluation of an Expression — defer > Similar to on.exit(), but allows one to attach an expression to be evaluated when exiting any frame currently on the stack. This provides a nice mechanism for scoping side effects for the duration of a function’s execution.
Aaron Lun (04:36:54): > yes, something like that, but in base; preferably as an argument toon.exit.
Milan Malfait (06:32:19): > No idea about that:confused:
Aaron Lun (11:08:23): > might make a patch to R and see how it goes down
2021-01-16
rohitsatyam102 (03:19:02) (in thread): > Wow Sir. Thanks for this
rohitsatyam102 (03:28:02) (in thread): > Already going gaga on this resource
rohitsatyam102 (03:28:18) (in thread): > I am attending too
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2021-01-18
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Friederike Dündar (09:54:40) (in thread): > I don’t have a visual, I think, but is something like this table along the lines of what you’re envisioning:
Friederike Dündar (09:54:44) (in thread): - File (PNG): image.png
Friederike Dündar (09:55:12) (in thread): > Happy to hear latest updates to the details, that table was prepared in 2015, which feels like eons ago
Friederike Dündar (09:56:51) (in thread): > Oh, and in terms of making the point that “choices matter”, I like to show this figure:https://www.nature.com/articles/s41467-017-00050-4/figures/1
Friederike Dündar (09:57:19) (in thread): > It’s sufficiently cluttered to make the point
Friederike Dündar (09:57:47): > Is there a BioC equivalent of Seurat’s HTODemux() function?
Friederike Dündar (09:58:37): > https://satijalab.org/seurat/v3.1/hashing_vignette.html - Attachment (satijalab.org): Satija Lab > Lab Webpage —
Dario Righelli (11:11:21): > Hi I’m trying to setup the GHA for installing the magick package, but maybe the lib-magick++ libraries have to be previously installed. > Does someone knows how to do that on each of the three main platforms inside a GHA workflow? > Thanks > p.s. I don’t know if there is a dedicated channel for this kind of questions
Aaron Lun (13:46:24) (in thread): > DropletUtils::hashedDrops might do what you want.
Aaron Lun (13:47:02) (in thread): > check outhttp://bioconductor.org/books/release/OSCA/droplet-processing.html#cell-hashing - Attachment (bioconductor.org): Chapter 15 Droplet processing | Orchestrating Single-Cell Analysis with Bioconductor > Or: how I learned to stop worrying and love the t-SNEs.
Charlotte Soneson (14:14:12) (in thread): > (assuming this is aboutSpatialExperiment) I think for mac you could use homebrew (https://formulae.brew.sh/formula/imagemagick ). > The errors for Windows and Linux appear unrelated to magick.
FelixErnst (14:19:53) (in thread): > Have a look at thebiocthis.@Leonardo Collado Torresset up the GHA with an OS specific rule
Friederike Dündar (14:34:30) (in thread): > excellent, will check it out
Friederike Dündar (17:37:28) (in thread): > Is there a way to use batchelor’smultiBatchNormwith ADTs? I.e. specifying that it should take thesizeFactorsfrom thealtExp, too?
Aaron Lun (17:53:32) (in thread): > Hm… option 1 is to setnorm.args=list(use.altexps=TRUE), which is passed tologNormCounts(). Option 2 is to just callmultiBatchNormon youraltExp(sce), which has the benefit of rescaling that as well. > > TBH the bigger problem is that there is no one-line function to perform batch correction on ADT-containing data. It’s not particularly hard to do so - some combination ofmumosa::rescaleByNeighbors()andfastMNN()would do the job - but I’ve never tried it myself.
2021-01-19
Dario Righelli (04:00:52) (in thread): > Thanks@Charlotte Soneson, yes it’s for theSpatialExperiment. > I’ll try with brew, I didn’t know it was possible to use it on the GHA.
Dario Righelli (04:01:12) (in thread): > Thanks@FelixErnst
Friederike Dündar (07:40:47) (in thread): > thanks, will tinker with it
Friederike Dündar (10:24:40) (in thread): > Just for future reference, this package also seems quite relevant for ADT/HTO-scRNA-seq datahttps://bioconductor.org/packages/3.12/bioc/vignettes/CiteFuse/inst/doc/CiteFuse.html
Aaron Lun (12:07:23) (in thread): > TBH they probably use a more sensible approach for demultiplexing thanhashedDrops, at the expense of having to generate more plots to show diagnostics.
Friederike Dündar (12:09:19) (in thread): > Did you gather that from their source code? The documentation is a bit scarce on the details of what they’re actually doing
Aaron Lun (12:09:39) (in thread): > oh, no, I just looked at their documentation and guessed their algorithm.
Friederike Dündar (12:09:49) (in thread): > of course you did
Aaron Lun (12:10:13) (in thread): > Probably fitting a two-component mixture to define a per-HTO threshold; everything above the threshold is considered “positive” for that HTO. So if a cell has two positives, it’s a doublet, etc.
Aaron Lun (12:10:41) (in thread): > In any case, I should probably work that into the book somewhere.
Hervé Pagès (13:09:33) (in thread): > The magick libraries should only be needed on Linux. If you are on Windows or Mac, you should preferably install package binaries. They are statically linked so don’t require any external library. Now there is the gotcha that CRAN doesn’t provide package Mac binaries for R-devel yet. See herehttps://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-macOS-Mojave-HOWTO.md#what-if-cran-doesnt-provide-package-binaries-for-macos-yet for a workaround that still doesn’t require to install any external library.
Hervé Pagès (13:12:27) (in thread): > The big benefit of this approach is that you don’t need to pollute your system with dozens of brewed components that are likely to mess up your system at some point.
Mike Smith (16:04:45) (in thread): > Although I totally agree using the pre-built binaries is the preferable way to go, is the pollution effect as much of a concern on a GA runner as it is on a standard workstation? Since it’s transient and dedicated only to the task of running build/check on this package, you shouldn’t run into the “what’s changed on my system since I ran this successfully 6 months ago?” problem.
Alma Hernandez de Rojas (16:18:57): > @Alma Hernandez de Rojas has joined the channel
Hervé Pagès (17:21:54) (in thread): > It’s more than just a pollution concern. It’s a “brewing random stuff will mess up your system” concern. I don’t know these days, but in the pastbrew imagemagickwas no exception to the rule (seehttps://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-macOS-Mojave-HOWTO.md#420-install-imagemagick ). Yeah, maybe less of a concern in the context of GHA, for some well-tested brew recipes, and if you know what you are doing. Otherwise, stay away from brew as much as you can, especially if you can install package binaries.
Hervé Pagès (17:31:41) (in thread): > Interesting. Looks like the R equivalent of a very nice feature of the GO language:https://tour.golang.org/flowcontrol/12
2021-01-20
Luke Zappia (03:22:27): > None of the buttons (“Add comment”, “Add answer” etc.) seem to be working for me on the support site. Possibly I’m doing something wrong but I’ve tried Chrome/Safari/incognito without any luck. If I inspect the page I see a bunch ofjQuery reference not founderrors. Anyone else having issues or is it just me?
Mike Smith (03:25:32) (in thread): > I’m seeing the same behaviour. Maybe worth opening an issue athttp://github.com/bioconductor/support.bioconductor.org/issues or mention it in#support-site
Martin Morgan (05:56:18) (in thread): > @Lori Shepherd^^ (not working for me, either…)
Lori Shepherd (06:35:12) (in thread): > Yikes. Okay. Investigating.
Lori Shepherd (06:35:42) (in thread): > @Natay Aberranumber 1 priority for our meeting today!
Mike Smith (07:07:35) (in thread): > They seem to be back working for me now. If it’s helpful I can share the error message I was getting.
Natay Aberra (07:10:25) (in thread): > We are improving the page speeds and defered some content to help with the load times. This broke some core functionalities but that has been fixed. > Thank you for your patience.
Jenny Drnevich (15:30:09): > Hi all. I am sharing this Life Science trainers survey as I know quite a few of us on here teach workshops. Please consider filling out the survey!Global Survey for Instructors Who Deliver Training For Life Scientists lifescitrainers.org community is available in several languages and will be open until March 20, 2021. Thank you and please shareNow Open: Global Survey for Instructors Who Deliver Training For Life Scientists > If you have instructed life scientists using workshops or short courses, please take this first-ever global survey.
Aedin Culhane (16:12:11): > Rstudio conference is tomorrow. Registration is free and still openhttps://global.rstudio.com/student/catalog Bioconductor will host a chat Q&A networking sessions (via spatial chat) after John Burn-Murdoch’s talk on the FT visualization of COVID19 data. So please watch John’s talk and join us afterwards in Spatial chat to meet Bioconductor folks. - File (PNG): Screen Shot 2021-01-20 at 4.10.26 PM.png - File (PNG): Screen Shot 2021-01-20 at 4.09.45 PM.png
Aedin Culhane (17:49:23): > @Susan Holmeswill be hosting a second spatial chat at 1:20am PST, which will work better for Europe and Asia (8:20am GMT, or 9:20am Central European time, 7:20pm Sydney)
Aedin Culhane (17:50:31): > So join at 1:20pm or 1:20am PST to connect with Bioconductor developers, users and those who want to get started with Bioconductor
Aedin Culhane (18:41:39): > What time is 1:20pm Thurs or 1:20am Fri in yourtime zone .. - File (PNG): Screen Shot 2021-01-20 at 6.40.18 PM.png - File (PNG): Screen Shot 2021-01-20 at 6.39.14 PM.png
Dario Strbenac (18:45:19): > Yay, it’s not 2 a.m. Sydney time for once!
Aedin Culhane (18:52:10): > Yes, RStudio are repeating all keynotes and asking organizations where possible to accommodate times zones. Luckily Bioconductor is global… as are its CAB members so we can do 2 times 12 hours apart.
Mike Smith (19:29:13): > If your in the zone for talks just a reminder we also have a Developers Forum talk tomorrow with a data scientist & software engineer from Microsoft Research Genomics. (Only live once I’m afraid!). - Attachment: Attachment > The next Bioconductor Developers’ Forum is this Thursday 21st January at 09:00 PST / 12:00 EST / 18:00 CET - You can find a calendar invite attached to this post and at https://tinyurl.com/BiocDevel-2021-01 @Nitesh Turaga) to provide access to Bioconductor and other genomics tools in the Azure cloud. If you’re interested in discussing scalable platforms for running analysis workflows, interactive notebook environments, or accessing large-scale public datasets this should be a great event. > > We will be using BlueJeans and the meeting can be joined via: > https://bluejeans.com/114067881 (Meeting ID: 114 067 881)
Aedin Culhane (23:19:12) (in thread): > In Spatial Chat, you’ll go torstd.io/chat >> look for “Life Sciences 4” among the rooms on the lefthand side.
2021-01-21
Aaron Lun (02:14:44) (in thread): > batchelor devel now has anas.altexp=argument to make it easy to apply it to the alternative experiments in the input SCE(s). So you can just callmultiBatchNorm()once for the RNA and another time withas.altexp="adt"(or whatever).
Nicholas Knoblauch (10:20:25) (in thread): > Would the Global Condition Handlers Luke Tierney mentioned at useR! 2020 match your use case?https://youtu.be/X_eDHNVceCU?t=3466 - Attachment (YouTube): useR! 2020: Welcome and R core event
Román Pérez (15:54:14): > @Román Pérez has joined the channel
2021-01-22
Kozo Nishida (00:51:49): > I would like to updatehttps://github.com/Bioconductor/bioconductor.org/blob/master/content/about/community-advisory-board.md to look likehttps://ropensci.org/about/ (tiled pictures of people). > But I don’t know the syntax (or some config file?) to do that forhttps://github.com/Bioconductor/bioconductor.org . > Please let me know if there is a suitable channel for this discussion (about requesting the website update). - Attachment (ropensci.org): About us > rOpenSci’s vision and mission, team, and collaborators
Aaron Lun (01:39:40) (in thread): > all correctino functions now also haveas.altexp=. But for MNN methods, this probably doesn’t quite do what you want, so I will write amumosa::multiModalMNN()tomorrow.
Aaron Lun (01:43:05) (in thread): > … I don’t think so, but I’ll have to read the docs a bit more to be sure.
Martin Morgan (04:46:09): > http://bioconductor.org/about/core-team/ provides an example, athttps://raw.githubusercontent.com/Bioconductor/bioconductor.org/master/content/about/core-team.md which is just HTML in a markdown file; images are inhttps://github.com/Bioconductor/bioconductor.org/tree/master/assets/images . Maybe there is a more clever way; the site uses (an older) version of nanochttps://nanoc.ws/ as described in the README of the repository (I’m not sure if that is completely up-to-date; there is a docker file also at the top level of the repository but actually I personally do not use it).
Martin Morgan (04:50:24): > A more programmed example is the Annual Reports page, derived from content/about/annual-reports.html and using lib/helpers.rb to publish whatever is in assets/about/annual-reports ; this approach could also be used for the minutes of the CAB / TAB if that is interesting to you…
Kozo Nishida (04:56:39) (in thread): > Thank you for the information! First, I will imitate core-team.md!
Jonathan Speh (05:08:37): > @Jonathan Speh has joined the channel
Friederike Dündar (09:05:00) (in thread): > Why does MNN need its own ADT spin-off?
Aaron Lun (11:19:05) (in thread): > For all other methods, the correction is done on a per-gene basis, so it’s okay that they’re applied independently to the main/alternative Experiments. For MNN, the correction depends on a neighbor search that uses information across features. You can imagine that the choice of neighbors will depend on whether information is used from RNA, ADT or both datasets at once; in principle, the best correction would use both datasets to identify the best neighbors for each cell.
Annajiat Alim Rasel (15:38:41): > @Annajiat Alim Rasel has joined the channel
2021-01-23
Aaron Lun (01:41:15) (in thread): > Man, designing this interface is a total headache. You havesubset.rowfor the main Experiment, and alsosubset.rowfor each of the alternative experiments, and also different choices ofdfor the PCA in each experiment… ugh.
Vince Carey (14:53:52): > New channel:#gwas-data– sign up, and help devise the next generation of high-performance data containers and workflows for GWAS summary statistics, phewas, etc.
2021-01-24
Aaron Lun (01:56:18) (in thread): > I’ve got it.
2021-01-26
Alexander Toenges (04:59:51): > Are the ArrayExpress maintainers here? This (https://www.biostars.org/p/366760/ ) question at Biostars gets quite some traffic and is unanswered. > I tracked this down to these lines in theparseMAGE.r. Could someone look into this / ping the maintainers? > > ph = ph[gsub(" ", "", ph$Array.Data.File) != ""] > sampleNames(ph) = ph$Array.Data.File >
Martin Morgan (05:33:59) (in thread): > maintainer("ArrayExpress")provides contact information; are they responsive?
Pablo Rodriguez (05:51:49) (in thread): > This is also their github repo , so you can live an issue or get the mainteiner’s mail
Alexander Toenges (05:52:48) (in thread): > https://github.com/ebi-gene-expression-group/bioconductor-ArrayExpress/issues/2
Alexander Toenges (05:53:24) (in thread): > Tagged the maintainer in this one, not sure if this or the one you linked is the correct repo.
Pablo Rodriguez (05:58:08) (in thread): > I reached the one I linked by googling “ArrayExpress github” and saw this repo is from the same person who is assigned as mainteiner, but couldn’t say which one is the official bioconductor repo
Alexander Toenges (05:58:45) (in thread): > I went for “bioconductor github arrayexpress”:slightly_smiling_face:We will see.
Lori Shepherd (07:57:14) (in thread): > anyone that saw my previous post – sorry – I was confusing AffyExpress with ArrayExpress –
2021-01-27
Vince Carey (06:45:50) (in thread): > I did a little debugging onrawset = ArrayExpress("E-MTAB-4451")… The data at ArrayExpress are non-standard. A column ‘Array.Data.File’ is expected by the software, but instead the sdrf file has ‘Array.Data.Matrix.File’. This sort of thing happens in data repositories. Validity checking is not adequate to protect against such events. Maybe standards/conventions have changed since ArrayExpress was coded. The ArrayExpress readPhenoData certainly needs more defensive programming to avoid such events. I don’t know if the content will ultimately parse successfully with its unexpected naming convention. If the developers don’t respond, it may be possible to revise the code in an afternoon or so to defeat the discovered failures. Please report back to the thread if you don’t hear from them in the next couple of days.
Shannan Ho Sui (11:54:22): > @Shannan Ho Sui has joined the channel
Lambda Moses (14:50:03): > I’m writing a package with a S4 class that has a slot that is a data frame, and I’m debating whether to use DataFrame or data.frame. Some Bioconductor packages use S4 DataFrame rather than regular data.frame. Besides features like rle and IRanges in DataFrame, why use DataFrame instead of data.frame or tibble?
Hervé Pagès (16:21:15): > Make sure you really need a new class. If you have a fixed set of columns that is known in advance and if that set is small (e.g. < 10 columns), then you might also consider storing them in individual slots. Also depends on how you want things to be presented to the end user. Doesn’t have to be the same as how things are represented internally e.g. it doesn’t matter so much what you use internally (DataFrame, data.frame, data.table, tibble, one slot per column), as long as you provide accessor functions that hide how things are internally. The accessors can have anasargument that can be set to"DataFrame","data.frame", etc… Of course that’s just replacing your original question with “what should the accessors return by default?” Hard to tell without knowing a little bit more about the kind of data, its size, and the typical downstream usage.
2021-01-28
Magali Michaut (04:24:14): > @Magali Michaut has joined the channel
Friederike Dündar (14:29:15) (in thread): > Those antibodies used for hash tagging – could those be used for the control-based normalization described in OSCA?
Aaron Lun (14:31:17) (in thread): > probably not. One problem that comes to mind is that the concentrations of antibodies labelled with different tags are often different, so the underlying assumption of control-based normalization (same molar quantity per cell) is already broken.
Aaron Lun (14:31:49) (in thread): > If you had IgG’s, you could use those. But coverage tends to be pretty low for those guys, given that they are explicitly non-specific binders; so they get worse as your experiment gets better!
Lambda Moses (19:28:28): > Again, about writing the S4 class. I findBiocGenerics:::replaceSlotsandS4Vectors:::selectSomeincredibly useful. Then why aren’t those functions exported? If you have trouble with using:::in a package (but I learnt about these two internal functions fromSummarizedExperiment’s source code), then I can copy the source code of those two functions into my package.
2021-01-29
FelixErnst (02:48:54): > Without having be able to look at your code and know what you are doing/want to do, I think you are working on the internals of S4 objects. The next step might be to look up the implementation ofreplaceSlots, which has a bunch of useful comments next to it. Maybe you want to move such discussion to the#developers-forumchannel.
Martin Morgan (09:25:12) (in thread): > @Hervé Pagès^^ any comments?
Hervé Pagès (11:16:17) (in thread): > I guess I could export them. What’s been refraining me from doing so in the case ofreplaceSlotsis that we’ve always consideredBiocGenerics
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2021-01-31
Yue Cao (05:34:42): > @Yue Cao has joined the channel
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Aaron Lun (21:11:36) (in thread): > Eventually addedmumosa::multiModalMNN.
2021-02-01
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Mahmoud Ahmed (19:26:56): > Are there any Bioconductor packages that interact with BEL (biological expression language) or similar specifications?
2021-02-02
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2021-02-04
MARC SUBIRANA I GRANÉS (08:10:15): > @MARC SUBIRANA I GRANÉS has joined the channel
Leonardo Collado Torres (17:59:08): > Hi! Today at the joint TAB and CAB meeting we talked about sharing more success stories, which reminded me that I didn’t tell you that CDSB got a grant from Code from Science and Society (CS&S) for organizing a series of 2 hour mini-courses throughout the year + our summer 1 week-long workshops. Here’s the announcementhttps://comunidadbioinfo.github.io/post/cs_and_s_event_fund_award/#.YBx5EGRKgdk (also available in Spanish) > > This means that we have more support for teaching R/Bioc this year. Joselyn@Joselyn Chávez& Erick@Erick Cuevasare organizing the presenters for the mini-courses. For the summer, CDSB will lead 2 week-long workshops instead of 1. Joselyn & Erick will teach a workshop related to organizing your R code (github, RStudio projects, etc, maybe a primer on R package dev) while I’ll likely teach one on sc/snRNA-seq based on the OSCA book (+ some scientific applied talks would be nice). If you are interested in presenting a session on these courses (around 1.5 to 2 hrs) please let us know! We are aiming to have Spanish presenters this time, though we are always flexible. Once we have a more detailed proposed syllabus, I’ll share it with you. > > Bioconductor has supported us in different ways since we got started in 2018, which is partially why we had a body of previous work to show in our grant application. Thank you Bioc!!!@Alejandro ReyesShirley Alquicira, Alejandra Medina, Irma Martinez, Yalbi Balderas are also involved in this grant. - Attachment (CDSB): CS&S Event Fund award announcement | CDSB > We are delighted to announce that Code for Science and Society has selected our application for their first cohort of Event Fund grant recipients as announced on January 25, 2021. The CS&S Event Fund program is made possible through award number GBMF8449 from the Gordon and Betty Moore Foundation (https://doi.org/10.37807/GBMF8449 ). Thanks to this support, CDSB along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG) will be able to carry out a series of short courses throughout 2021 (including one event from December 2020) that will end with the National Bioinformatics Meeting 2021 that will be composed of 6 week-long courses.
2021-02-05
Aedin Culhane (02:31:19): > For any interested folks. The Rstudio conferences talks are online athttps://info.rstudio.com/UeMQ0rN0SX0NYT027C010lU
rohitsatyam102 (04:05:33) (in thread): > I was about to share that too:fiesta_parrot:. Thanks@Aedin Culhane
rohitsatyam102 (04:09:21) (in thread): > However, I was finding difficulty watching the workshop sessions that were held prior to the meet-up. Are they yet to uploaded?
Mikhail Dozmorov (10:41:54): > I encountered a strange bug withrtracklayer::liftOver. In R, it takes one region and lifts it into 21 regions! Using the UCSC genome browser and the command line tool with the identical liftover chain, that one region is correctly lifted into one region. I posted this on theBioC support site , but wonder if anyone ever noted such behavior? - File (PDF): liftover_test.pdf
Ludwig Geistlinger (12:08:08): > yep: see here:https://support.bioconductor.org/p/99306/
rohitsatyam102 (12:38:14) (in thread): > Yes sir. Even I started with rtracklayer and then that’s why shifted to liftover.exe and/or CrossMap.
rohitsatyam102 (12:39:34) (in thread): > I thankfully came across this wonderful link onBiostars when I was starting to learn liftover.
Mikhail Dozmorov (13:06:54) (in thread): > Thanks,@rohitsatyam102 . The link Ludwig posted explains the potential reason, but yes, for practical purposes, command line seems to be most reliable
Mikhail Dozmorov (13:08:28) (in thread): > Thanks,@Ludwig Geistlinger. I didn’t know that, and it sounds severe enough to clarify in the vignette.
Ludwig Geistlinger (16:08:06) (in thread): > I am with you on this one.
2021-02-06
saskia (22:16:34): > <!channel>We have updated theCode of Conduct to include more examples of bullying and intimidation. We have also changed the instructions to reporters of Code of Conduct violations to include screenshots or copies of the incidents whenever possible and without compromising their anonymity.
2021-02-08
Larry Cai (04:02:39): > @Larry Cai has joined the channel
Michael Love (07:56:49) (in thread): > the examples are very useful. I noticed a typo i think “deliberately inflammatoryof
Dario Righelli (15:00:40): > Hi all, does anyone knows to what this error could be related? > > > load_all() > Loading SpatialExperiment > ... > Error in add_classes_to_exports(ns = nsenv, package = package, exports = exports, : > object 'lev' not found > > we don’t have any export with this name in our NAMESPACE > It seems appeared from nowhere
Spencer Nystrom (15:11:05) (in thread): > if you grep your codebase forlevdo you get anything? even if not exported?
Dario Righelli (15:12:12) (in thread): > I tried, nothing
Spencer Nystrom (15:12:27) (in thread): > weeeeeird.
Dario Righelli (15:12:49) (in thread): > I got some “levels” though:joy:
Spencer Nystrom (15:13:00) (in thread): > Could it be in yourtest/folder?
Spencer Nystrom (15:13:29) (in thread): > Oh, maybe check those “levels” and see if they appear in Roxygen headers. Sometimes if things are out of order that can do weird things to your exports.
Dario Righelli (15:14:07) (in thread): > I’ll check it
Martin Morgan (16:33:31) (in thread): > > > pkgload:::add_classes_to_exports > function (ns, package, exports, nsInfo) > { > hasS4m <- .hasS4MetaData(ns) > if (.isMethodsDispatchOn() && hasS4m && !identical(package, > "methods")) { > if (lev > 1L || lev == -5) > message("-- processing S4 stuff for ", dQuote(package)) > > seems to uselevwithout defining, so a bug in pkgload…?
Martin Morgan (16:37:03) (in thread): > …except that pkgload has not been updated recently, with publication date 2020-05-29 …https://cran.r-project.org/web/packages/pkgload/index.html and > > > packageDescription("pkgload") > Package: pkgload > Title: Simulate Package Installation and Attach > Version: 1.1.0 > ... > Packaged: 2020-05-28 17:51:35 UTC; jhester > ... > Date/Publication: 2020-05-29 05:10:08 UTC > - Attachment (cran.r-project.org): pkgload: Simulate Package Installation and Attach > Simulates the process of installing a package and then attaching it. This is a key part of the ‘devtools’ package as it allows you to rapidly iterate while developing a package.
Martin Morgan (16:46:28) (in thread): > …ah but pkgload is being too clever and is importing something?? from base::loadNamespace athttps://github.com/r-lib/pkgload/blob/161ba01e1c02ddc462bb6780b7bec30a2c9cd369/R/namespace-env.r#L148 . I guess there is a recent commit > > R-devel/src/library/base/R$ svn log -c79912 > ------------------------------------------------------------------------ > r79912 | ripley | 2021-01-31 12:34:54 -0500 (Sun, 31 Jan 2021) | 1 line > > allow tracing of loadNamespace, show calls for missing namespace warnings > ------------------------------------------------------------------------ > > that is causing problems… > > I’ll report this tohttps://github.com/r-lib/pkgload/issues since it is getting pretty complicated!
2021-02-09
Dario Righelli (04:07:23) (in thread): > Thanks@Martin Morgan, I was discussing about it also with@Marcel Ramos Pérezand@Lukas Weberand we found that previous versions of R-devel worked! > broken version seems to be:R Under development (unstable) (2021-02-07 r79964) -- "Unsuffered Consequences"latest woking version in my hands is: > Thanks@Martin Morgan, we were discussing about it also with@Marcel Ramos Pérezand we found that previous version of R-devel worked! > broken version seems to be:R Under development (unstable) (2021-02-07 r79964) -- "Unsuffered Consequences"latest woking version in my hands is (which is the Bioconductor docker devel version):R Under development (unstable) (2021-01-07 r79806) -- "Unsuffered Consequences"
Martin Morgan (04:22:38) (in thread): > @Dario Righellithe work-around seems to be to install pkgload from githubBiocManager::install("r-lib/pkgload")
Dario Righelli (04:30:27) (in thread): > it worked! thanks again@Martin Morgan!!!
Lukas Weber (09:05:36) (in thread): > thanks@Martin Morgan!
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saskia (23:06:42) (in thread): > thank you mike
2021-02-10
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Vince Carey (12:05:46): > Here’s a question to pkgdown aficionados – have you noticed adverse interaction between mathjax-based math notation and plotly graphic usage in Rmd? There has been an issue raised and closed on pkgdown.
Federico Marini (12:15:07): > Yes!
Federico Marini (12:16:33): > Not really limited to pkgdown, actually. > A colleague of mine had a function generating a plotly plot, with some latex formulas to make it nice to read. Works nicely as standalone plot. > Plays nasty when trying to put the plotly thing into a vignette and render that, if the vignette has formulas as well.
Federico Marini (12:17:18): > For us it went down to the point that we removed the tex-part from the plotly function, because the issue was not solvable as they were suggesting
Federico Marini (12:19:01): > … also because this:https://github.com/ropensci/plotly/blob/master/inst/examples/rmd/MathJax/index.Rmd did not really work as expected in our hands
FelixErnst (15:53:24): > Just out of curiosity: Did someone figure out, whycrosstalk.min.js.mapwas not load/generated?
FelixErnst (16:13:21): > I am not sure about this, but the name suggest a play-nice-with-each-other function. From 5 min of debugging in a browser, I think that this breaks the javascript interpretation before the MathJax stuff is done. Removing the reference tocrosstalk.min.js.mapdoesn’t solve the problem, but I am not sure how engrained crosstalk is in plotly.@Vince Careydoes your browser complain in your scenario aboutcrosstalk.min.js.mapas well?
Vince Carey (16:26:36): > @FelixErnsti haven’t run into that.
FelixErnst (16:28:12): > It only appears as output in the debugging console of your browser
2021-02-11
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2021-02-12
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2021-02-13
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2021-02-14
FelixErnst (09:55:28): > Hi. Does anybody know of a R implementation of testing for overlapping rectangles using the separating axis theorem?
Aaron Lun (14:26:59): > there’s probably something insf.
Aaron Lun (14:27:14): > I remember seeing something to this extent when creatingfindOverlaps()equivalents for thier polygons.
Aaron Lun (14:27:34): > But if your rectangles are properly orientated, you could just do this yourslef with ease.
FelixErnst (15:44:35): > Thanks. I will take a look
FelixErnst (15:45:13): > They are not necessarily oriented correctly, so thats why I didn’t want to implement something again if it can be avoided
2021-02-15
Espen Riskedal (10:30:06): > What are recommended packages for doing pathway enrichment analysis given a set of CpG sites (for example from an EWAS or developing a classifier)? So far I’ve usedgometh from missMethyl - Attachment (rdocumentation.org): gometh function | R Documentation > Tests gene ontology enrichment for significant CpGs from Illumina’s Infinium HumanMethylation450 array, taking into account the differing number of probes per gene present on the array.
Vince Carey (11:18:19): > @Ludwig Geistlinger^^ ?
Ludwig Geistlinger (12:24:05): > This will largely depend on how you want to assign your CpG sites to nearby genes for which you then test for gene set / pathway enrichment along the usual lines. If you are thinking of doing that, then you might wanna checkout therGREATpackage. For more general genomic region enrichment analysis where you not necessarily map to nearby genes, you might wanna give theregioneRor theLOLApackage a look.
2021-02-16
Kasper D. Hansen (03:18:24): > It is also critical to account for the array design in that all genes do not have the same number of associated probes. That fact has been republished many times. I believe gometh deals with that.
Espen Riskedal (03:29:20): > Yes, gometh does deal with that, at least for 450k
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2021-02-17
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2021-02-18
Luke Zappia (08:04:57): > I have a question about the code of conduct (couldn’t see a more appropriate channel but happy to be redirected if there is one). Are there any guidelines about including it on GitHub repositories for individual packages? For example, I currently have a link to the Contributor Code of Conduct on a package README and was thinking about replacing this with a link to the Bioconductor CoC for consistency but wasn’t sure if this is appropriate/recommended?
Kasper D. Hansen (08:30:02): > This is a good point, but I am not sure it has been fully thought through. Would be nice with a standard approach which people can use and (perhaps) some debate about pros and cons, in case people don’t like it.
Federico Marini (10:43:44): > Could this be a specific item for@Leonardo Collado Torres’sBiocthis?usethishas theusethis::use_code_of_conduct(), so it could be a sensible addition to that
Luke Zappia (10:46:22) (in thread): > Actually adding it is easy (but automation would be nice I guess). The bigger question is whether the CoC is actually designed for this or not and I can see pros and cons either way.
Federico Marini (10:52:41) (in thread): > are you suggesting a package-focused version of the Bioc-CoC?
Levi Waldron (10:53:52): > Submit an abstract for a talk, digital poster, or Birds-of-a-feather session, or a syllabus for a software demo or long workshop at BioC2021 on Aug 4-6! The conference will most likely again be virtual this year.https://bioc2021.bioconductor.org/submissions/ - Attachment (bioc2021.bioconductor.org): Submissions > Submissions
Luke Zappia (10:54:22) (in thread): > I’m not suggesting anything, just wondering if this is something that was considered when it was designed.
Federico Marini (10:58:53) (in thread): > k:wink:would be an interesting addition indeed
Luke Zappia (11:00:36) (in thread): > So I see the main pro as consistency but I’m not sure whether Bioconductor would want to try and enforce it on a platform they don’t really have any control over.
Heather Turner (11:06:08) (in thread): > Not my playground, but I would say that package maintainers are responsible for enforcing CoC on their own package. The Python community have one of the broadest CoCs that I know of and they restrict it to “Code repositories, issue trackers, and pull requests made against any Python Software Foundation controlled GitHub organization” (https://www.python.org/psf/conduct/ ). - Attachment (Python.org): Python Community Code of Conduct > The official home of the Python Programming Language
Kasper D. Hansen (11:29:29) (in thread): > Of course this is the purview of package developers, but some general recommendations would be influential here.
Kasper D. Hansen (11:30:21) (in thread): > Im not saying that having a specific CoC ought to be a requirement at all, but from practice we know that a recommendation would probably be taken up by a large degree of the community
Heather Turner (15:38:58) (in thread): > That’s a fair point and it’s a good thing to encourage!
Federico Marini (16:00:22) (in thread): > Could this become an item for BiocCheck (NOTE-wise), or is it too stringent?
Kasper D. Hansen (16:13:41) (in thread): > As I say above, it is not clear to me that it makes sense torequire a package CoC
Federico Marini (16:31:41) (in thread): > Yes, I also meant that as a simple recommendation
saskia (20:30:28) (in thread): > Hmmm that is a good question I will discuss it with the CoC committee
2021-02-19
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2021-02-22
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saskia (23:13:23) (in thread): > I agree that this should be a recommendation at most.@Leonardo Collado Torresmight be able to include the current CoC in Biocthis (or someone could simply make a pull request). Also it was suggested from the CoC committee to link@Lori Shepherdinto this thread and see whether she thinks this amounts to something the package review panel wants to look at.
2021-02-23
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Leonardo Collado Torres (22:40:10) (in thread): > I’ll look into this next week. But yes, it’s very doable to include a function inbiocthisthat will help developers add a code of conduct in their packages that links to the BioC code of conduct.
saskia (23:58:57) (in thread): > Thanks Leo
2021-02-25
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2021-02-26
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2021-02-28
saskia (18:42:57): > The CoC committee received an anonymous complaint of an answer posted 1.5 years ago onsupport.bioconductor.org containing a malicious code snippet requiring only addition of a comma in order to recursively delete the user’s home directory that had the effect of mocking an inexperienced user. The post pre-datedBioconductor’s Code of Conduct but would be considered a violation of our current standards. We expect the Bioconductor community to maintain a welcoming and respectful environment for users of all experience levels, and ask that any instances of intimidation and bullying, or other Code of Conduct violations, be reported immediately via our email (code-of-conduct@bioconductor.org ) oranonymously . - Attachment (bioc.wufoo.com): Anonymous harassment complaint > Please use this form to report incidents of harassment at any Bioconductor-sponsored event or platform. It will automatically be forwarded to the Code of Conduct committee. Please include as much detail as you can, including time, location, and the names of any participants or witnesses to the event. You may include your name or remain anonymous.
saskia (18:46:40) (in thread): > I should add that the answer was deleted.
Lori Shepherd (18:48:39): > I will mention also we try to catch spam posts and malicious posts as moderators of the support site as quickly as possible to moderate, delete and ban users. Please report any violations on the support site to both the CoC committee andwebadmin@bioconductor.org so we can take immediate action.
saskia (18:49:28) (in thread): > Thank you@Lori Shepherd
2021-03-01
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2021-03-02
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Alexander Toenges (07:20:14): > @Mike SmithAs a suggestion for biomart, maybe in future versions when making a query it should return a message indicating the genome version that was used. > Now that GRCm39 is out and the default I guess many people will run into coordinate incompatibilities as they assume it was still GRCm38. > With a little message users will notice the mistake right away. > I ran into it myself recently as I missed that 39 is now default.
Lucy (07:24:46): > Thats a good idea!
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Stephanie Hicks (13:06:55): > https://chanzuckerberg.com/rfa/essential-open-source-software-for-science/ - Attachment (Chan Zuckerberg Initiative): Essential Open Source Software for Science - Chan Zuckerberg Initiative
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2021-03-03
Aedin Culhane (00:57:21): > We created a new channel#humble-bragfor announcements of “today I learnt”, your gists, talks, achievements, awards, funding awards and links to your blog, viral tweet, news articles on your institute (or even your mom’s) website, etc.In
2021-03-05
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Mike Morgan (13:21:31): > I have a conceptual question about edgeR; I’m not sure if this is quite the right place, but here goes: > I would like to know about some of the practicalities ofglmQLFTestwhen there is a global shift in the log fold-change distribution, such that it is no longer zero-centered. This arises as a consequence of a bias in data ascertainment, such that data are collected more from one condition than another. This isnot a case of gene expression, but the analogy would be if sequencing was performed consistently more on one condition over another (say 10X more), and library size normalisation is insufficient at handling this due to the 100% confounding with the experimental variable. > > Intuitively, I would expect that re-centering the log-fold change distribution would account for this, e.g. > > dge <- DGEList(counts, lib.size=log(colSums(counts))) > dge <- estimateDisp(dge, model) > > i.fit <- glmQLFit(dge, model, robust=TRUE) > n.coef <- ncol(i.model) > > i.est.coeff <- i.fit$coefficients[, n.coef, drop=FALSE] - median(i.fit$coefficients[, n.coef, drop=FALSE]) > > By replacing the relevant coefficients with the median-centered coefficients as in the code block above, we now have a zero-centered distribution of log fold changes. However, the significance testing in glmQLFTest does not seem to use these coefficients, and the subsequent results have very small p-values as if they are derived from the origin unshifted coefficients. What am I missing here, so that I can compute the correct test statistics and p-values?
Hervé Pagès (15:41:03) (in thread): > This is the type of question that is better asked on our support site:https://support.bioconductor.org TheedgeR
2021-03-06
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2021-03-08
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2021-03-10
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2021-03-11
USLACKBOT (08:45:56): > This message was deleted.
Lluís Revilla (08:52:13) (in thread): > Hi, I think this will be better answered onsupport.bioconductor.org as there are some questions and answers about how to do this. Perhaps I would clarify what do you mean with longitudinal comparison that it is not a pairwise comparison.
2021-03-12
Mike Morgan (07:59:03) (in thread): > Thanks Hervé - it was sort of a development question as we’re using edgeR under the hood for a package we’re developing. I’ll post it on the forum and see what comes back.
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2021-03-15
Life Science Alliance (06:25:28): > @Life Science Alliance has joined the channel
Life Science Alliance (06:29:45): > #jobsHi everyone, for prospective postdocs, there is are fellowships available for a joint EMBL - Stanford postdoc position. Applications close on June 6 2021 > > Postdoctoral Fellows – Bridging Excellence FellowshipMake your mark as a transatlantic scientist! EMBL | Stanford Life Science Alliance invites researchers to submit an application to the Bridging Excellence Postdoctoral Program. With a network of over 50 labs from across EMBL and Stanford University, we believe in working together to leverage the know-how, technologies and opportunities at both leading institutions to accelerate biological research. > Our Bridging Excellence Fellowships support ambitious and creative joint projects, defined by postdoctoral applicants. The fellowships provide funding for a 3-year EMBL stipend, lab consumables, a generous travel and accommodation supplement for visit(s) to Stanford, and funds for presenting at an international conference.Your role Eligibility our website for full eligibility criteria. - Attachment (med.stanford.edu): Life Science Alliance > The Stanford | EMBL Life Science Alliance is a non-profit cross-institutional research initiative dedicated to the advancement of science and technology development.
2021-03-16
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2021-03-17
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2021-03-18
Aedin Culhane (03:20:47): > Hi. Has anyone else had issues trying to use ggplot with both stat_ellipse and gghighlight? gghighight seems to create a new group, which override my intended group.@Dan Bunis
Helena L. Crowell (04:02:09) (in thread): > Not sure if this is what you need, but maybe this works? > > library(ggplot2) > library(gghighlight) > > ggplot(faithful, aes(waiting, eruptions)) + > geom_point() + > gghighlight(waiting > 50, use_group_by = FALSE) + > stat_ellipse( > data = faithful, inherit.aes = FALSE, > aes(waiting, eruptions, col = eruptions > 3)) > - File (PNG): image.png
Helena L. Crowell (04:07:23) (in thread): > Actually puttingcol = ...in the firstggplot(..., aes(...))also retains the point colors, but non-highlighted points are still grey.
Helena L. Crowell (04:48:14): > Quick question… I’m aware a version bump is required to trigger a new built. Now say I bump 1.1.0 -> 1.1.1 and there’s a build error. I then fix the bug and re-push. Will the daily builder try and rebuilt my package continuously until it succeeds, or does this require another version bump (which would lead to skipped versions from a user-perspective)?
Kasper D. Hansen (05:00:41): > As far as I know, it will re-try until it succeeds.
Kasper D. Hansen (05:01:53): > However, I also think that skipped versions from a user-perspective is kind of irrelevant. IMO you should increase versions every time you do something, including fixing a bug, but a user has no easy way of knowing what is in a version change. So I say, forget about this, and just bump versions aggressively
Kasper D. Hansen (05:04:30): > You can also say that if you have a version X that doesn’t work. You fix the issue and don’t bump the version. Do you then have two version X of the package - one that works and one that doesn’t? That is not true if your only interaction is through the built packages and binaries. But you can argue its true if you have the POV of someone interacting with the git repository.
Helena L. Crowell (05:09:25): > Thanks for your thoughts! I guess I’ll anyways see in a couple days if it rebuilt or not… I tend to agree and disagree: Yes, there shouldn’t be untraced changes under the same version. On the other hand, there are cases where everything works and the error is e.g. due to a dysfunctional roxygen link in the documentation, and I would like to not make a new version for this. Then again, you’re probably right and it doesn’t really matter to bump versions aggressively.
FelixErnst (06:43:30) (in thread): > Just a comment: I think the two branches for release and devel also offer the option for both types of approaches. On release I want to keep all version functional, whereas on devel I bump version more often.
Dan Bunis (12:59:59) (in thread): > I haven’t used gghighlight at all, so can’t add much here. Hopefully Helena’s code helps!
Aedin Culhane (17:08:00) (in thread): > Thanks@Helena L. CrowellHere are the plots on the same data in which I use stat_ellipse and scale_color_gradient (to color a gene) on PCA coordinates. But if I use gghighlight I see 2 issues, the gradient of color is dark (1) to light (4) and second the ellipses highlight the subset of cells in each group that express the gene. - File (PNG): image.png
Aedin Culhane (17:13:19) (in thread): > Your solution fixed the ellipse issue Thanks. I reorder the code so gghighlight first and later I call stat_ellipse with inherit.aes = FALSE. However I still need to fix the colors
Aedin Culhane (17:13:46) (in thread): > Thanks
2021-03-19
Helena L. Crowell (08:17:56) (in thread): > If you can tell me what you’d like to highlight and ellipse I’d be happy to give it a try if it’s not yet resolved
Aedin Culhane (14:15:33) (in thread): > Got it resolved. Thanks so much for your help
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2021-03-22
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2021-03-23
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2021-03-24
Jeroen Ooms (06:54:39): > Hi all! R-universe now supports bioconductor packages:https://r-universe.dev/ . This means that if you own a bioc package that is developed on Github, you can enable your universe by installing the R-universe Github-app on your Github account. Seehttps://r-universe.dev/help/
Jeroen Ooms (06:55:26): > Here is the full list of eligible Github users:https://github.com/r-universe-org/cran-to-git
Kasper D. Hansen (07:02:28): > @Jeroen OomsI read the pageshttps://ropensci.org/r-universe/ andhttps://r-universe.dev/help/ and I still don’t understand what this is and what advantage it delivers to me as a package developer.
Kasper D. Hansen (07:03:22): > I am pretty sure this is great and something I should check out, but I’m just giving you the feedback that I have read these pages and I have no clue what this is. Is it for searching packages? A build system? A CI tool for Github?
Jeroen Ooms (07:22:17): > A bit of everything:slightly_smiling_face:It’s still very early, but if you have 20 minutes, the linked talk at rstudio-conf explains a bit more about the sort of things we want to do. In a nutshell, it is mostly intended to let (potential) users easily browse and discover R packages/articles across ecosystems, get a view of development activity, the people behind the packages, etc. Later this year we want to add more metrics and indicators about the health, popularity and impact of packages.
Jan Stanstrup (10:19:17): > @Jan Stanstrup has joined the channel
Gonçalo Graça (12:18:20): > @Gonçalo Graça has joined the channel
Janani Ravi (14:47:31): > Hello everyone, > We (R-Ladies East Lansing and R-Ladies Chicago) are hosting our final Spring event,Fun with R Apr 23, 2021 https://forms.gle/jnQrYSnimLvehRuD9 :rladies:Event details:https://www.meetup.com/rladies-east-lansing/events/276152415/ DM me (@Janani Ravi) if you have any questions/speaker suggestions.
Peter Hickey (16:21:51) (in thread): > I’m in the same boat as Kasper.
Peter Hickey (16:22:29) (in thread): > More concretely, one of my initial reactions/concerns was “oh dear, another way for someone to install a BioC package that isn’t via the officially supportedBiocManager::install().BiocManager::install()handles BioC’s release cycle but it’s not uncommon as a developer to get reports of”your package doesn’t work” which ultimately boils down to the user having installed the package usingremotes::install_github()or some other mechanism that doesn’t respect or isn’t aware of the BioC release cycle.
Peter Hickey (16:26:47) (in thread): > I was also confused by the availability of packages onhttps://bioconductor.r-universe.dev/ui#builds . TakeDelayedArray https://bioconductor.org/packages/3.10/bioc/html/DelayedArray.html ). > And other key packages likeIRanges
Peter Hickey (16:29:18) (in thread): > I don’t mean this to sound negative,@Jeroen Ooms, and I hope this feedback is helpful
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2021-03-25
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2021-03-26
Jeroen Ooms (06:39:13) (in thread): > Thanks for your feedback, it makes sense. This is very much work in progress.
Jeroen Ooms (06:40:29) (in thread): > Indeed the system currently focuses on development of individual packages, without taking into account the release cycle of the entire bioconductor ecosystem.
Jeroen Ooms (06:41:11) (in thread): > My idea was that many bioconductor packages are also dependencies of CRAN packages, so it maybe useful to also build them for older versions of R
Kasper D. Hansen (07:01:23) (in thread): > Historically, Bioconductor has been pretty quick to take advantages of changes in R (and indeed has been the cause of such changes), so we don’t really expect current release to work with older versions.
Jeroen Ooms (07:39:12) (in thread): > Yes I see, I need to think a bit how we can make this work better for packages tied to a strict release cycle like bioc. But we plan to stop building for 3.6 very soon, so that should solve the immediate issue,
2021-03-30
Albert Kuo (11:54:47): > Has the schedule for the next Bioconductor 3.13 release been posted yet? The one I found on the website is for Bioconductor 3.12 (http://bioconductor.org/developers/release-schedule/ ), but I’m guessing the deadlines for 3.13 are coming soon?
Lori Shepherd (11:58:16): > We do not have a schedule yet for Bioconductor 3.13 release. We expect to have a schedule soon but are waiting on the announcement of the next R release.
Laurent Gatto (16:54:36): > Does anyone know of the licence of theSummarizedExperiment vignette figure ? Could it be re-used/adapted (with attribution), for example to illustrate aVarientExerimentuse case?@Martin Morgan- as a SE author, you might know.
Albert Kuo (16:59:47) (in thread): > OK thank you!
Alan O’C (17:00:18) (in thread): > The package license is Artistic-2.0https://www.bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html - Attachment (Bioconductor): SummarizedExperiment > The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Laurent Gatto (17:10:43) (in thread): > The Artistic licence is a software license, which, as far as I know, doesn’t necessarily include documentation such as vignettes, or is even applicable to such documents.
Martin Morgan (17:15:08) (in thread): > I don’t have insight, but if someone tells me what to do I’ll do it…; I’m actually not sure of the origins of the figure…
Vince Carey (18:14:21) (in thread): > I think Wolfgang might know…@Wolfgang Huber
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2021-03-31
Hervé Pagès (02:42:57) (in thread): > FWIW Jim Hester made that figure back in 2015 and added to the vignette. See:https://github.com/Bioconductor/SummarizedExperiment/commit/bb0a99dc9c7b7a0833f3140fde9231f9f8a3cc33
Laurent Gatto (05:46:25) (in thread): > Thank you, Hervé.
Geet (11:25:17): > Hi All, > I am trying to get the unmapped reads for paired end samples using hisat2 and command is : > hisat2
Alan O’C (11:28:44) (in thread): > What snakefile are you using
Alan O’C (11:29:05) (in thread): > Also probably better to look for support for stuff like this on biostars/support site
Laurent Gatto (11:30:52) (in thread): > Follow-up on twitter -https://twitter.com/lgatt0/status/1377196594236424197?s=20 - Attachment (twitter): Attachment > @jimhester_ https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html ). Are you ok with me re-using/adapting it to illustrate the VariantExperiment class. Will cite the SE package and give you credit for it.
Lisa Cao (12:49:09): > @Lisa Cao has joined the channel
Geet (12:56:55) (in thread): > Hi@Alan O’CI am using snakemake-5.17.0. Thank you, I’ll look on the support sites.
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2021-04-04
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2021-04-05
Sean Davis (11:22:09): > For job seekers and posters, note that we have a#jobschannel available for posting positions that are of interest to the Bioconductor community.
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2021-04-06
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2021-04-08
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Kozo Nishida (09:45:06): > (To this Slack workspace admin users) > Can I ask you to move#biocasia2021_private from public to private? > Since we will exchange financial information in the channel, I would like to ask it.
Marcel Ramos Pérez (10:20:01): > Hi Kozo Nishida! AFAIK, it is not possible to make a public channel private. I recommend using encrypted email.
Simina Boca (10:25:34): > It looks like it can be donehttps://slack.com/help/articles/213185467-Convert-a-channel-to-private - Attachment (Slack Help Center): Convert a channel to private > If a channel’s conversation is better suited for a closed audience, it can be converted to private. This type of channel is best for discussions that shouldn’t be open to everyone. Keep in mind On…
Simina Boca (10:25:54): > We converted another channel to private (to discuss conference decisions/scheduling)
Marcel Ramos Pérez (10:52:49): > Thanks for the info!
Kozo Nishida (11:12:19): > @Simina BocaThank you for the information!
Nicholas Cooley (11:25:02): > Does anyone have a good source or guide for running two versions of R side-by-side on Mac? I have an instance of my code blowing up the r-devel container and would like to test it outside the container in a more familiar environment.
Charlotte Soneson (11:26:14) (in thread): > https://rud.is/rswitch/ works nicely - Attachment (rud.is): RSwitch > A lightweight menubar utility for macOS R users
Alexander Toenges (11:26:55) (in thread): > You could create two different environments, e.g. via conda.
Lucy (12:00:55) (in thread): > RSwitch works nicely for me:slightly_smiling_face:
Hervé Pagès (12:22:43) (in thread): > Here is how this works. You can have as many versions of R as you want installed side-by-side on a Mac. They all get installed in/Library/Frameworks/R.framework/Versionsand a symlink is created to point to the last one you installed. The content of/Library/Frameworks/R.framework/Versionstypically looks like this: > > mymac:Versions me$ pwd > /Library/Frameworks/R.framework/Versions > mymac:Versions me$ ls -l > total 0 > drwxrwxr-x 6 root admin 192 Apr 7 12:22 4.0 > drwxrwxr-x 6 root admin 192 Dec 28 2020 4.1 > lrwxr-xr-x 1 root admin 3 Apr 7 12:22 Current -> 4.0 > > AFAIK all what RSwitch does is change that symlink to point to the selected version.
Kasper D. Hansen (12:42:35) (in thread): > I did what Herve points to, but have now switched to just installing into /usr/local/R/version
Kasper D. Hansen (12:43:13) (in thread): > Depends on whether you want the R to work with eg. Rstudio or just command line access
Nicholas Cooley (12:51:16) (in thread): > thanks that’s all super helpful!
Nicholas Cooley (12:52:13) (in thread): > just to make sure i understand, a symlink is always updated when you untar a new R version?
Hervé Pagès (12:58:55) (in thread): > A symlink is actually a file (a special one, it’s very small) and in that case it’s included in the tarball. When you extract a tarball into a folder, by default files in the tarball will replace files already present in the folder. Other files in the folder that are not present in the tarball are preserved. This applies to any file, including symlinks. This is just how extracting a tarball works in general.
Nicholas Cooley (13:00:19) (in thread): > great, that’s very helpful!
Kasper D. Hansen (13:26:21) (in thread): > changing symlink is not enough, or at least didn’t use to be enough, but it isalmost enough
Kasper D. Hansen (13:26:48) (in thread): > and its only pretty specific things which fails if all you do is changing the symlink
Dan Bunis (13:27:21) (in thread): > Depending on how you install different R versions, this may or may not be helpful. It also may be outdated cuz I used it a year ago now:shrug:, but I’d found that installing a new R version actually broke my other versions even for RSwitch until I ran the code chunk in the middle of thishttps://jacobrprice.github.io/2019/09/19/Installing-multiple-parallel-R-versions.html before each new version install.
Hervé Pagès (14:56:58) (in thread): > @Kasper D. HansenChanging the symlink inR.framework/Versionsworks as intended. The special design/layout of the R.framework makes this possible. Has always worked fine for me. All this is if you stick to using the official R-*.pkg distributions available on CRAN or athttps://mac.r-project.org/ of course.
Hervé Pagès (15:06:11) (in thread): > Although when I tried this it was on the Mac builders many years ago and I was running R in a terminal. No GUI, no RStudio.
Nicholas Cooley (15:06:54) (in thread): > As long as the symlink changes correctly for the R and Rscript terminal commands that will be more than fine.
Kasper D. Hansen (15:15:05) (in thread): > It could well be that it was because I compiled R myself. It was also a pretty arcane; a path was contained inside a text script. I used it for years before discovering I needed to do more than symlink.
Kary Oetjen (15:45:20) (in thread): > I use docker to run rocker containers of other R versions when I need to troubleshoot
Marcel Ramos Pérez (16:27:13) (in thread): > Perhaps the BiocManager vignette can provide some help using aliases (with native installations):https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#multiple-versions bioconductor/bioconductor_dockeris also a good option.
Hervé Pagès (16:39:19) (in thread): > Looks like in his original post@Nicholas Cooleymentioned that he tried to troubleshoot using the r-devel container already but that he wanted to try to troubleshoot in a more familiar environment.
Nicholas Knoblauch (21:39:25) (in thread): > This might be overkill but I’m a really big fan of spack:https://spack.readthedocs.io/en/latest/
2021-04-09
António Domingues (08:16:20): > Any recommendations for a shiny app to look at gene expression, say select one or a few genes and plot their expression in different samples of a dataset (boxplot)? Ideally group (color) the samples by covariates. Nice to have: input is a DESeq2 object. I know of ideal (cc’@Federico Marini) but it seems too feature rich for this simple use case:slightly_smiling_face:
António Domingues (08:17:12) (in thread): > Of course I can always develop my own solution, but this is one those things I would have thought a better coder has done before
Alan O’C (08:18:01) (in thread): > https://twitter.com/jokergoo_gu/status/1373638176250675200 - Attachment (twitter): Attachment > Didn’t expect it gets so popular:stuck_out_tongue_winking_eye:. Today I added a new func interactivate() which can be directly applied to the DESeq2 object to generate this app: > > library(DESeq2) > library(airway) > data(airway) > > dds = DESeqDataSet(airway, design = ~ dex) > dds = DESeq(dds) > > interactivate(dds) https://twitter.com/jokergoo_gu/status/1373013068821725189 - Attachment (twitter): Attachment > Wrote an article on how to implement interactive heatmap for visualizing DESeq2 results :rocket::rocket: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/deseq2_app.html > > If you want to try, please install the newest version from GitHub.
António Domingues (08:32:57) (in thread): > Cheers| I have seen this on twitter but because I was thinking of boxplots + dotplots it didn’t come to mind. I will explore it.
Charlotte Soneson (09:04:47) (in thread): > You could also feed yourDESeqDataSetobject directly toiSEE():slightly_smiling_face:
António Domingues (09:05:39) (in thread): > oh nice! iSEE is always on my radar but I keep think that it’s too advanced for what I do:slightly_smiling_face:
Alan O’C (09:12:47) (in thread): > I imagined iSEE would do the job but wasn’t sure so didn’t want to oversell
Charlotte Soneson (09:25:12) (in thread): > I tend to actually convert theDESeqDataSetto aSingleCellExperimentobject so that I can store/display the PCA as well…apart from that, making sure that you have a suitable assay for the violin plots and optionally appending the result table to therowDatatypically does the job.iSEEuadditionally has some panels for MA plots and volcano plots if you want to add those.
Kevin Rue-Albrecht (09:34:19) (in thread): > > oh nice! iSEE is always on my radar but I keep think that it’s too advanced for what I do:slightly_smiling_face: > There was i time I would have been proud to write a package that appears “too advanced”, but this makes me wonder whether we’re somehow selling too much iSEE’s advanced features:sweat_smile:In essence,iSEE(object)is all you need to start toying with all of the built-in panels. > Beyond that, it’s all about pre-configuring the initial state of the app when it launched, e.g. selecting a subset of panels to display:slightly_smiling_face:
Federico Marini (10:27:49) (in thread): > Note to ourselves#isee’ers - Would it make sense to add a small vignette demonstrating this use case? I think it can gain a lot of traction, given the number of people usingDESeq2. Plus, we can do some kind of bridging over from limma/edgeR, if the dependency burden does not become too much. > We can take it to the channel and see more from there, it is indeed something that I have been doing already a couple of time out-of-package
Tiago C. Silva (10:28:01) (in thread): > We worked with a student on a shinny app to use DESeq2 and visualize the results some years ago. The input is raw counts.https://junkdnalab.shinyapps.io/GENAVi/ https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6073-7 - Attachment (BMC Genomics): GENAVi: a shiny web application for gene expression normalization, analysis and visualization > Background The development of next generation sequencing (NGS) methods led to a rapid rise in the generation of large genomic datasets, but the development of user-friendly tools to analyze and visualize these datasets has not developed at the same pace. This presents a two-fold challenge to biologists; the expertise to select an appropriate data analysis pipeline, and the need for bioinformatics or programming skills to apply this pipeline. The development of graphical user interface (GUI) applications hosted on web-based servers such as Shiny can make complex workflows accessible across operating systems and internet browsers to those without programming knowledge. Results We have developed GENAVi (Gene Expression Normalization Analysis and Visualization) to provide a user-friendly interface for normalization and differential expression analysis (DEA) of human or mouse feature count level RNA-Seq data. GENAVi is a GUI based tool that combines Bioconductor packages in a format for scientists without bioinformatics expertise. We provide a panel of 20 cell lines commonly used for the study of breast and ovarian cancer within GENAVi as a foundation for users to bring their own data to the application. Users can visualize expression across samples, cluster samples based on gene expression or correlation, calculate and plot the results of principal components analysis, perform DEA and gene set enrichment and produce plots for each of these analyses. To allow scalability for large datasets we have provided local install via three methods. We improve on available tools by offering a range of normalization methods and a simple to use interface that provides clear and complete session reporting and for reproducible analysis. Conclusion The development of tools using a GUI makes them practical and accessible to scientists without bioinformatics expertise, or access to a data analyst with relevant skills. While several GUI based tools are currently available for RNA-Seq analysis we improve on these existing tools. This user-friendly application provides a convenient platform for the normalization, analysis and visualization of gene expression data for scientists without bioinformatics expertise.
António Domingues (11:20:00) (in thread): > Thanks a lot for your suggestions! I will do a tour of all of those before choosing one. This is not for me to use, but biologists, so I will have to choose something isjust
Aaron Lun (11:28:00) (in thread): > note iSEEu also provides anMAPlotandVolcanoPlotoff the shelf.
António Domingues (11:38:22) (in thread): > Noice!
2021-04-11
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2021-04-12
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2021-04-13
Martin Morgan (09:02:47): > Thishttps://anvilproject.org/news/2021/04/12/announcing-anvil-cloud-cost-credits-program could be a great way to get into cloud computing for large-scale analysis, both workflows and interactive / R / Bioconductor. There’s a training component too so an excellent way to introduce students to the future… - Attachment (The AnVIL): Announcing the AnVIL Cloud Credits Program (AC2) > NHGRI’s Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) cloud genomics platform is pleased to announce the availability of the AnVIL Cloud Credits Program (AC2).
Lori Shepherd (09:29:54): > Registration for Bioc2021 is now Open!! Please see theConference Website for more information. - Attachment (bioc2021.bioconductor.org): Registration > Registration
Mariela (09:40:17): > Hi all, I am trying to install some packages for Bioconductor that require the latest version. The cluster on my institution runs several versions of R, the one I use the most is 3.6 and I have installed in my personal path (I don’t have admin permissions) Bioconductor v3.9. However, now that I want to use R 4.0.0 because of the packages that only run in BioC 3.12, I don’t want to update the BioC 3.12 globally. Is there any way to have another version of BioC given that I have not permissions to change the original installation?
Lori Shepherd (09:59:53): > Nominations for Bioconductor 2021 Awards now Open. SeeAwards Page for more details or fill out thisnomination form ! Deadline for nomination is May 31, 2021. - Attachment (Google Docs): Bioconductor Awards 2021 > Nomination form for the Bioconductor Awards (see https://bioconductor.org/about/awards/ for more details). Please fill out all the fields in the following sections. In the Nominator section, please provide your own contact information in case we need to contact you with any question. In the Nominee section, please indicate how the nominee provides outstanding contributions for each of the selected nomination criteria. Four awards will be given using the selected criteria as justification.
Marcel Ramos Pérez (10:33:24) (in thread): > Hi Mariela, Bioconductor versions are tied to specific R versions and one recourse is to have admin install R > 4.0 on the cluster. You may also be able to install R on your account without admin privileges but this might be a bit more difficult to manage. See this vignette for managing multiple versions of R and Biochttps://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#multiple-versions
Martin Morgan (10:52:01) (in thread): > Another possibility is to use singularity (Docker requires permissions that are prohibitive on a cluster) to run the Bioconductor docker image; docker instructions including a section on using singularity are athttps://bioconductor.org/help/docker
Dario Strbenac (17:00:09) (in thread): > Definitely ask them to get with the times. > > $ module avail R > -------- /apps/Modules/modulefiles -------- > R/3.6.1 R/4.0.0 >
Martin Morgan (17:22:09) (in thread): > R 4.0.5 was released a couple of weeks ago and represents the culmination of the 4.0 release cycle — it would be a perfect candidate for ‘long term’ support.
2021-04-14
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2021-04-15
Mike Smith (05:41:27): > Just wanted to share that we’ll be discussing the upcoming release schedule in the Developers’ Forum later today. Come along if you have any questions about how the release process works. - Attachment: Attachment > The next Bioconductor Developers’ Forum is this Thursday 15th April at 09:00 PST / 12:00 EST / 18:00 CEST - You can find a calendar invite attached and at https://tinyurl.com/BiocDevel-2021-04 > > • As we’re fast approaching the release of Bioconductor 3.13 we’ll use this meeting to go over the current release schedule, and give some reminders of the things package developers might need to be aware of. If you’re relatively new to supporting a Bioconductor package (or just want a refresher!) this is a great chance to ask any questions you may have to members of the core team that manage the version transition. If you’ve got questions about version numbering :1234:, deprecation cycles :recycle:, or the last day you can make a change :hourglass_flowing_sand:this is the opportunity to ask! > • @Lori Shepherd will also present some proposed major changes to BiocFileCache and how those might affect packages you’re maintaining or using. > • If anyone else has another topic they’d like to discuss or present, please let me know.
António Domingues (15:40:49) (in thread): > Hi@Mariela, if I understood your questions correctly, one workaround I found is to use conda environments - assuming that option is available in the cluster. Create one for any given R version and install packages as usual. These will be place in a separate Rlib for each environment.
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2021-04-19
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Aedin Culhane (12:24:20): > Please tweet, email and tell all your colleagues on zoom about the Bioconductor community awardshttps://bioconductor.org/about/awards/ . Nominations are open. Please nominate yourself or others in the community
2021-04-21
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2021-04-23
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2021-04-27
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Mahmoud Ahmed (19:58:35): > A package I am working on wraps a java program to capture and explore the output in R. I included the.jarfile in the package and wrote a function to call it usingsystem2. The file size is large, so the package fails Bioconductor checks (the 5MB limit). What do you recommend I do? I thought of including instructions to download the file and specify the path in the wrapper function, but this makes testing and writing examples complicated. It also increases the time it takes to check the package and makes it dependent on the internet connection.
Hervé Pagès (20:43:18): > I think I remember seeing some package contributors putting the.jarfile in a separate data-experiment package to work around the 5MB limit. Personally I don’t really like this because this solution is obviously not driven by good software design considerations, it’s only a hack to bypass the 5MB limit. How big is the package source tarball with the.jarin it? If it’s only a few MB above the 5MB limit, say no more than 10MB, you could try to convince your reviewer to make an exception. Otherwise, you could put the.jarin a separatesoftware .jarwill be bigger but also typically very stable so people won’t have to re-download/re-install it often), (2) the.jaris software, not data, so having it wrapped in a software package is the right thing to do, and this will make it more likely to be reused by another software package than if it’s hidden in a data-experiment package.
Mahmoud Ahmed (21:12:30): > Thanks@Hervé Pagèsthis is very helpful. The.jarfile itself is about 4MB, and since I need to include other data files (genome annotation in a custom format, and sample input data) the package size is much bigger. > So if I go with your suggestion, > I would need to submit another software package with the.jarand a data package with the data file?
Hervé Pagès (21:17:30): > It depends. The worst case scenario is a split in 3 parts but maybe you can do 2 parts only if after moving the data to their own package you end up with a software package that has a “reasonable” size (i.e. < 5MB or close to that). Note that you need to look at the size of thepackage source tarballs .jarin one of them doesn’t necessarily translate into a 4MB increase in its size.
Mahmoud Ahmed (21:22:04): > Okay. I will try splitting into two pieces first. I am thinking, the data files should be added ininst/extdata. What if I also need to make a separate package for the.jar, should it be treated as a data file or is it different in the case a software package?
Hervé Pagès (21:33:05): > Note that we don’t like data-experiment packages that are too big either i.e. if its size is going to be more than 15MB or 20MB (can’t remember the exact limit) we usually ask people to put the data files on ExperimentHub and to make a light data-experiment package associated with these files. > I don’t think that we have specific guidelines for where to put the.jarin a software package. This is not data so I wouldn’t put it ininst/extdata/. Maybe put it directly ininst/? Please check the “Writing R Extensions” manual for that. This is the primary reference for this type of question. Maybe they provide some guidance about where to put things like a.jarfile. Alternatively maybe therJava
Mahmoud Ahmed (21:50:25): > Okay. I will check the manual. Is there guidelines on how to submit more than one package simultaneously, especially that one would depend on the others? For example do the dependencies have to be accepted first?
Peter Hickey (21:54:00) (in thread): > https://github.com/Bioconductor/Contributions#submitting-related-packages
Mahmoud Ahmed (21:58:03) (in thread): > Great. Thanks@Peter Hickey
2021-04-28
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Mike Smith (08:02:14) (in thread): > You can use any name you like for folders underinstand that folder name will be preserved and copied when the package is installed. It seems to be quite common for packages to put a.jarunderinst/javabut I don’t think there’s a hard and fast rule. There’s some examples athttps://code.bioconductor.org/search/search?q=f%3Ajar
Mike Smith (08:25:30): > I’m excited to announce a new addition to the Bioconductor online presence:https://code.bioconductor.org The site currently provides two things: > 1. Tools to browse the contents and git history of all current Bioconductor software packages. > 2. Functionality to search for words or phrases across all software packages at once, and to filter results by file names, types, or packages. > A big thank you to everyone who’s helped make this project happen. In particular the EMBL IT-services team for providing and supporting the hosting environment, and@Martin Morganfor managing the domain. > > Hopefully these are useful tools to the community and I’d appreciate any feedback to make sure that’s the case. - Attachment (code.bioconductor.org): Bioconductor Code > Search and browse the source code of Bioconductor packages.
Mike Smith (08:26:38) (in thread): > There’s some more details on the current implementation athttps://code.bioconductor.org/about.html If you find problems, please create an issue onGitHub so I can keep track of them.
Frederick Tan (09:03:15) (in thread): > Looks great! Are there other features being considered e.g. links to notable/curatedsupport.bioconductor.org posts?
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Michael Lawrence (13:06:40) (in thread): > Would be cool to make the search more semantic around code structures, like classes and methods.
Hervé Pagès (17:19:05): > <!channel>Hi all, we’ve created a new channel#package-submissionfor all questions regarding the submission process, including questions about the output of the reports generated by the SPB (Single Package Builder). You’re welcome to join, whether you’re in the process of submitting a new package, or planning to contribute one, or just willing to help others with the process. See you there. Thanks! H.
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2021-04-29
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Aedin Culhane (13:07:30): > We have created a new channel#biocwebsiteto discuss redevelopment of the Bioconductor website. What do you need from the website? What are the best/worst aspects of the current site? We are putting in a funding application to redesign it and want community input. Is there a website you love that would form a good template for Bioconductor website redesign?
2021-04-30
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2021-05-01
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2021-05-04
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2021-05-05
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2021-05-06
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Chris Fields (12:21:07): > Hi everyone! H3ABioNet, the bioinformatics support network for the Human Heredity and Health in Africa (H3Africa) initiative, is looking for volunteers to help with reviews on node accreditation work. In particular, we are looking for anyone with expertise or background in: > > * Human variant calling analysis > * Genome-wide association studies > * Gene expression using RNA-Seq > * 16S rRNA microbiome analysis > > It’s a great opportunity to help with developing open science infrastructure and efforts all across Africa. If you are interested we have a simple sign-up form:https://forms.gle/RhnfstHbKPJCo4EK7 If you have any questions feel free to reach out to me here on Slack, via email atcjfields@illinois.edu , or viaTwitter Links:H3ABioNet H3Africa - Attachment (Google Docs): Node Accreditation Reviewer Sign Up > H3ABioNet (h3abionet.org ), the bioinformatics support network for the Human Heredity and Health in Africa (H3Africa) initiative (h3africa.org ), is looking for reviewers with expertise or background in: * Human variant calling analysis * Genome-wide association studies * Gene expression using RNA-Seq * 16S rRNA microbiome analysis Reviewers will assess network research nodes who undertake a six-week accreditation exercise performing one of the above common bioinformatics tasks following basic standard operating procedures (h3abionet.github.io/H3ABionet-SOPs/index.html ). A final report is generated by the node that details the step-by-step process used for the analysis, along with relevant code and results. Reviewers would review the final report to evaluate the Node’s ability to process, analyze, and interpret these data using the reviewer guide (h3abionet.github.io/H3ABionet-SOPs/reviewers.html ). - Attachment (twitter.com): Chris Fields (@cjfields ) | Twitter > The latest Tweets from Chris Fields (@cjfields ). Director: @HPCBio . Practitioner: open-source/open-science (@OBF_News ) Genomics: #metagenomics #microbiome #BlackLivesMatter Moar Coffee!. In some corn field, Urbana, IL - Attachment (H3ABioNet - Pan African Bioinformatics Network for the Human Heredity and Health in Africa): Home > H3aBioNet website - Attachment (H3Africa): H3Africa | Human Heredity & Health in Africa | Human Genomic Research > H3Africa empowers African researchers in genomic sciences. It generates unique data that can be used to improve African and indeed global health!
Krithika Bhuvanesh (13:54:34) (in thread): > It seems to similar to a peer review for a journal article ? Is my understanding correct ?
Chris Fields (13:57:15) (in thread): > Somewhat, but the focus is more on data preparation and analysis.
Krithika Bhuvanesh (14:08:19) (in thread): > okay thanks
Chris Fields (15:32:29) (in thread): > @Krithika Bhuvaneshlet me know if you need more details, happy to discuss via PM if needed
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2021-05-07
Charlotte Soneson (04:54:13): > Nominations for joining theBioconductor Technical Advisory Board are now open. Nominate yourself or someone else (please first confirm that they are interested), by completing thisshort form . Nominations close on May 31, at midnight in a time zone of your choice. > If you have questions, feel free to ask them in the#tech-advisory-boardchannel. Please help spread the word!
2021-05-08
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2021-05-09
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2021-05-10
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2021-05-11
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2021-05-12
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2021-05-13
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2021-05-15
Janani Ravi (14:45:37): > Hello all, I thought many of you might be interested in this really cool conference. It will be great if you can share it with your units. Please feel free to DM me if you have any questions!useR! 2021 is here Attachment > :loud_sound: After a 24h maintenance break, registrations are open again! > > :calendar: We have extended the Early Bird Deadline until May 28th. > > Don’t miss this chance and register now! :point_down: > > :pushpin:https://user2021.r-project.org/participation/registration/
Dipanjan Dey (15:24:27): > Hi@Janani Ravi, can people who are currently not affiliated to any university register for the conference?
Janani Ravi (15:49:04) (in thread): > Absolutely! Yes, they can – anyone and everyone is free to register!
Dipanjan Dey (16:30:13) (in thread): > Thanks
2021-05-17
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2021-05-18
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2021-05-19
António Domingues (07:51:08): > Hi@Leonardo Collado Torres, quick questions aboutrecount2: 1, are there plans to regularly update the datasets that have been processed as more data comes into SRA? And 2, is there bulk download (of counts tables + metadata) from anywhere? Cheers.
Frederick Tan (08:07:57) (in thread): > Leo can definitely answer better, but in the meantime note recount3http://rna.recount.bio
Kasper D. Hansen (08:10:29): > We’re about to release the preprint of recount3 which will superseede recount2 and have tons more data.
Kasper D. Hansen (08:11:03): > However, the expression values are different in recount3, so if you have (say) trained models on recount2 you will need to retrain on recount3.
Kasper D. Hansen (08:11:47): > As@Frederick Tansays, you can access recount3 right now. You just have to wait a week (perhaps less) for the preprint
António Domingues (08:29:09) (in thread): > Nice. Thanks.
António Domingues (08:30:11) (in thread): > That’s good news. This would be my first foray into recount, so no I am worried about inconsistency with recount2.
António Domingues (08:30:58) (in thread): > I am more interested in having a fairly large and comprehensive dataset for exploration.
António Domingues (08:32:31) (in thread): > So I guess you will be mining SRA on a semi regular basis for new datasets?
Kasper D. Hansen (11:40:18) (in thread): > Yes. Our new pipeline should make this significantly easier than recount2 (where it turned out to be too much work). I would hope updates every 6mo, but that may be optimistic.
António Domingues (12:21:02) (in thread): > That is impressive! Cheers.
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Leonardo Collado Torres (19:09:25): > Thanks@Frederick Tanand Kasper! I think that they both answered your question@António Domingues:smiley:
2021-05-20
FelixErnst (04:26:59): > Is anybody in contact with Cristobal Fresno at INMEGEN in Mexico City?RDAVIDWebServiceis/will be deprecated and I had no luck getting in touch. He is still publishing, so I am not sure, whether he is aware of this development or not.
Guido Barzaghi (07:45:11): > @Guido Barzaghi has joined the channel
Federico Marini (12:16:01) (in thread): > I’m quite sure@Lori Shepherddid reach out already a couple of times when she regularly checks the in-progress list for the candidates to deprecation. > Probably a somewhat older/not often checked maintainer email?
Lori Shepherd (12:17:59) (in thread): > Yes I reached out several times before deprecating. and encouraged the few packages that depended on RDAVIDWebService to do the same. It might be a bad/outdated email
FelixErnst (13:23:39) (in thread): > I tried that as well
FelixErnst (13:24:28) (in thread): > But he is publishing so my guess would be a case of “old institute mail address”
FelixErnst (13:25:20) (in thread): > Maybe someone from INMEGEN is here or somebody knows someone at INMEGEN?
FelixErnst (13:25:34) (in thread): > Offline contact might be the solution:slightly_smiling_face:
Lori Shepherd (15:29:50): > Bioconductor 3.13 is Released!! Thank you to all developers and community members for contributing to the project. See fullrelease announcement
2021-05-22
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2021-05-23
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2021-05-24
Lori Shepherd (12:51:48): > <!channel>The deadline for nominating someone (or self nomination) for a Bioconductor annual award is one week away, May 31, 2021! Please see theawards page for full list of criteria. Use the followingnomination form to submit your candidates. Cheers! - Attachment (Google Docs): Bioconductor Awards 2021 > Nomination form for the Bioconductor Awards (see https://bioconductor.org/about/awards/ for more details). Please fill out all the fields in the following sections. In the Nominator section, please provide your own contact information in case we need to contact you with any question. In the Nominee section, please indicate how the nominee provides outstanding contributions for each of the selected nomination criteria. Four awards will be given using the selected criteria as justification.
2021-05-25
Charlotte Soneson (04:46:07): > Also nominations for the Bioconductor Technical Advisory Board close on Monday, May 31Attachment > Nominations for joining the Bioconductor Technical Advisory Board are now open. Nominate yourself or someone else (please first confirm that they are interested), by completing this short form . Nominations close on May 31, at midnight in a time zone of your choice. > If you have questions, feel free to ask them in the #tech-advisory-board channel. Please help spread the word!
Quang Nguyen (12:17:59): > @Quang Nguyen has joined the channel
2021-05-26
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2021-05-27
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Mike Smith (06:54:50): > A reminder that we’ll be discussing some of the changes in R-4.1 later today in the Developers Forum. Anyone interested is welcome to join. - Attachment: Attachment > The next Bioconductor Developers’ Forum is this Thursday 27th May at 09:00 PST / 12:00 EST / 18:00 CEST - You can find a calendar invite attached and at https://tinyurl.com/BiocDevel-2021-05 > > I thought it might be fun to go through some of the changes introduced in R-4.1 together, with different people highlighting the change they’re most interested in or affected by. > > The full list of changes in this version can be found at: https://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html > > If you’d be willing to talk for between 1 and 5 minutes on anything introduced in R-4.1 please reply here so we don’t all pick the same topic. I think @Martin Morgan has already selected the native pipe - thanks Martin!
Aedin Culhane (13:12:50): > Do you need better support for multiple languages from core Bioconductor packages such as BiocManager? Do you wish to contribute to translation and language support in Bioconductor. Join the discussion on the#community-advisory-boardchannel
Aedin Culhane (13:13:16) (in thread): > Excellent excellent session. I learned lots.. Thank you
Peter Hickey (22:55:05): > anyone had trouble/success installingRhdf5lib https://github.com/grimbough/Rhdf5lib/issues/40
2021-05-28
Robert Castelo (03:17:06) (in thread): > hi Peter, i have a CentOS7 box and have no trouble installing and loading Rhdf5lib. I’m attaching the output of the installation in case it helps you identifying the problem. > > > library(Rhdf5lib) > > sessionInfo() > R version 4.1.0 (2021-05-18) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: CentOS Linux 7 (Core) > > Matrix products: default > BLAS: /projects_fg/soft/R/R-4.1.0/lib64/R/lib/libRblas.so > LAPACK: /projects_fg/soft/R/R-4.1.0/lib64/R/lib/libRlapack.so > > locale: > [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8 > [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8 > [7] LC_PAPER=en_US.UTF8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Rhdf5lib_1.14.0 colorout_1.2-2 > > loaded via a namespace (and not attached): > [1] compiler_4.1.0 > - File (Plain Text): Rhdf5lib.txt
Pablo Rodriguez (03:40:00) (in thread): > I’ve also work on CentOS 7 and have no problem installing it. > What is the output ofrhdf5::H5get_libversion()in your session? > > Mine is:> rhdf5::H5get_libversion()``majnum minnum relnum `` 1 10 7
Peter Hickey (04:33:14) (in thread): > Thanks both. It seems to be something to do with the R being installed with link time optimisation (LTO), as Mike noticed.
Sharanya Manoharan (06:29:35): > @Sharanya Manoharan has joined the channel
Mike Smith (08:56:20) (in thread): > Thanks for the replies. We’re tracking this athttps://github.com/grimbough/Rhdf5lib/issues/40 for now.
Lori Shepherd (14:32:53): > Deadline for nominating someone for a Bioc2021 award is this weekend! May 31st. See more information athttp://bioconductor.org/about/awards/ . The nomination form can be found athttps://forms.gle/d9PyAjAw62yVKxjL8 - Attachment (Google Docs): Bioconductor Awards 2021 > Nomination form for the Bioconductor Awards (see https://bioconductor.org/about/awards/ for more details). Please fill out all the fields in the following sections. In the Nominator section, please provide your own contact information in case we need to contact you with any question. In the Nominee section, please indicate how the nominee provides outstanding contributions for each of the selected nomination criteria. Four awards will be given using the selected criteria as justification.
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2021-05-29
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2021-05-30
Wes W (11:24:52) (in thread): > I have had troubles recently (only like in the last month) with Ubuntu 20.01 LTS
2021-06-01
Aaron Lun (13:00:59): > @Mike Smithare some of the biomaRt endpoints busted?
Aaron Lun (13:01:07): > e.g. > > out <- biomaRt::useMart("ensembl", host = "[https://aug2017.archive.ensembl.org](https://aug2017.archive.ensembl.org)", dataset = paste0("hsapiens_gene_ensembl")) > ## Error: Unexpected format to the list of available marts. > ## Please check the following URL manually, and try ?listMarts for advice. > ##[https://aug2017.archive.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt](https://aug2017.archive.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt) >
Gurpreet Kaur (13:08:05): > @Gurpreet Kaur has joined the channel
Mike Smith (13:44:31) (in thread): > That doesn’t look great! AFAIK there was some server outage that took everything on the mainwww.ensembl.org site out from Friday. The site came back this morning, but in a limited form. I guess the archives are one of things still out of action. - File (PNG): Screenshot_20210601-193944.png
Hervé Pagès (16:24:20) (in thread): > Can we vote the Ensembl BioMart the most unreliable Bioinformatics service ever? (After BBS of course:sweat_smile:.) I wonder if the Ensembl Rest API couldn’t be used as a replacement. Has someone started to experiment with it?
Mike Smith (17:32:45) (in thread): > This wasn’t just BioMart, it was all Ensembl services. So VEP, REST API, etc were all out of action. However a REST API package has been on my to-do list for about 3 years. I got as far as sharing some prototypes in a code-review at some point, but it’s not made it to the top of the list.
Hervé Pagès (18:29:32) (in thread): > Okthis time it wasn’t just BioMart, I was unfair. Maybe I’ve become a little bit biased after so many years of dysfunctioning Ensembl BioMart.
2021-06-03
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2021-06-04
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2021-06-08
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2021-06-09
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2021-06-10
Jenny Drnevich (17:36:09): > I am interested in switching to the native R pipe|>but realize I already have%>%hardwired into my brain!
Haichao Wang (17:57:43): > I read somewhere before|>is not totally the same with%>%
Haichao Wang (17:58:43): > but forgot where I read that!
Mikhail Dozmorov (18:08:28): > https://twitter.com/AedinCulhane/status/1398007351387508736?s=20 - Attachment (twitter): Attachment > |> or %>% > > help(“|>”) for help > |> no need to library magrittr or dplyr > |> may be quicker to type or easier to read > |> requires () after functions df |> nrow() > |> do not accept . arguments after 1st > > @grimbough https://hackmd.io/Fm8OhgvxTyKTWm1xTLN1-g?view#New-Syntax > > #RStats > @Bioconductor
Alan O’C (18:13:22): > > library(magrittr) > mtcars %>% lm(mpg~cyl, data=.) > #> > #> Call: > #> lm(formula = mpg ~ cyl, data = .) > #> > #> Coefficients: > #> (Intercept) cyl > #> 37.885 -2.876 > mtcars |> lm(mpg~cyl, data=.) > #> Error in is.data.frame(data): object '.' not found > mtcars |> (\(x) lm(mpg ~ cyl, data=x))() > #> > #> Call: > #> lm(formula = mpg ~ cyl, data = x) > #> > #> Coefficients: > #> (Intercept) cyl > #> 37.885 -2.876 >
USLACKBOT (18:14:50): > This message was deleted.
Alan O’C (18:15:39): > I’m not going to use it, I’m just amused by the people who’ve been clamouring for a native pipe for years deciding that a different lambda syntax means it’s all for nought
Alan O’C (18:16:06): > Not mentioning the possibility to do lovely things likemtcars %>% lm(mpg~., data=.)
Alan O’C (18:27:08): > For those so inclined I believe there’s an RStudio option to change the pipe shortcut (ctrl+shift+m or something?) from%>%to|>
Dirk Eddelbuettel (18:41:02): > Not amagrittruser but less opposed to|>for the main reason that itreally is just functional composition . As in the following snippet:
Dirk Eddelbuettel (18:41:09): - File (Plain Text): Untitled
Alan O’C (18:43:30): > Is=>still experimental?
Dirk Eddelbuettel (18:48:25): > Yes. Word is that the semantics may not be final, hence the env.var opt-in I use on line 1. Otherwise you get a ‘no pipebind for you’ error message.
Alan O’C (18:49:40): > Interesting, thanks. It’s certainly more readable than the current lambda syntax
Martin Morgan (19:36:47): > I like the pipe for interactive work, especially when doing data transformation. It fits well with composing short ‘phrases’ of thought. Easy to abuse, I guess, with long sequences, but it’s also easy to write complicated nested code. > > I know the use of pipes in package code has been discouraged, and I guess it’s hard (too hard for me, so my packages do have piped code) and error-prone to re-write the piped code in a more traditional manner. > > For me, though, the ‘lambda’ anonymous function notation\(x)and the need to use parentheses in a pipe(\(x) x)()seems too hard to easily parse, and I’ll stay away from it. This means that|>is restricted to functions where the LHS is the first argument of the RHS, at least for the current release of R.
2021-06-11
Sebastian Worms (07:10:09): > I’m sticking to%>%,but if I’m honest it’s only because|>is harder to type on AZERTY keyboards ^^
Janani Ravi (08:08:24) (in thread): > Any particular reasons why piped code isn’t recommended within package functions? We have been using it – easier to write and interpret!
Mercedeh Javanbakht Movassagh (11:22:08): > @Mercedeh Javanbakht Movassagh has joined the channel
Henrik Bengtsson (12:00:23) (in thread): > One argument is, if using the new pipe syntax,|>, in your package, the package will require R (>=4.1.0).
Martin Morgan (12:33:57) (in thread): > I guess the requirement on R (>=4.1.0) is not important for Bioconductor (release and devel of Bioconductor depend on R >= 4.1.0). It could definitely cause problems for CRAN packages that depend on Bioconductor packages.https://r4ds.had.co.nz/pipes.html#when-not-to-use-the-pipe provides some guidance on when pipes are inappropriate. Some of the reasons to avoid pipes, e.g., inhttps://stackoverflow.com/questions/38880352/should-i-avoid-programming-packages-with-pipe-operators , are negated by its implementation in base R. Dirk’s observation that|>represents true function composition addresses additional limitations. > > I think the remaining reservations are that it provides yet another syntax that those trying to help have to struggle with (I have an apocryphal story of an R-core developer being shown some code, cursing at the use of pipes etc making it unreadable, then realizing that it was actually matlab), and that it encourages a programming style where one has to understand highly ‘composed’ functions (cf Dirk’s examplehttps://community-bioc.slack.com/archives/C35G93GJH/p1623364862047500 ) rather simple single-line, linearly organized statements. In practical terms, from participating in StackOverflow, I’m confident that R programmers are able to write difficult-to-understand code in any paradigm! - Attachment (Stack Overflow): Should I avoid programming packages with pipe operators? > Are there any objective reasons for why pipe operators from the R package magrittr, such as %>%, should be avoided when I program packages in R? More specifically, I want to know if using pipe - Attachment: Attachment > Not a magrittr user but less opposed to |> for the main reason that it really is just functional composition . As in the following snippet:
Martin Morgan (13:00:31): > I want to create or re-use a channel to discuss translating package error / warning messages. Is there an existing channel that I should use? Do I (just a regular slack participant) have the ability to create new channels?
saskia (22:53:09) (in thread): > Just create a channel! You should have the ability
2021-06-14
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2021-06-15
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2021-06-17
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Mike Smith (10:36:04): > A reminder that our Developers Forum call on enabling multi-lingual error messaging in R packages is taking place in 90 minutes. It would be great to hear the opinions of both package users and developers on how valuable this might be. Everyone is welcome to listen or contribute. - Attachment: Attachment > The next Developers Forum will be this Thursday at 09:00 PST / 12:00 EST / 18:00 CEST - You can find a calendar invite attached and at https://tinyurl.com/BiocDevel-2021-06 > > We’ll be using BlueJeans at https://bluejeans.com/114067881/ > > @Martin Morgan will present some initial steps towards translating error messages in {BiocManager} into multiple languages. This isn’t something I’ve thought about before, and it will be great to have some idea how much work is required from a technical side, in addition to creating the actual translations. > > There are some notes available at https://github.com/Bioconductor/BiocManager/blob/po-translations/README-Translation.md that may be of interest. In particular it would be great to get the perspective of he community (both developers and users) on the points in the “<https://github.com/Bioconductor/BiocManager/blob/po-translations/README-Translation.md#concerns–next-steps|Concerns / next-steps>” section
Michael Lawrence (11:56:52): > Are you recording it?
Mike Smith (11:57:36): > Yes, that’s the plan.
2021-06-18
Lori Shepherd (07:20:27) (in thread): > This comment has been deleted as a violation of the Bioconductor Code of Conduct. Please review theBioconductor Code of Conduct
saskia (21:46:04): > The Code of Conduct (CoC) committee received a report about a slack post violating CoC rules against trolling and mocking behavior. The poster has been officially warned by the CoC and the post was deleted. > > We ask that everyone review the Bioconductor CoC (https://www.bioconductor.org/about/code-of-conduct ) and follow it in your interactions with the community, being aware that serious violations or repeated warnings can result in temporary or permanent suspension from Bioconductor platforms.
2021-06-21
Sebastian Worms (06:03:03): > Anyone attending/presenting at the world microbe forum?
Sebastian Worms (06:03:18): > I’m finding the expermient with pushing the boundaries of online conferences nice
2021-06-23
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2021-06-24
Ilaria Billato (08:13:21): > @Ilaria Billato has joined the channel
Kevin Blighe (13:52:48) (in thread): > Not attending that one@Sebastian Worms, but, generally, it has been good to ‘virtually’ attend various conferences / talks this past year-and-a-half. My last ‘in person’ conference was possibly 2016, and avoided them since then due to work loads.
2021-06-25
Janani Ravi (22:40:52): > In addition to the community-based incubators mentioned by@Heather Turner, we have one more that may be of interest to R developers here, esp. those interested in open source software solutions to R conferences/meetups: > > Dear all, > We would like to invite you to participate in our incubator “Stop reinventing the wheel Friday, July 09, 2021, 6:45–7:45 pm UTC janani@msu.edu ). > > We plan to split the event into two groups: > - the first group works to define a process on how to evaluate useR! 2021 in such a way that the learnings help future R conferences with a strong online component. The short-term goal would be to develop a debriefing strategy/guideline. > - the second group discusses the challenges of hybrid conferences since a strong online component is likely meant to stay. > > The ultimate goal would be to use technology and proven processes to package many bits and pieces of conference and abstract management in a modular yet deployable fashion. In other words, we’re looking for an architecture (stack) and process discussion beyond the potluck style of throwing together scripts and helpers. > > useR! 2021:https://user2021.r-project.org useR! 2021 schedule:https://user2021.r-project.org/program/schedule/ We are very excited to include folks from various R communities such as this to avoid reinventing the wheel with every conference ahead! > > Thanks a ton for your feedback and participation in advance! > Best,@Janani Ravi& Matt BannertP.S. Please let us know in case you can recommend others who are interested in this as well. - Attachment: Attachment > Hi Folks, There are several community-focused incubators at useR!, that I expect would be of high interest to this group: > • “Five principles to grow up your R community” (@Leonardo Collado Torres is co-organizing) > • “Strategies to build a strong AsiaR Community” (@Janani Ravi is co-organizing and I posted about here: https://community-bioc.slack.com/archives/C01S6BCPA5N/p1624608174000900 ) > • “Expanding the R community in the Middle East and North Africa (MENA)” (not sure it involves anyone on this Slack yet?) > See all incubators here: https://www.conftool.org/user2021/index.php?page=browseSessions&presentations=show&form_tracks=9&form_topic=0
2021-06-26
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2021-06-28
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2021-06-29
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2021-07-01
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2021-07-02
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2021-07-05
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2021-07-06
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2021-07-07
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2021-07-08
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2021-07-09
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2021-07-10
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2021-07-11
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2021-07-12
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Lori Shepherd (12:02:47): > Bioconductor is pleased to announce a call for community volunteers to > assist with Bioconductor Package Reviews. This is an excellent way to get > involved with and give back to the Bioconductor Community. The minimum > requirement to volunteer is to be actively maintaining an existing Bioconductor > package. Please readReviewer Expectations for full details and information.
Lluís Revilla (13:07:53) (in thread): > I have some questions about how it will work in practice. How will be shown who is a reviewer on the Github issue? Will the reviewers be assigned to the issue? On a package review done with an on-boarding member, will there be 3 reviewers or the review of the new reviewer and the experienced reviewer are enough? When two community reviewers are assigned, will there be an “editor” figure from the Bioconductor core team overviewing the review process?
Lori Shepherd (13:12:29) (in thread): > The review process assignment and how a reviewer is shown is still the same as it has been. Until a prospective reviewer is official they will not be assigned a package and will work with the paired reviewer on one of their assigned issues. In practice only one reviewer is assigned and giving a review; a paired review will only be used in the on-boarding process and for evaluation.
Lluís Revilla (13:20:10) (in thread): > Awesome! Many thanks. I thought there would be 2 reviewers for each package, but this is on rOpenSci.
Sophie Arogbonlo (14:03:30): > @Sophie Arogbonlo has joined the channel
Jianhai Zhang (15:40:55): > Hello guys, is there a channel of Bioc virtual conference 2021?
Mike Smith (16:46:02) (in thread): > I don’t want to speak for Lori, but my understanding is that the hope for this drive is to ease the burden on the current team by expanding the number of reviewers and hopefully speed up the existing reviews. If we get a ton of volunteers (no idea on an exact number but a “surplus”) then it’d be great to have two reviews per package. However for now the aim is to relieve the existing team and leave reviews the same, rather than making a more comprehensive review process.
Lluís Revilla (18:22:06) (in thread): > I understand that this is one of the few works that can be done by outsiders and at the same time help building more interoperable packages. (I have pointed out on several packages submission that a package wasn’t reusing existing classes). But I also think that one person spending just 1.5 hours on a package might not be enough for the great detail that the Bioconductor review was providing (Many thanks!!). Thus the quality of new packages might be lower. Even with semi-automatic checks and templates like on rOpenSci the usual self-reported time is longer. You might have already discussed this so feel free to ignore this comment.
Lluís Revilla (18:23:30): > Yes#bioc2021
2021-07-16
rohitsatyam102 (05:49:01): > I was trying to make a violin plot and I wish to remove the upper tail (vertical line) in each of the violins. When I usetrim=TRUEit removes the lower tail but not the upper tail. I see a similar issue reportedhere . Is there a workaround ? - File (PNG): image.png
Gavin Rhys Lloyd (06:44:16) (in thread): > One option might be to find the “outliers” equivalent to a box plot, then exclude them from the violin > > library(ggplot2) > > # some data with outliers > df=data.frame(value=c(rnorm(23),5,-5,rnorm(23),7,-7),group=c(rep('A',25),rep('B',25))) > > # function corresponding to boxplot outliers > is_outlier [ x ](- function(x) { > return(x < quantile(x, 0.25) - 1.5 * IQR(x) ) quantile(x, 0.75) + 1.5 * IQR(x)) > } > > # get outliers > OUT=is_outlier(df$value) > > # violin the inliers, and plot the outliers in red > g= ggplot(data=df[!OUT,],aes(x=group,y=value))+ > geom_violin() + > geom_point(data=df[OUT,],aes(x=group,y=value),color='red') > > g >
Gavin Rhys Lloyd (06:44:50) (in thread): - File (PNG): image.png
rohitsatyam102 (06:48:36) (in thread): > Wow, this works flawless. What I tried meanwhile was to useylim(0,0.010)to trim the y axis
Gavin Rhys Lloyd (06:49:35) (in thread): > Personally I prefer not to ‘hide’ some data points
rohitsatyam102 (06:52:16) (in thread): > Yes but I can’t help my boss asked to do. Thanks@Gavin Rhys Lloydfor helping me out.
Heather Turner (07:07:26) (in thread): > If you want to trim the y axis it would be better to usecoord_cartesian(ylim = c(0, 0.010)); this zooms in on the area of interest rather than excluding data, seehttps://ggplot2.tidyverse.org/reference/coord_cartesian.html for examples. - Attachment (ggplot2.tidyverse.org): Cartesian coordinates — coord_cartesian > The Cartesian coordinate system is the most familiar, and common, type of coordinate system. Setting limits on the coordinate system will zoom the plot (like you’re looking at it with a magnifying glass), and will not change the underlying data like setting limits on a scale will.
Pariksheet Nanda (12:26:22): > Hi Bioconductor developers! DoesS4Vectos::IntegerList()have a C API? I see a little ofList()in the exported headers of the S4Vectors package. Asking because I’m trying to vectorize a function that currently takes as input an integer vector, but I want a variant that takes as input an IntegerList. The underlying implementation is in C, and my current R interface usesendoapply()on the IntegerList, but I would like to directly process the IntegerList in the C layer and subsequently parallelize with OpenMP. For what it’s worth, here are the relevant files: > * Current call toendoapply()https://gitlab.com/coregenomics/tsshmm/-/blob/master/R/hmm.R#L172 > * R interface:https://gitlab.com/coregenomics/tsshmm/-/blob/master/R/viterbi.R > * C interface:https://gitlab.com/coregenomics/tsshmm/-/blob/master/src/R_wrap_tsshmm.c - Attachment (GitLab): R/hmm.R · master · coregenomics / tsshmm > Bioconductor package for de-novo transcription start site discovery from nuclear run-on sequencing data - Attachment (GitLab): R/viterbi.R · master · coregenomics / tsshmm > Bioconductor package for de-novo transcription start site discovery from nuclear run-on sequencing data - Attachment (GitLab): src/R_wrap_tsshmm.c · master · coregenomics / tsshmm > Bioconductor package for de-novo transcription start site discovery from nuclear run-on sequencing data
Pariksheet Nanda (12:31:49) (in thread): > In other words, is there anything special I need to do for accessing for theIntegerListS4 objects to getINTEGER()andLENGTH()from the theInegerListS-expression, or do traditional operations for R’slist()work just as well forIntegerList?
C_viterbi(SEXP hidden_states,
SEXP observations)
{
viterbi(INTEGER(hidden_states),
INTEGER(observations),
LENGTH(observations));
return R_NilValue;
}
Pariksheet Nanda (14:00:10) (in thread): > I’ll try this:https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Handling-lists - Attachment (cran.r-project.org): Writing R Extensions > Writing R Extensions
Martin Morgan (15:16:13) (in thread): > I know@Hervé Pagèsis traveling and probably better to wait for him, but I think you would rather pass theunlist()andlengths()of theIntegerList()to your C code. These operations will be fast / memory efficient, and you’ll be dealing in C with familiar objects that do not require knowledge of the (complicated / non-intuitive) *List classes. You’d use thelengths()as offsets into theunlist()data to get each element of the list.
Michael Lawrence (15:24:09) (in thread): > Yes, that would be efficient if you have a CompressedList. For a SimpleList, it’s just a matter of callingas.list()and using the existing C API for base R lists. Callingas.list()would also handle the compressed case, but obviously less efficiently. Seems like there is an opportunity for a C-level abstraction here, like a way to iterate over elements represented as int pointers and lengths (thus avoiding constructing R vectors).
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2021-07-17
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2021-07-21
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2021-07-23
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2021-07-26
Dario Strbenac (08:00:02): > I am looking ata question about BiocParallel’s reproducibility when changing the number of cores that didn’t have any answer on the mailing list. What is the answer?
Martin Morgan (09:27:30) (in thread): > Seehttps://github.com/Bioconductor/BiocParallel/pull/140 . This has not been implemented yet but will be in the next weeks.
2021-07-27
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Alan Murphy (17:53:53): > Have the multi platform build checks for bioc 3.14 ran the last two nights? Thelanding page still seems to show Saturday
Lori Shepherd (18:30:58): > @Andres Wokatyit seems like there is a build issue. Can you check if the cause is known?
Andres Wokaty (19:00:29): > The builds failed for the same reason the past two days, but I need some help with git before I can rerun them. Maybe@Lori Shepherdor@Nitesh Turagacan help?
Lori Shepherd (20:26:30): > @Alan Murphythank you for making us aware.@Andres Wokatyidentified the issue and it should be fixed. We expect build reports to resume normal schedule.
2021-07-28
FelixErnst (12:12:44): > I am looking for info on communicating a change in maintainership for single package. Is this info up-to-date:https://bioconductor.org/developers/how-to/git/change-maintainer/ ?
Lori Shepherd (12:13:54): > yes
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Hervé Pagès (20:51:30) (in thread): > @Pariksheet NandaThere’s a C-API but for the CompressedList flavor only (for the SimpleList flavor, follow Michael’s suggestion or turn it into a CompressedList withas(x, "CompressedList")). > If you’re only trying to access the elements of an CompressedIntegerList, the C-API is easy to use. First addIRanges_stubs.cto your<pkg>/src/(e.g. copy it fromBiostrings/src/) andIRanges LinkingTo:field. Then: > > #include "IRanges_interface.h" > > SEXP foo(SEXP x, ...) > { > CompressedIntsList_holder x_holder; > Ints_holder x_elt_holder; > > x_holder = hold_CompressedIntegerList(x); > x_len = get_length_from_CompressedIntsList_holder(&x_holder); > /* Loop over x's list elements and > access the data in each of them. */ > for (int i = 0; i < x_len; i++) { > x_elt_holder = get_elt_from_CompressedIntsList_holder(&x_holder, i); > /* x_elt_holder is a Ints_holder structure with 2 members: > - x_elt_holder.ptr: a const int * that is a pointer to an array of ints; > - x_elt_holder.length: the length of the array of ints. > } > ... > } > > Now if you also want to construct a new CompressedIntegerList at the C level, things are a little bit more complicated. Let me know if that’s something you need to do. > Finally please note that vectorizing a function to make it work efficiently on an IntegerList can be donemost of the times
2021-07-29
Pariksheet Nanda (12:40:57) (in thread): > @Hervé PagèsWow, thank you! This is really useful. I had implemented Martin’s way of unlisting and using an offset index, but this way should save me from having to unlist and relist in R. Your API actually makes it trivial to apply Martin’s logic of using the length offsets. Yes, I’m working withCompressedIntegerList. Typically I do all my memory allocations in the R layer. Yes, I do need to create an identically shapedCompressedIntegerListwhich I do here:https://gitlab.com/coregenomics/tsshmm/-/blob/master/R/viterbi.R#L11 but I think it’s fine as is to use a vector, because I have the function either return an atomic vector or a list (feel free to boo my API, but it’s internal to the package and so really only matters for the unit tests). I’ll probably get around to working on the code again in a couple of days to useIRanges_stubs.c. to save myself from using unlist. > > Is there a canonical way to inspect theSEXPobject to query if it’s aCompressedIntegerList? > > While I have you, I was wondering what your thoughts are about patching GenomicRanges and IRanges to natively generate reversedtile()output? Basically I only need a single line changed, that would greatly speed up my use case:https://gitlab.com/coregenomics/tsshmm/-/blob/master/R/hmm.R#L226 - this would be useful to folks doing any DNA sequencing assay where one runs into the need for generating reverse ordered windows for the negative strand to run models on (add having the model support non-reversed data adds a lot of ugly complexity than simply reversing the data). - Attachment (GitLab): R/viterbi.R · master · coregenomics / tsshmm > Bioconductor package for de-novo transcription start site discovery from nuclear run-on sequencing data - Attachment (GitLab): R/hmm.R · master · coregenomics / tsshmm > Bioconductor package for de-novo transcription start site discovery from nuclear run-on sequencing data
2021-07-30
Ludwig Geistlinger (04:23:50): > I’d like to announce two Bioc-community challenges. > (Also posted on the bioc-devel mailing list, apologies for the cross-posting).
Ludwig Geistlinger (04:23:59): > 1. BioPlex challenge https://bioplex.hms.harvard.edu ) has created two > proteome-scale, cell-line-specific protein-protein interaction (PPI) networks: > the first in 293T cells, including 120k interactions among 15k proteins; and > the second in HCT116 cells, including 70k interactions between 10k proteins. > The BioPlex R package (https://github.com/ccb-hms/BioPlex , submitted to Bioconductor) > implements access to the BioPlex PPI networks and related resources from within R. > Besides PPI networks for 293T and HCT116 cells, this includes access to CORUM > protein complex data, and transcriptome and proteome data for the two cell lines. > > The goal of this challenge is to introduce the BioPlex data and package to the > community, and work together on several analysis and programming challenges around > the data including: (a) transcriptomic and proteomic data integration > on the BioPlex networks, (b) assessing the impact of alternative splicing on > bait proteins of the networks, (c) integration with public databases for > disease-associated genes and variants, (d) implementing a GraphFrames backend > for efficient representation and analysis of the networks, and (e) designing an > R/Shiny graph viewer that allows flexible inspection of experimental data and > metadata for nodes and edges of the networks. > > We will introduce the challenge at Bioc2021,Wed, Aug 4, 2:30-3:30 PM EST
Ludwig Geistlinger (04:25:23): > 2. BugSigDB challenge https://bugsigdb.org ) is a manually curated database of microbial > signatures from published differential abundance studies, providing standardized > data on geography, health outcomes, host body sites, and experimental, > epidemiological, and statistical methods using controlled vocabulary. > To date, BugSigDB provides more than 2,000 signatures from over 500 published > studies, allowing systematic assessment of microbiome abundance changes within > and across experimental conditions and body sites. > > The bugsigdbr package (https://github.com/waldronlab/bugsigdbr , submitted to Bioconductor) > implements access to BugSigDB from within R/Bioconductor. This includes import of > BugSigDB data into R/Bioconductor, utilities for extracting microbe signatures, > and export of the extracted signatures to plain text files in standard file formats > such as GMT. > > The goal of this challenge is to introduce the BugSigDB database and package to > the community, and work together on several analysis and programming challenges > around the data including: (a) identification of body site-specific signatures > from healthy samples, (b) efficient calculation of similarity measures between > signatures across the whole database or specific subsets of it, (c) automatic > identification of candidate papers for curation based on recently proposed text > mining approaches, (d) ontology-based queries to the database using controlled > vocabulary for experimental factors and body sites, and (e) inference of abundance > changes along the taxonomic hierarchy using phylogenetic approaches such as > ancestral state reconstruction. > > We will introduce the challenge at Bioc2021,Thu, Aug 5, 2:30-3:30 PM EST
Hervé Pagès (05:15:48) (in thread): > If you need to create an identically shaped CompressedIntegerList, this is actually the easy case: > > #include "IRanges_interface.h" > > /* Implement the transformation of an int > array. 'in' and 'out' are both int > arrays of length 'n'. foo() reads the > input values from 'in' and write the > transformed values to 'out'. */ > static void foo(const int *in, int *out, int n, ...) > { > ... > return; > } > > /* Apply the foo() transformation on each > list element of CompressedIntegerList > object 'x'. */ > SEXP vectorized_foo(SEXP x, ...) > { > CompressedIntsList_holder x_holder, ans_holder; > Ints_holder x_elt_holder, ans_elt_holder; > int x_len; > SEXP ans; > > x_holder = hold_CompressedIntegerList(x); > x_len = get_length_from_CompressedIntsList_holder(&x_holder); > PROTECT(ans = duplicate(x)); > ans_holder = hold_CompressedIntegerList(ans); > > for (int i = 0; i < x_len; i++) { > x_elt_holder = get_elt_from_CompressedIntsList_holder(&x_holder, i); > ans_elt_holder = get_elt_from_CompressedIntsList_holder(&ans_holder, i); > /* 'x_elt_holder.length' and 'ans_elt_holder.length' should always > be the same. */ > foo(x_elt_holder.ptr, (int *) ans_elt_holder.ptr, x_elt_holder.length, > ...); > } > > UNPROTECT(1); > return ans; > } >
rohitsatyam102 (13:37:44): > Hi My shiny app shows'Disconnected from Server'Reload. Is it normal because otherwise my network is working fine and shiny app is running fine too!! I am assuming that it might be because of my inactivity on shiny app because when I browse on other tabs for a while the above mentioned message appear!!
Jared Andrews (13:42:59): > Yes, it will timeout. You can change that setting if using Shiny Server Pro or Shiny Connect.
Jared Andrews (13:44:39): > Probably onshinyapps.io too.
FelixErnst (15:02:21) (in thread): > I have send a mail tomaintainer@bioconductor.org , but haven’t got a reply, yet. I am not sure, whether this is normal, since it has been a week, but I know you are always busy. Any update would be welcome. Thanks!@Leo Lahti
Lori Shepherd (15:05:40) (in thread): > Sorry for the delay. I have notified the personnel that normally takes care of these issues.
FelixErnst (16:20:19) (in thread): > Not a problem at all. Thank you for raising the issue.
rohitsatyam102 (16:35:33) (in thread): > I am a student and I can’t purchase subscription. I am using free hosting service ofshinyapps.io . Is it possible to set something in the code?
Jared Andrews (16:36:25) (in thread): > I don’t know, I don’t useshinyapps.io . If you can do it in the free version, it’ll be somewhere in the app settings. Look for connection timeout or similar settings.
rohitsatyam102 (16:36:52) (in thread): > It would be great if shiny had student subscriptions that are affordable for hosting apps that are not data intensive!!
Jared Andrews (16:39:02) (in thread): > I mean, 9 bucks a month isn’t insane or anything.
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2021-07-31
Chris Vanderaa (05:16:15) (in thread): > If you are usingshinyapps.io , go to your dashboard and click on your app that is failing. You may give a look at 2 tabs. 1) TheLogstab: it can help you identify why your app is disconecting ( for instance, I got the same message as you because of a out of memory error) and 2) theSettingstab: you can increase the timeout settings or other settings.
2021-08-01
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2021-08-03
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Arjun Krishnan (10:53:23) (in thread): > @Ludwig GeistlingerThis is really interesting! Is there more info on the BioPlex challenge, including instructions on how to join the meeting on the virtual conference platform?
Ludwig Geistlinger (10:55:43) (in thread): > @Arjun KrishnanThere is now a detailed description of the challenge here:https://kevinrue.github.io/BiocChallenges/articles/challenges/bioplex.html - Attachment (kevinrue.github.io): Integrative analysis of proteome-scale protein-protein interaction networks from the BioPlex project > BiocChallenges
Arjun Krishnan (10:56:07) (in thread): > Super, thank you:slightly_smiling_face:
Ludwig Geistlinger (10:56:34) (in thread): > I am about to find out how to join the meeting from the conference organizers and will get back to you.
Ludwig Geistlinger (12:17:40) (in thread): > @Arjun KrishnanI have been told that once you login to the airmeet conference platform that there will be a table in the virtual lounge area called “BioPlex”. This would be the one where we are meeting at the indicated time.
Arjun Krishnan (13:08:55) (in thread): > Thank you!
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Hervé Pagès (20:26:00) (in thread): > For your other questions: > > Is there a canonical way to inspect theSEXPobject to query if it’s aCompressedIntegerList? > > > if (isObject(x) && strcmp(CHAR(STRING_ELT(GET_CLASS(x), 0)), "CompressedIntegerList") == 0) { > ... > } > > However, please note that this is the equivalent to doing something likeidentical(class(x), "CompressedIntegerList")in R, which is rarely the right thing to do. It’s almost always better to check that an object extends some class e.g. > > is(x, "CompressedIntegerList") > > There is probably a way to do this in C but I never bothered to investigate. I just got into the habits of doing most of the argument checking in R, just before passing them to my .Call entry points. > > While I have you, I was wondering what your thoughts are about patching GenomicRanges and IRanges to natively generate reversedtile()output? Basically I only need a single line changed, that would greatly speed up my use case > Please open an issue on GitHub (https://github.com/Bioconductor/GenomicRanges/issues ) to request the feature. It’ll be easier to discuss it there. Thanks!
2021-08-04
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Ambarish S. Ghatpande (09:50:43): > Hi great to be here, I am a clinical neurophysiologist quite interested in single cell omics in the brain context. I am attending bioc2021. Ping me if you think we share interests
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Michael Lawrence (12:46:26) (in thread): > You can useinherits()at the C level.
Stephanie Hicks (13:39:09): > Welcome everyone!:wave:
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2021-08-05
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Aarthi Ravikrishnan (05:40:57) (in thread): > Sure, I will email you! Thanks.
2021-08-15
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2021-08-16
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2021-08-18
Charlotte Soneson (08:23:49): > Would you like to join the organization committee for EuroBioC2022 (plans are for an in-person/hybrid conference in Heidelberg, Germany, on March 16-18 2022)? The conference committee meets biweekly; if you’re interested in helping out with communication, program development, sponsorship, technical development, code of conduct enforcement, local organization in Heidelberg, or any other aspect, please fill out this short survey with your contact information and interests:https://forms.gle/5YsKh5GwtEgRwHcR7 - Attachment (Google Docs): EuroBioC2022 Committee Application > The organizing committee for EuroBioC2022, to be held in Heidelberg, Germany, on March 16-18 2022, needs organizers to help in planning the event. Participation involves attending approximately biweekly remote meetings plus taking on responsibilities in one or more of the areas listed below.
Aedin Culhane (09:41:19): > If you have developed a Bioconductor Package and learned the challenges along the way If you have tips and tricks for would-be developers. Please consider joining the new Bioconductor Mentorship program to help new would be developers get from R scripts to Bioconductor package. Expression of interest form athttps://forms.gle/fya5JEArTT5kNEGr9 - Attachment (Google Docs): Bioconductor Developer Mentorship Program - Expression of Interest > Please indicate your interest to learn more and potentially become a mentor in the Bioconductor Developer Mentorship program. The Bioconductor Developer Mentorship Program will form a part of the Bioconductor “welcome mat” that the Bioconductor Community Advisory Board are developing. It will be a group-mentorship/buddy program for would-be, new, or hesitant developers or for developers who wish to refresh their skills. The goal of the program is to welcome and onboard new developers, develop educational material to assist new developers, improve the quality of packages submitted to Bioconductor, and strengthen community and interactions between Bioconductor developers. Mentors should have at least 1 package either in the release or accepted in the development branch of Bioconductor. Each program cycle would run for 6 months (or the development cycle of Bioconductor package release). For more information about the program see the Bioconductor Website [link].. or Google doc [https://docs.google.com/document/d/1Q-Hxmy0ZcKzKSbB-dtg02gJRlZ0Vi6WNOTF-W3bwjmY/edit?usp=sharing ]
2021-08-19
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2021-08-21
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2021-08-25
Pariksheet Nanda (14:44:17): > Hi all, I’m writing a somewhat complex HMM that requires using the GHMM C library (http://ghmm.org ). What are the Bioconductor core developer / maintainer opinions on bundling 3rd party library dependencies vs using OS dependencies? Looking at RStudio’s packages as reference, one can see that thefspackage bundles thelibuvdependency [1], and that thexml2package only ever uses the OS package [2]. The last stable release for GHMM was many years ago and it seems up-to-date on most distros, so it comes down to making it easier to install on Windows and MacOS. > > On a related note, what would be the best way to test the package builds on MacOS and Windows in addition to Linux that I’ve been testing on? Should I just sign up for a bioconductor developer account at this point and spam the build machines, or fiddle with the Rube Goldberg machine that is GitHub CI? > [1][https://github.com/r-lib/fs/blob/master/src/Makevars](https://github.com/r-lib/fs/blob/master/src/Makevars)[2][https://github.com/r-lib/xml2/blob/master/configure](https://github.com/r-lib/xml2/blob/master/configure)(edit: s/system/machines)
Kasper D. Hansen (15:26:08): > I would not always look at the RStudio way as the “one true way to do this”. It is a tradeoff. By depending on a system library you’re essentially trading your time for your users time. It’ll be much easier for you, but the downside is that it will be much more difficult for your end users.
Kasper D. Hansen (15:27:32): > For your end users perspective, bundling ghmm (or making a separate package just with that library) is much preferable, but you take on a lot of responsibility because you’re now responsible when the library breaks on some OS. How much responsibility that is, really depends on details on GHMM.
Kasper D. Hansen (15:29:06): > Some years ago I switch Rgraphviz from depending on an external Graphviz, to bundling it. It came with a lot of work, but the end product was MUCH easier to install for users. Prior to this, Rgraphviz installation was a major hurdle. So I have some experience, but the decision also really depends on the specifics of GHMM and its dependencies
Kasper D. Hansen (15:30:21): > Finally, the Bioc build system is not really a substitute for access to a development environment on OS X or Windows. I mean, you can try, but it won’t be a pleasant experience. It works well if you’re 98% of the way, but I would not think that’s the case for your use case.
Kasper D. Hansen (15:33:26): > ok, GHMM depends on libxml2 and optionally on GSL. That’s workable. Do you depend on GSL?
Pariksheet Nanda (15:33:36): > The only hard dependency of GHMM is libxml2 which if I’m not mistaken is also required for Bioconductor? I’m not using GSL
Pariksheet Nanda (15:34:06): > Actually they only tested against GSL 0.7. The current GSL 2.5 breaks with GHMM and would need some maintenance, but I don’t see GSL as necessary.
Kasper D. Hansen (15:35:19): > ok, so if you’re happy to build without GSL it seems doable. The package uses autoconf which is good, but the installation instructions suggests runningsh autogen.shwhich seems pretty weird and lowers my confidence a bit
Kasper D. Hansen (15:35:53): > Windows may be an issue
Kasper D. Hansen (15:36:36): > Rtools do not give you full autoconf support out of the box (or at least didn’t use to) and the installation instructions suggests limited / no work on building on mingw32
Kasper D. Hansen (15:37:04): > You’re guarenteed to need a windows development environment if you want to do this
Kasper D. Hansen (15:37:26): > You could probably make OS X and linux work without that much hassle
Kasper D. Hansen (15:37:32): > that’s my prediction
Kasper D. Hansen (15:38:14): > Windows will be somewhere between “some work” to “near impossible”, and I predict a most likely to be a “substantial amount of work”. Whatever I mean by that
Kasper D. Hansen (15:39:07): > But since there are no windows binaries I can see, you cannot do Windows support as external library I think
Kasper D. Hansen (15:40:08): > You sidestep this to some extent by using python and basilisk to install a full conda environment with GHMM. But that’s not what you asked for above
Pariksheet Nanda (15:40:33): > Ok, I’ll look into bundling the dependency. I’m not finding the documentation on setting up Bioconductor for Windows development, but presumably I would need to refer to R’s instructions for setting up a Windows development environment.
Kasper D. Hansen (15:42:17): > yes, that’s what you need.
Kasper D. Hansen (15:42:28): > It might be a pain btw
Kasper D. Hansen (15:42:44): > I would start by concentrating on Linux + OS X
Kasper D. Hansen (15:42:59): > recognizing that windows might be unobtainable
Kasper D. Hansen (15:43:14): > depending on how much you know the GHMM codebase
Dirk Eddelbuettel (15:43:16): > It’s a known hard problem, and@Kasper D. Hansenand I discussed (even in public at a useR:slightly_smiling_face:) Embedding is one solution, I mention it here too (for the case of a small+simple library) in “Thirteen Simple Steps for Creating An R Package with an External C++ Library”:https://arxiv.org/abs/1911.06416 Doing it in general terms, across OS, is still hard. I recently helped an undergrad deal with an external HTS dependency. > > Embedding is of course most portable but also … hardest. You ownall the build woes. Users pay with longer compile times (unless binaries). > > In short, (still) no free lunch. - Attachment (arXiv.org): Thirteen Simple Steps for Creating An R Package with an External… > We desribe how we extend R with an external C++ code library by using the Rcpp package. Our working example uses the recent machine learning library and application ‘Corels’ providing optimal yet…
Pariksheet Nanda (15:50:43): > Ok, I see what you meant by rtools for building on Windows:https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-Windows-toolset - Attachment (cran.r-project.org): R Installation and Administration > R Installation and Administration
2021-08-26
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Gavin Rhys Lloyd (04:34:53): > is there a way to automatically be notified if a Bioc Core Team member pushes changes upstream?
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Hervé Pagès (06:11:22) (in thread): > Hi@Gavin Rhys Lloyd, yup, that’s me… I pushed a change tostruct https://bioconductor.org/developers/gitlog/ ). Then use some fancy feature in your RSS Feed Reader to get notified when the name of one of your package shows up in the feed.
Gavin Rhys Lloyd (06:17:54) (in thread): > Is it standard practice for the core team to make changes and push upstream instead of using a github pull request?
Gavin Rhys Lloyd (06:18:26) (in thread): > I guess if you have a lot of packages to fix, then thats a lot of pull requests
Lori Shepherd (07:40:47) (in thread): > If we made a change in a core package we occasionally try to fix some based on the nature of the change. In general we don’t change people’s packages and would write to maintains to fix…except for the version bumps at release time which the core team always does automatically
Gavin Rhys Lloyd (08:16:46) (in thread): > I am grateful that the code was fixed (thank you!), but I dont think changes should be pushed upstream without the package maintainers knowledge. I will try the RSS feed filtering as suggested.
Kasper D. Hansen (08:34:08) (in thread): > Not everyone uses Github
Kasper D. Hansen (08:34:23) (in thread): > (I mean in practice many do, but the setup is not github dependent)
Gavin Rhys Lloyd (08:35:24) (in thread): > fair, but an (automated?) email would be enough
Kasper D. Hansen (08:51:19): > @Pariksheet NandaPerhaps it is time for me to write a short tutorial on how to do what you want to do (incorporate an autoconf-based library in an R package). Now is not a great time (semester / school start) but then again its never a great time. In the meantime, you could look atRgraphviz/configure.acto get an idea about what is happening.
Dirk Eddelbuettel (08:53:15) (in thread): > If you’re interested, I’d be happy to help. It has come up before, and it keeps comping up. Simple(r) examples relying onpkg-configare not that hard, and leading up to harder example likeRgraphvizis good.
Kasper D. Hansen (09:05:14) (in thread): > Thanks
Kasper D. Hansen (09:07:57) (in thread): > I’ll try to use this as a lever to get going and I’ll hope to reach out sometime in the next week with a github repos.
Dirk Eddelbuettel (09:09:39) (in thread): > Happy to help at any stage. I something it helps to start with bullet points for big picture items, sometimes I just when I think it is more linear. All good. “This was only overdue by two decades” but hey we kept busy.
Hervé Pagès (12:51:25) (in thread): > Hi Gavin, this change tostruct metabolomicsWorkbenchR struct https://github.com/const-ae/glmGamPoi/pull/29 ) but I was not able to find your package on GitHub. I didn’t see the GitHub URL in the DESCRIPTION file of the package and searching for “struct” on GitHub gives 170112 repository results. I should probably have tried to look up your name on GitHub (I see now that this would have allowed me to find your package). > Anyways, yes we sometimes push changes upstream. That’s kind of part of the deal of having your package on Bioconductor.
Gavin Rhys Lloyd (12:54:12) (in thread): > Thanks for making the changes, your contribution is appreciated. I will make a note to update the DESCRIPTION files so that the GitHub repo can be found more easily.
Pariksheet Nanda (16:05:47) (in thread): > I feel I’m well covered with autotools, but certainly the tutrorial would be handy for others in the community. I used to write packages for Gentoo Linux and one of their developers, Diego, wrote the bookautotools.io which I’ve found useful besides the autoconf and m4 manuals.
Kasper D. Hansen (19:18:23) (in thread): > Sounds like you probably know more about autotools than I do (but perhaps less about using it in an R package). A key thing you should remember is that if you have a configure file, that you want to inherit the C compiler from the R installation using code like > > CC=`"${R_HOME}/bin/R" CMD config CC` > > (see R-exts section 1.2)
Kasper D. Hansen (19:25:19) (in thread): > That book seems good
2021-08-27
Lluís Revilla (07:09:21): > I thinkhttps://code.bioconductor.org/browse/ is down:thinking_face:
Andres Wokaty (07:25:42) (in thread): > Thanks for mentioning that. We’ll look into it.
Lluís Revilla (08:05:04) (in thread): > If it helps the first time I tried I got an error about mathjax, but din’t thought to copy it
Lluís Revilla (08:05:31) (in thread): > And thank you for providing this service
Andres Wokaty (08:12:22) (in thread): > Thanks for the additional information.@Mike Smith
Mike Smith (10:19:27) (in thread): > @Lluís Revillais it working for you now?
Lluís Revilla (10:20:52) (in thread): > Yes, not it is working back! I used this to check the availability of the website:https://downforeveryoneorjustme.com/code.bioconductor.org - Attachment (Down For): code.bioconductor.org down? Current problems and status. - DownFor > code.bioconductor.org won’t load? Or, having problems with code.bioconductor.org ? Check the status here and report any issues!
Lluís Revilla (10:20:56) (in thread): > Thanks for the quick fix
2021-08-31
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2021-09-01
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2021-09-06
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2021-09-07
Kozo Nishida (23:02:32): > We launched the dedicated website for BioC Asia 2021.https://biocasia2021.bioconductor.org Join us if the time-zone is right for you. - Attachment (biocasia2021.bioconductor.org): BioC Asia 2021 > Site template made by devcows using hugo
2021-09-10
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2021-09-12
Vince Carey (10:59:46): > Pondering AnnotationHub metadata. > > > ahtags = sort(unique(unname(unlist(mcols(AnnotationHub::AnnotationHub())$tags)))) > snapshotDate(): 2021-05-18 > > ahtags[32:40] > [1] "[CL] MEL (Gata1/ER)" > [2] "[CL] T6E T Lymphocyte" > [3] "[CL] Tot2 (Irf8 KO)" > [4] "[PC]" > [5] "[PC] " > [6] "[PC] B-Cells" > [7] "[PC] B-Cells (Rag2-/-)" > [8] "[PC] Bone Marrow Macrophage" > [9] "[PC] Bone Marrow Macrophage (Stat1 KO)" > > Does anyone know where the[PC]tokens come from?[CL]would seem to refer to cell ontology.
Charlotte Soneson (11:25:19) (in thread): > Just a guess, but this suggests that it means “primary cell” - Attachment (codex.stemcells.cam.ac.uk): CODEX > CODEX: a functional genomic portal developed by the Gottegens lab, Department of Haematology, University of Cambridge.
Vince Carey (15:40:44) (in thread): > Thank you. Indeed the dataprovider in the metadata is “Haemcode”. And so[CL]denotes only Cell Line and not a cell ontology term.
2021-09-13
Kozo Nishida (18:22:34): > @Sean DavisWhich channel is appropriate for question about Orchestra?
Sean Davis (19:17:29): > Hi,@Kozo Nishida. There isn’t such a channel, but just tagging me from#biocworkshopsmight work.
2021-09-15
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2021-09-16
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2021-09-17
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2021-09-19
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Vince Carey (19:04:36): > bioc aficionados in manhattan: core devs will be at amsterdam ale house around 830pm monday plz slack to<#C02FMPPNFCY>if interested
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2021-09-20
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2021-09-21
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2021-09-23
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2021-09-28
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2021-09-29
Stephanie Hicks (21:30:08): > hello! I’m preparing a lecture on object oriented programming and reading through Hadley Wickham’sAdvanced R book on S4 (https://adv-r.hadley.nz/s4.html#learning-more ). He notes that Bioconductor has some of the best material for S4 and points to a link from 2017 from@Martin Morgan@Hervé Pagès(https://bioconductor.org/help/course-materials/2017/Zurich/S4-classes-and-methods.html ). Do people have fav recs on more recent S4 material?
Peter Hickey (21:31:52) (in thread): > i remember enjoying this blog post by@Stuart Leehttps://stuartlee.org/2019/07/09/s4-short-guide/ - Attachment (stuart lee): S4: a short guide for the perplexed > I recently attended the Bioconductor 2019 conference in New York City, where I was lucky enough to give a workshop on my Bioconductor package plyranges and present some new ideas I’m working on. After some discussion with both Bioconductor veterans and new-comers there was general agreement that it was hard to find good resources or even a beginner’s guide for learning S4. This blog-post is an attempt to rectify that.
Stephanie Hicks (21:32:27) (in thread): > thanks@Peter Hickey@Stuart Lee!
Stephanie Hicks (21:40:36) (in thread): > lil_turtle,okTurtle:joy::purple_heart:
Dirk Eddelbuettel (21:45:02) (in thread): > Can’t compete with that but I still have Gentleman (2009, CRC), “R Programming for Bioinformatics”, here along with Chambers (2008, 2016). And was wondering if/where it was dated when I re-read some stuff last week…
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Stuart Lee (22:59:10) (in thread): > I really like Chambers 2008 too , maybe@Michael Lawrencehas more up to date materials - Attachment (springer.com): Software for Data Analysis - Programming with R | John Chambers | Springer > John Chambers has been the principal designer of the S language since its beginning, and in 1999 received the ACM System Software award for S, the only statistical software to receive this award. He is author or coauthor of the landmark books on S. Now he turns to R, the enormously successful…
2021-10-02
saskia (06:01:59): > The Code of Conduct Committee is looking for new members! We are a friendly bunch and would love more input from the community. So if you feel passionate about the Bioconductor community, please apply by the 21st of October. Of course if you know someone, please forward. To apply fill outthis form . - Attachment (Google Docs): Bioconductor Code of Conduct Committee Elections 2021 > The Bioconductor Code of Conduct Committee updates, disseminates, upholds and enforces the Code of Conduct (http://bioconductor.org/about/code-of-conduct/ ) across all platforms of the Bioconductor project. Each year the Code of Conduct Committee invites applications to become a new member of the committee. If you are interested in becoming a member of the committee, please fill out the following short application. The applications are then voted on by the current committee. The Bioconductor Code of Conduct Committee strives for a diverse and inclusive committee and thus encourages applications from members of underrepresented groups. Find out more about the Code of Conduct Committee and its work! (https://docs.google.com/presentation/d/11c1_LjiZbEJ-4S5jgcJnEzdcVo5yhxHICKdI4e95oVM/edit?usp=sharing ) Applications close 21st of October. If you have any questions regarding serving on the Bioconductor Code of Conduct Committee or the application process, please contact Saskia Freytag (mailto:sas.freytag@gmail.com|sas.freytag@gmail.com ).
2021-10-03
Vince Carey (09:28:50) (in thread): > Very nice to see these S4-oriented resources. I paid a visit toDrS4 to explore issues related to discovery of coercion method and autogeneration of getters and setters. - Attachment (vjcitn.github.io): DrS4 > Provide assistance in examining S4 classes
2021-10-04
Pariksheet Nanda (09:11:04): > I’m hoping to submit my first package for review this week, and I feel it would really help to also schedule a chat with at least one person on the Bioconductor team who will be reviewing the package because I have a growing list of slightly complex questions - 12 so far - that I need to dive into and likely make further revisions. Is it possible / reasonable to schedule this type of discussion for the package submission? Maybe sometime over Slack or video conferencing? If so, I’ll mention that in the new package submission issue . If not, I’ll just toss in the questions I have in the issue and explain that I’m happy to make those revisions.
Laurent Gatto (09:35:29) (in thread): > There’s a mentoring scheme being set up, which looks like would be the right fit for your request. Also, providing some basic info about your package (like the DESCRIPTION file) could help finding a good match to help out.
Lluís Revilla (09:36:11) (in thread): > Those kind of questions might have been already answered on the mailing list and if not it would be on the interest of everybody to have them on the open/searchable. You could also make those question on the#package-submissionor#package_submissionschannels if they are unique questions about your package and you don’t enter on the mentor program.
Pariksheet Nanda (10:01:30) (in thread): > Here’s the DESCRIPTIONhttps://gitlab.com/coregenomics/tsshmm/-/blob/master/DESCRIPTION - Attachment (GitLab): DESCRIPTION · master · coregenomics / tsshmm > Bioconductor package for de-novo transcription start site discovery from nuclear run-on sequencing data
Pariksheet Nanda (10:07:04) (in thread): > I may as well post the list of questions here to help provide an idea: > 1. Either overloading the tile() function in some way with the optional rev argument, or changing IRanges and GRanges.> N checking dependencies in R code (2.4s) > ':::' call which should be '::': ‘IRanges:::PartitioningByWidth’ > See the note in ?`:::` about the use of this operator. > Unexported object imported by a ':::' call: ‘S4Vectors:::diffWithInitialZero’ > See the note in ?`:::` about the use of this operator. > > 2. Whether I should have an assert() in model.c or use some other error mechanism. If the assertion fails, it crashes R!! Would never happen to a user but can happen to a developer messing around with the model probabilities in that C file. > 3. Proper place for developer documentation? HACKING.md / README.md / …? > 4. Be brutal with feedback. > 5. Especially about class structure or function names. For example, should I overload the S4Vectors::params() generic instead of using parameters()? Should I make parameters slots that are “read-only” somehow? > 6. Should I replace new("TSSHMM") with TSSHMM()? Kasper mentions it’s not a good idea for complicated classes (https://kasperdanielhansen.github.io/genbioconductor/html/R_S4.html ), but this is a simple class, I think. > 7. create_batches() is the only non-S4 function. Should I something like a BatchList class to store the list of IntegerList batches? That way the input to train() will also have an S4 object instead of list as the second argument. > 8. I know I have a lot of underscores and can change to camel case: Maybe limit to user facing functions and options? Hard to read camel case. > 9. CRAN complaints about extra autotools files like libtool, the non-portable file name lt~obsolete.m4 file (containing that tilde). > > W checking for portable file names ... > Found the following file with a non-portable file name: > tools/lt~obsolete.m4 > These are not fully portable file names. > See section ‘Package structure’ in the ‘Writing R Extensions’ manual. > ... > W checking top-level files ... > Non-standard files/directories found at top level: > ‘aclocal.m4’ ‘libtool’ > ... > N checking compilation flags used > Compilation used the following non-portable flag(s): > ‘-module’ > > 10. Not tested on Mac OS or Windows: don’t know how to because I don’t have access especially to Windows system. Didn’t hear good suggestions from Slack discussion. > 11. How do I serialize parmeters() instead of erroring out when they don’t match the model? Should there be an API field? > 12. In TSSHMM-class I mention the external pointer because that might surprise people; I know it’s generally considered better not to talk about implementation:https://www.bioconductor.org/help/course-materials/2017/Zurich/S4-classes-and-methods.html#documenting-an-s4-class
Pariksheet Nanda (10:28:34) (in thread): > Mentoring is not really what I’m looking for. I see the value of posting some of the non-package specific questions piecemeal on the mailing list or a separate Slack channel. I’ll prune the list to package specific questions and post them with the new package submission issue. Thanks!
Lluís Revilla (11:08:09) (in thread): > 1. You shouldn’t use internal function of other’s package. > 2. Having more checks is better > 4. Check past reviews, it is usually extensive and sincere but not brutal. You can also check the points reviewers will check athttps://contributions.bioconductor.org/index.html 7. It is okay to have S4, S3 and other non object oriented functions. > 10. You can use continuous integration test to do that. Or you could use r-hub for similar approach (although they don’t have the same environment variables and checks as Bioconductor). > 11. Without seeing the code will be hard to answer. - Attachment (contributions.bioconductor.org): About Bioconductor | Bioconductor Package Guidelines for Developers and Reviewers > This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook.
Kevin Rue-Albrecht (12:13:05) (in thread): > @Lluís Revillacan I ask you to open issues onhttps://github.com/kevinrue/bioc-mentorship-docs/issues , preferably one issue per point of Q&A? > I need more time to think about how to implement it (i.e., how to add and organise the individual points into the existing contents), but I feel that at least some of those points of Q&A could be useful additions to the mentoring materials
Kevin Rue-Albrecht (12:14:21) (in thread): > My idea being that the book might become a nice resource of Q&A’s for mentors, mentees, and package developers generally
Pariksheet Nanda (12:31:32) (in thread): > @Lluís RevillaI appreciate the comments! It’s helpful to know that the reviewers also use that contributions as their checklist.
Hervé Pagès (14:36:45) (in thread): > I feel like some of your questions cannot be properly discussed/answered on Slack. Most of them (2, 3, 6, 8, 10) should probably be asked on the bioc-devel mailing list which is still the preferred place for questions about package development. Maybe 1, 4, 5 can be asked there too, hard to know, I don’t understand them. Make sure you formulate them clearly. Would have been better to ask these things as you develop your package rather than accumulating them and ask them all at once just before submitting.
Pariksheet Nanda (15:29:44) (in thread): > @Hervé PagèsSounds good; I’ll reformulate and ask those questions on the bioc-devel mailing list.
Hervé Pagès (15:52:51) (in thread): > For your question abouttile(), see my answer herehttps://community-bioc.slack.com/archives/C35G93GJH/p1628036760010700?thread_ts=1626452782.009900&cid=C35G93GJH (from 2 months ago): - Attachment: Attachment > For your other questions: > > Is there a canonical way to inspect the SEXP object to query if it’s a CompressedIntegerList? > if (isObject(x) && strcmp(CHAR(STRING_ELT(GET_CLASS(x), 0)), "CompressedIntegerList") == 0) { > ... > } > However, please note that this is the equivalent to doing something like identical(class(x), "CompressedIntegerList") in R, which is rarely the right thing to do. It’s almost always better to check that an object extends some class e.g. > is(x, "CompressedIntegerList") > There is probably a way to do this in C but I never bothered to investigate. I just got into the habits of doing most of the argument checking in R, just before passing them to my .Call entry points. > > While I have you, I was wondering what your thoughts are about patching GenomicRanges and IRanges to natively generate reversed tile() output? Basically I only need a single line changed, that would greatly speed up my use case > Please open an issue on GitHub (https://github.com/Bioconductor/GenomicRanges/issues ) to request the feature. It’ll be easier to discuss it there. Thanks!
Alex Wolfe (19:37:14): > @Alex Wolfe has joined the channel
Kasper D. Hansen (20:34:23) (in thread): > Yes, you should post on bioc-devel for this
2021-10-05
Michael Love (05:17:06) (in thread): > I started a simple demo package with contributions from@Martin Morgan. For those who learn by copy:laughing:https://github.com/mikelove/s4demo
Stephanie Hicks (07:22:40) (in thread): > that’s a fantastics idea@Michael Love@Martin Morgan!
Stephanie Hicks (07:25:15) (in thread): > fwiw, my lecture last week ended up being mostly S3, but there is a bit of S4. It includes making abusandparty_busS4 class:joy::bus: > > setClass(Class = "bus_S4", > slots = list(n_seats = "numeric", > top_speed = "numeric", > current_speed = "numeric", > brand = "character")) > setClass(Class = "party_bus_S4", > slots = list(n_subwoofers = "numeric", > smoke_machine_on = "logical"), > contains = "bus_S4") > > https://www.stephaniehicks.com/jhustatcomputing2021/posts/2021-09-30-object-oriented-programming/index.html - Attachment (Statistical Computing): Statistical Computing: Object Oriented Programming > Introduction to S3, S4, or reference class with generics and methods.
Michael Love (07:42:55) (in thread): > #:loud_sound:= detectWoofers()
Michael Love (07:43:31) (in thread): > Did Chris approve the number and placement of bus woofers:joy:
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2021-10-06
JiefeiWang (12:43:46): > Hi channel, we are looking for suggestions forBiocParallel. If you think there is any new feature we can add to next release ofBiocParallel, please feel free to leave your comments here:https://github.com/Bioconductor/BiocParallel/issues/160
Kasper D. Hansen (13:20:20) (in thread): > You never sent that email right? I don’t see it
claudiozanettini (14:12:48): > @claudiozanettini has joined the channel
Pariksheet Nanda (16:23:50) (in thread): > Not yet, but it’s on my list and thanks for the follow up! Working on higher priority of processing data for my advisor:sweat_smile:
Dario Strbenac (19:00:00): > Is there an annotation package that stores the genomic coordinates of any popular commercial exome capture kit as a GRanges object? I am aiming to calculate tumour mutation burden in a comparable way to the majority of previous studies of the same cancer type which don’t use whole genome sequencing.
2021-10-07
Vince Carey (08:25:18): > Might be a good question for the support site.
2021-10-09
Michael Love (07:18:24) (in thread): > Sounds like a useful addition if they aren’t there
2021-10-10
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2021-10-11
Laurent Gatto (07:30:13): > I haven’t seen any report so far, but the Bioconductor server seems to be down, at least from Belgium - can’t access the website nor install packages.
Alan O’C (07:35:07) (in thread): > Yep same here,bioconductor.org times out when updating packages
Stuart Lee (07:35:13) (in thread): > Same
İrem B. Gündüz (07:40:15): > @İrem B. Gündüz has joined the channel
Lluís Revilla (07:44:41) (in thread): > It seems it is down for everybody: currentlyhttps://downforeveryoneorjustme.com/bioconductor.org shows “It’s not just youbioconductor.org down? Current problems and status. - DownFor > bioconductor.org won’t load? Or, having problems with bioconductor.org ? Check the status here and report any issues!
Maria Angeles Martinez Rodriguez (07:50:37): > @Maria Angeles Martinez Rodriguez has joined the channel
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Mike Smith (08:44:02) (in thread): > Seems very intermittent for me. The website is horribly slow, but I was able to download a package withBiocManager::install().
Alan O’C (08:44:47) (in thread): > Website loads after >30s for me
Alan O’C (08:45:12) (in thread): > Probably could get packages downloaded if you setoptions(timeout=10000)or something equally silly
Alan O’C (08:46:45) (in thread): > Also see a ns_error_dom_bad_uri in the network inspector fwiw
Vince Carey (09:13:45) (in thread): > sorry about this. i am seeing AWS Cloudfront errors. This is a US holiday so I don’t know how quickly this can be resolved but we are aware in core.
Laurent Gatto (09:37:34) (in thread): > Thank you for following up, Vince. No worries at all. This is, as far as I can remember, the only issue with the Bioc server(s) I have experienced in 18 years or so.
Lori Shepherd (11:06:02): > The site should be back up sorry for the inconvenience – we will monitor closely over the next day as we investigate the cause
Lori Shepherd (11:07:33): > The build reports do appear to be present for Friday for release and Saturday for devel – I’m not sure if the downtime will effect the posting of today’s report
Vince Carey (11:54:38): > Thanks a million to Lori. Also to Joshua K of AWS tech support who very quickly diagnosed complex issues with our server setup.
Alan Murphy (12:23:10): > Is there any way to get a package tested on the 3 machines again now? It appears my package (MungeSumstats) failed to build with new changes I pushed on Saturday. I can’t replicate the error so I want to rule out the server issue today:https://bioconductor.org/checkResults/3.14/bioc-LATEST/MungeSumstats/nebbiolo2-buildsrc.html I would wait for tomorrow’s build generally but with the code freeze I want to ensure it won’t result in an error then
Alan O’C (12:31:17) (in thread): > Aren’t the package builds meant to run without internet access?
Alan Murphy (12:32:01) (in thread): > My package needs it for certain actions in the vignette
Alan O’C (12:32:22) (in thread): > Well, then the build will fail.
Alan Murphy (12:33:28) (in thread): > Yeah the issue is I made other changes which I need to make sure resolved previous build errors I was having. I can’t see if this was the case since the builds failed at the vignette stage
Alan O’C (12:39:17) (in thread): > Probably best to save the results of the query in the package, then?
Alan O’C (12:47:21) (in thread): > Also it might be good to output the original warning/error fromdownload.filealong with the one you’ve added regarding ID/URL, because that might tell you why it fails in the vignette
Alan Murphy (12:55:30) (in thread): > These are useful for future reference and thank you for them but I still really need to know the code I have will pass checks now before the freeze tomorrow (either with or with these changes incorporated)
David Mateo García (13:45:51): > @David Mateo García has joined the channel
Vince Carey (13:51:30) (in thread): > Today is a holiday in the US.@Alan MurphyI do think you should write the code so that failure to connect is handled and does not lead to an error state for your package check. It would also seem that the file that was unavailable is pretty small and you could just stash it in the package for demonstration purposes. As for beating the freeze, we may have some flexibility on that. Just get the package to the best state you can.
Alan Murphy (13:57:31) (in thread): > I’ll do that now, thanks@Vince Carey!
2021-10-12
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Dario Strbenac (05:00:09) (in thread): > As a challenge, I decided to try to obtain the Agilent Human SureSelect coordinates. To get a BED file, it requires registration for Agilent’s SureDesign portal and that didn’t work for me. Now I understandwhy there aren’t such Bioconductor packages. Attempting to (unsuccessfully) register also triggers a notification to your local Agilent sales representative. - File (PNG): Targeted Advertising
Martin Morgan (13:16:13): > https://chanzuckerberg.com/rfa/single-cell-data-insights/ sounds like an excellent fit for Bioconductor software development! - Attachment (Chan Zuckerberg Initiative): New Funding Opportunity for Single-Cell Computational Biology > Advancing tools and resources for analyzing single-cell biology datasets to gain greater insights into health and disease.
2021-10-13
Laurent Gatto (06:12:34) (in thread): > I would be keen to contribute with respect to proteomics single-cell.
2021-10-14
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2021-10-16
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2021-10-17
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saskia (21:08:00): > The Code of Conduct Committee, a friendly bunch, is looking for new members! This is a really great opportunity for anyone (any level of expertise and any level of career stage) to get leadership experience. So if you feel passionate about the Bioconductor community, please apply by the 21st of October. Of course if you know someone, please forward. To apply fill outthis form . Only 3 more days to go!!! - Attachment (Google Docs): Bioconductor Code of Conduct Committee Elections 2021 > The Bioconductor Code of Conduct Committee updates, disseminates, upholds and enforces the Code of Conduct (http://bioconductor.org/about/code-of-conduct/ ) across all platforms of the Bioconductor project. Each year the Code of Conduct Committee invites applications to become a new member of the committee. If you are interested in becoming a member of the committee, please fill out the following short application. The applications are then voted on by the current committee. The Bioconductor Code of Conduct Committee strives for a diverse and inclusive committee and thus encourages applications from members of underrepresented groups. Find out more about the Code of Conduct Committee and its work! (https://docs.google.com/presentation/d/11c1_LjiZbEJ-4S5jgcJnEzdcVo5yhxHICKdI4e95oVM/edit?usp=sharing ) Applications close 21st of October. If you have any questions regarding serving on the Bioconductor Code of Conduct Committee or the application process, please contact Saskia Freytag (mailto:sas.freytag@gmail.com|sas.freytag@gmail.com ).
2021-10-18
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2021-10-21
Martin Morgan (11:24:45) (in thread): > For those interested — please jot down availability for an orientation meeting next week athttps://www.when2meet.com/?13358750-LGxyt
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2021-10-23
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2021-10-24
Martin Morgan (09:53:01) (in thread): > Thanks for the responses. There’s a new channel#hca-data-insightswith a link for the first meeting.
Gavin Tomlins (20:02:28): > @Gavin Tomlins has joined the channel
2021-10-25
Davide Risso (13:02:38): > Sharing this with the main channel as people may have missed the thread: a group of us interested in this RFA are meeting this Wednesday at 8am Eastern. Feel free to join and/or reach out if you’re interested in participating. See the#hca-data-insightschannel for details including Google Meet link - Attachment: Attachment > https://chanzuckerberg.com/rfa/single-cell-data-insights/ sounds like an excellent fit for Bioconductor software development!
2021-10-26
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2021-10-27
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Lori Shepherd (16:55:52): > Bioconductor 3.14 is Released!! Thank you to all developers and community members for contributing to the project. See fullBioconductor 3.14 Release Announcmenet
2021-10-28
itTan (02:48:08): > @itTan has joined the channel
Michael Love (06:31:07) (in thread): > Thanks to the core team as well!
2021-10-29
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2021-11-01
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2021-11-02
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2021-11-04
saskia (18:58:18): > The Code of Conduct Committee is changing.@Aedin Culhane,@Matt Ritchie,@Levi Waldronand@Stephanie Hicksare leaving the committee after two years. (Thanks for all the awesome work!) They are replaced by 5 new members (@Lluís Revilla,@Anna Quaglieri (she/her),@Sowmya Parthiban,@Federico Mariniand@Michael Love). Part of the Committee change is also a slight change to theCode of Conduct : > * fixed typos > * included new reporting form > * rules around account names in Bioconductor spaces
2021-11-05
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2021-11-08
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2021-11-09
Aedin Culhane (09:33:29): > Hi. Have people experience with Orange for sc. Does it only use python or does it also use R/Bioconductor at its backend. seems like the former… but maybe other know morehttps://github.com/biolab/orange3-single-cell https://singlecell.biolab.si/ Its a nice use of visual programming - Attachment (singlecell.biolab.si): scOrange – Single Cell Analysis Single Cell Analysis > Orange Data Mining Toolbox
GuandongShang (20:32:09): > Hi. I developed a package in Bioc 3.13 and now its version is bumped by 1.0.0, but I am little confused about Git release branch and bump version of packages development. I am wondering whether someone can help me see if what I do is correct. > According to thehttps://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ , first, I sync my local repo with Github and Bioconductor > > git fetch --all > git checkout master > git merge upstream/master > git merge origin/master > > git checkout -b RELEASE_3_14 upstream/RELEASE_3_14 > git checkout RELEASE_3_14 > git merge upstream/RELEASE_3_14 > git merge origin/RELEASE_3_14 > > Then I modify some code in master branch > > git checkout master > # modify code > # bump version in DESCRIPTION into 1.1.1 > git add code file and DESCRIPTION > git commit -m "modify code" > > And then I switch to RELEASE_3_14 and cherry-pick the commits from master > > git checkout RELEASE_3_14 > git cherry-pick master > # Now the conflict appears in version section in DESCRIPTION file like this > > <<<<<<< HEAD > Version: 1.1.1 > ======= > Version: 1.0.0 > >>>>>>> upstream/master > > So I delete other line and only keep the Version 1.0.0 and bump it into 1.0.1. And I git add and commit > > git add DESCRIPTION > git commit -m "update RELEASE version number" > > Then I push my changes to Github and Bioconductor > > git checkout master > git push upstream master > git push origin master > > git checkout <RELEASE_X_Y> > git push upstream <RELEASE_X_Y> > git push origin <RELEASE_X_Y> >
Marcel Ramos Pérez (21:32:50) (in thread): > Hi@GuandongShangThis is a good question for the#bioc_gitchannel.
GuandongShang (21:34:53) (in thread): > Thanks!
2021-11-10
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2021-11-11
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2021-11-15
Mike Smith (18:35:47): > Just wanted to highlight this exciting talk on Thursday to those that aren’t members of the#developers-forumchannel. - Attachment: Attachment > After a hiatus the Developers Forum will be back next Thursday 18th November at 09:00 PST / 12:00 EST / 18:00 CET - You can find a calendar invite attached and at https://tinyurl.com/BiocDevel-2021-11 > > @Jeroen Ooms will give an overview of the R Universe project (https://r-universe.dev/ ). This project offers individuals or organisations a platform to build, test and release R packages outside of CRAN or Bioconductor. As well as being potentially useful to those who are developing packages, there’s also a tonne of infrastructure engineering to create the build system, and it should be really interesting to learn more about this. > > Please note the meeting details have changed; We’re now on Zoom: > https://embl-org.zoom.us/j/99712225827?pwd=ZUdWRGhqalgzRmsxbjY3RkRGRHMzZz09
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2021-11-16
Henrik Bengtsson (20:39:47): > WISH: Have you thought about linking to Bioc::CodeExplore on each Bioc package page? For example, onhttps://bioconductor.org/packages/affxparser/ add a link tohttps://code.bioconductor.org/browse/affxparser/ ? (I’m sure it’s been discussed already, but I must have missed it) - Attachment (code.bioconductor.org): Bioconductor Code: Browse > Browse the content of Bioconductor software packages.
Marcel Ramos Pérez (23:00:38) (in thread): > Yes we have and we haven’t gotten around to implementing it. The landing page, the code, and the build result should all reference each other consistently. Thanks for putting this back on our radar.
2021-11-17
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2021-11-18
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2021-11-19
Christian Arnold (05:06:22): > @Christian Arnold has joined the channel
Christian Arnold (05:08:03): > Hi guys, Christian here. Is this the right place to ask a question regarding a warning I get with BiocCheck() for a Bioconductor package preparation?
Lluís Revilla (05:13:30) (in thread): > Hi Christian! It might be okay, but probably it is better if you ask (and search before) on the mailing list.
Christian Arnold (05:30:28) (in thread): > I did, while the error has been discussed before, I wanted to check here for options and related questions, so I’ll just go ahead, might be useful for others also
Christian Arnold (05:34:26): > With BiocCheck(), the only warning left is the famous “The following files are over 5MB in size” warning, which in my case related to various Vignette files in the “workflow” vignette. I cant easily bring it down to < 5 MB, for various reasons, so looking for alternatives. The package will have a dedicated website where the Vignettes are also shown (up-to-date versions which are automatically build whenever I push a change). So I dont necessarily need the Vignette as part of the package, I am thinking about referencing it in the Intro vignette which is built as part of the package which compiles quickly. So my question is: Is there any big disadvantage I am overseeing with this approach (Providing only the Intro Vignette as part of the package, and cross-referencing the Workflow vignette and keeping it up-to-date on the external package website with no file size limitations)? How do specify to ignore one Vignette but not the other for say BiocCheck()?
Lluís Revilla (05:49:40) (in thread): > On Bioconductor vignettes are build every 2-3 days when all the packages are tested (not only when you push a new version). If you separate your vignettes from the Bioconductor testing framework your users following that vignette might find errors not caught by your setup. (I found this frequently on packages that moved their vignette to be built outside Bioconductor.) You might find interesting reading the section of the Bioconductor package development book:http://contributions.bioconductor.org/docs.html?q=vigne#vignettes As per the guide, if you leave one vignette on Bioconductor your reviewer might allow the other’s on your site. Good luck! - Attachment (contributions.bioconductor.org): Chapter 11 Documentation | Bioconductor Packages: Development, Maintenance, and Peer Review > Package documentation is important for users to understand how to work with your code. Bioconductor requires: a vignette with executable code that demonstrates how to use the package to accomplish…
Christian Arnold (07:56:18) (in thread): > Thanks for the link. When reading this: “Only the source vignette file (.Rnwor.Rmd) and any necessary static images should be in the vignette directory. No intermediate files should be present.”, the warning in my case may comes from intermediate files actually. In the beginning or output, no file is > 5 MB, only what is produced in the various chunks in between is >5 MB. Only the final output file that I so far optionally store on disk as an rds file is > 5 MB, so I can just mark the chunk as “dontrun” or skip it altogether
Lluís Revilla (08:06:57) (in thread): > If you create files on the vignette, create them on the temporary directory. It is fine there (I don’t remember if you need to delete it later), but not on the source code of the package like you seem to have now. A link to the repository would help, but that will be addressed on the review too.
Christian Arnold (08:16:30) (in thread): > Indeed, right now, a “workflow_cache” directory is produces automatically within the vignettes subfolder, where intermediate files are stored that I cant control. Changing this to a temporary folder is a good idea; for me it is fine to solve such issues during a review process indeed
Christian Arnold (08:24:11) (in thread): > Thanks@Lluís Revillafor your help and insights
Lluís Revilla (08:57:18) (in thread): > I hope to see your package on Bioconductor on the next release! > hNo problem
Christian Arnold (09:06:08) (in thread): > Do you happen to know when the next submission deadline is for the next release?
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Lluís Revilla (09:08:18) (in thread): > It will be with next R release, so a month before, usually around February. You can submit whenever you are ready, the deadline is only to be included on the next release (sometimes packages are submitted before the deadline but they are not release on the next one because not all the issues are solved in time).
Alan O’C (10:15:54) (in thread): > Does BiocCheck respect.Rbuildignore?
Lluís Revilla (10:30:14) (in thread): > BiocCheck can also be used on an already built package, so I guess that when done on the repository it respects it.
2021-11-20
Vince Carey (08:41:32) (in thread): > Itcan
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Aedin Culhane (08:59:14): > Next week I will be the curator of the WomenInStat twitter account…. any suggestions… what should I tweet about? What would be most interesting to you?
2021-11-29
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2021-12-08
Lluís Revilla (04:24:58): > It seems that some packages from Bioconductor need changes for the new R-devel: > > authors of packages using native (C, C++ or Fortran) code should read the following lines. Some of them will have to update their packages… > https://developer.r-project.org/Blog/public/2021/12/07/upcoming-changes-in-r-4.2-on-windows/index.html
Alexander Bender (06:22:23): > @Martin Morganrelated to this issue (https://github.com/plger/scDblFinder/issues/53#issuecomment-988717262 ) — shouldn’t this be smoother / automatically handled byBiocParallel bpstart()/bpstop()?
Hervé Pagès (10:34:05) (in thread): > The CRAN folks are switching to the UCRT runtime for R 4.2 on Windows and to a new toolchain (RTools42). We’re currently working on setting up a new Windows builder to replicate this new setup. Some packages with native code are expected to break. Having the new Windows builder in the daily report will help us identify them.
Lluís Revilla (10:50:15) (in thread): > Thanks for replying, I wasn’t sure if CRAN team and the R core was talking only to individual package maintainers or directly with the Bioconductor technical board. Hope that the transition on the servers and checks will be smooth.
Mikhail Dozmorov (11:03:03): > This is a general R question, I wonder if anybody encountered it. After updating R to 4.1.0, I’m noticing lots of “NAs introduced by coercion to integer range” warnings while running simple commands. Everything works and knits, but clearly something is off. Restarting the session doesn’t help. Couldn’t google it. What may be going on? > > > print(paste("Total downregulated:", length(degs_DN))) > [1] "Total downregulated: 1390" > Warning messages: > 1: In paste(sig, collapse = "#") : > NAs introduced by coercion to integer range > 2: In paste(...) : NAs introduced by coercion to integer range > 3: In paste(...) : NAs introduced by coercion to integer range > 4: In print.default(paste("Total downregulated:", length(degs_DN))) : > NAs introduced by coercion to integer range > 5: In print.default(paste("Total downregulated:", length(degs_DN))) : > NAs introduced by coercion to integer range > 6: NAs introduced by coercion to integer range > 7: NAs introduced by coercion to integer range > 8: NAs introduced by coercion to integer range > 9: NAs introduced by coercion to integer range > 10: NAs introduced by coercion to integer range > > class(degs_DN) > [1] "character" > There were 50 or more warnings (use warnings() to see the first 50) >
Martin Morgan (13:45:28): > collapse = "#"is not the default value of thecollapse=argument to paste, so I’m guessing that the problem is in a package that has perhaps written apastefunction; what does the body of paste look like? I have > > > paste > function (..., sep = " ", collapse = NULL, recycle0 = FALSE) > .Internal(paste(list(...), sep, collapse, recycle0)) > <bytecode: 0x7f82fc879958> > <environment: namespace:base> >
Mikhail Dozmorov (13:48:22) (in thread): > Slightly different bytecode, otherwise - the same > > > paste > function (..., sep = " ", collapse = NULL, recycle0 = FALSE) > .Internal(paste(list(...), sep, collapse, recycle0)) > <bytecode: 0x7fbb2412f138> > <environment: namespace:base> >
Mikhail Dozmorov (13:48:58) (in thread): > The problem occurs in many other instances. It seems like something fundamental. Cannot understand what.
Martin Morgan (15:58:37) (in thread): > Is this in RStudio or just R? Can you provide sessionInfo() after a minimum reproducible example? you could also ‘promote’ the warning to an error, and then use traceback() — > > options(warn = 2) > ## make the error happen > traceback() > options(warn = 0) >
Henrik Bengtsson (18:48:18) (in thread): > There’s a: > > > methods:::.sigLabel > function (sig) > paste(sig, collapse = "#") > <environment: namespace:methods> > > in the R source code (https://github.com/wch/r-source/blob/e029bc70683a7cca2caedbecf93b5919a7e92427/src/library/methods/R/methodsTable.R#L443-L444 ). That could be a clue, but I have no idea what sorcery could cause that to inject itself here.
Martin Morgan (19:49:04) (in thread): > Iresponded to the issue . The TL;DR is to use the current version (3.14) of Bioconductor. > > > BiocManager::version() > [1] '3.14' > > BiocManager::valid() > [1] TRUE # or a message indicating how to make it valid > > Additional subtleties are in the comment.
Mikhail Dozmorov (21:11:32) (in thread): > This may be a localized situation that may be cured by reinstalling R/Rstudio from scratch, Which is a setback. This craziness can be reproduced, it may be one or a combination of packages. Still, it is super weird. Thetracebackapproach didn’t help, same message but with error. - File (PDF): Warnings.pdf - File (Plain Text): Warnings.Rmd
Henrik Bengtsson (21:58:02) (in thread): > I think Martin was after theoutput oftraceback(); that’ll help narrow down what’s going on. What does it show?
Mikhail Dozmorov (22:02:02) (in thread): > Not much, surprisingly: > > There were 50 or more warnings (use warnings() to see the first 50) > > options(warn = 2) > Warning messages: > Error: (converted from warning) NAs introduced by coercion to integer range > In addition: Lost warning messages > > ## make the error happen > > print("x") > Error in print.default("x") : > (converted from warning) NAs introduced by coercion to integer range > > traceback() > Error in deparse(x[[1L]]) : > (converted from warning) NAs introduced by coercion to integer range > > options(warn = 0) > > And, all the previous warnings are those NAs..
Henrik Bengtsson (22:29:15) (in thread): > Woohoo …, yeah, you’ve got something really weird going on. This is certainly not normal or expected. I would start by verifying thatprint("x")works in a vanilla R session, i.e. > > $ R --vanilla > ... > > print("x") > [1] "x" > > Then I would try to load your packages one by one and retry. Hopefully that’ll identify a single problematic package. > > BTW, what does.libPaths()show?
Henrik Bengtsson (22:37:29) (in thread): > Also, try the following: > > options(warn = 2) > print("x") ## trigger the error > options(warn = -1) ## disables all warnings > traceback() ## print traceback > options(warn = 0) ## re-enables warnings > > It might help show the realtraceback()
2021-12-10
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Alan O’C (06:09:01): > Is there any way for CRAN packages that depend on Bioc package(s) to ensure the deps are automatically installed? There’s an old trick of adding an empty biocViews that seems to not work any more, but curious if there’s anything else
Lluís Revilla (06:19:26) (in thread): > I have one CRAN package that suggests Bioconductor packages (and used them on examples and tests). I didn’t have to provide anything else (No biocViews, no Additional_repositories or remotes field) , they are automatically picked by CRAN. But most of the time there are some notes of missing packages on MacOS on the daily checks, so be ready to use them conditionally. Hope this helps
Alan O’C (06:22:58) (in thread): > I think CRAN finds them no problem, but users are a different story. eghttps://cran.r-project.org/web/packages/PhenotypeSimulator/index.html has snpStats as anImportsandinstall.packagesfails with no suggestion for how to fix if I don’t have snpStats installed locally
Lluís Revilla (06:31:51) (in thread): > To avoid this kind of problems I simply install all packages via BiocManager,BiocManager::install("PhenotypeSimulator")But the package could explain that it needs Bioconductor dependencies and how to install them on the README.
Alan O’C (06:33:50) (in thread): > Same here. Yeah seems best, although imo this shouldn’t really be necessary, or at least R should prompt users to use BiocManager
Lluís Revilla (06:45:32) (in thread): > It is hard to warn users, install.packages doesn’t know it needs a Bioconductor package, as there is no way to distinguish missing dependencies from Bioconductor than those from other sources. Maybe there could be a field on DESCRIPTION for that something like Repositories: CRAN, Bioconductor
Kevin Rue-Albrecht (08:05:17) (in thread): > @Alan O’Chave you tried to either runoptions(repos = BiocManager::repositories())or adding it to~/.Rprofile? > In some cases, I’ve used that to install Bioconductor packages usinginstall.packages()orrenv::install()I’m not going to get into hours of discussion why this isn’t best practices, but adding Bioconductor repositories to the “search path” should allow installation functions to pick up dependencies in any of the repositories
Alan O’C (08:06:14) (in thread): > I know how to install Bioc packages, I’m more asking about the general case for users who may not understand why a CRAN package has failed to install due to an unavailable (in this case Bioc) package
Kevin Rue-Albrecht (08:07:42) (in thread): > I’m not sure how that came across, but I wasn’t talking about installing Bioconductor packages, I was saying that changing thereposoption should pick up dependencies in those repos, even when installing CRAN packages
Kevin Rue-Albrecht (08:11:38) (in thread): > Explaining the relationship between CRAN and Bioconductor to novice users will always be a bit of a challenge (I’ve tried to illustrate this herehttps://carpentries-incubator.github.io/bioc-project/03-installing-bioconductor/index.html ) > What I’ve proposed is a relatively advanced workaround (that requires some prior knowledge of repos and options) to not fail when a CRAN package has a Bioconductor dependency. That said, reading your discussion so far, we would probably need to document a number of failed installation use cases to identify patterns that cause this behaviour and offer a proper fix or guide
Kevin Rue-Albrecht (08:14:02) (in thread): > Actually, more simply, doesn’tBiocManager::install("CRAN_package")just do what your original message asks? I mean BiocManager::install() naturally searches both CRAN and Bioconductor
Alan O’C (08:18:30) (in thread): > Perhaps I have not been clear. Take the case where somebody runsinstall.packages("PhenotypeSimulator"). The installation fails becausedependency ‘snpStats’ is not available for package ‘PhenotypeSimulator’. If the user knew to useBiocManager::installfor CRAN packages that depend on Bioc, or to setoptions(repos)this would not be a problem. However, without doing either, it is a problem, and there is no obvious suggestion for a resolution. I am asking is there something that package authors can do to ensure that this does not happen
Kevin Rue-Albrecht (08:22:24) (in thread): > Right - Then, to answer your question “is there something that package authors can do to ensure that this does not happen”, my answer would be that the author should declare in their installation instructions to use BiocManager::install() to install their package. > I don’t see any reason for CRAN to bother updatinginstall.packages()to track every other repository of R packages where dependencies might be found.
Kevin Rue-Albrecht (08:23:18) (in thread): > Error messages and diagnostics can only cover so many use cases, the rest is about educating users
Alan O’C (08:42:49) (in thread): > Feels off to me that packages from the primary R repository fail to install with an error amounting to “:shrug:”
Mike Smith (08:57:32) (in thread): > I’m with Alan. I’d never realised this behaviour happens, and it feels really odd. > > To me Bioconductor is large enough and been around long enough that it has achieved some level of “special status” in the R world. We all know CRAN have some fairly tricky criteria for inclusion in the repository, so if they’ve declared it’s fine for a CRAN package to depend on a Bioc package, installation shouldn’t then be difficult. It’s not like we’re talking about some one-off GitHub repo, which I presume a CRAN package can’t depend on (??). > > I’d also point to the existence of functions likeutils::chooseBioCmirror()as proof that there’s some level of acknowledgement for the existence of Bioconductor in the core R functionality.
Alan O’C (09:51:03) (in thread): > Yeah, it would be understandable to me if they didn’t trust Bioc packages as dependencies. What’s weird is trusting them, and including them in the build system, but not helping users actually install them
Henrik Bengtsson (14:05:45) (in thread): > FWIW, R andR CMD checkhas a formal concept ofmainstream repositories, to which they count CRAN and Bioconductor. I’m quite sure one thing this means is that you cannot have two different packages with the same name in these mainstream repositories. Also, you donot have to declareAdditional_repositoriesfor dependencies on Bioconductor packages. TheAdditional_repositoriesDESCRIPTION field was added some years ago to allow for R packages to depend on packages in third-party (formal) R package repositories, which is why we can (=are allowed to) depend on R packages that are hosted elsewhere, e.g.https://ropensci.org/r-universe/ ,https://neuroconductor.org/ , self-hosted drat repositories on GitHub, etc.
Henrik Bengtsson (14:10:07) (in thread): > To@Alan O’C’s point, yes, it would be awesome if one could install Bioconductor packages usinginstall.packages()out of the box. It’s definitely adds lots of issues for new comers to R and users who do not know the difference what CRAN and Bioconductor is, or even heard those terms. The only solution now is documentation. Unfortunately, you’renot allowed to add that to the ‘Description’ of your DESCRIPTION file, when submitting to CRAN. At least, I was asked to remove such instruction for packages some years ago. So, a README.md file, which are linked to on CRAN package pages, is probably the best bet right now.
Henrik Bengtsson (14:14:37) (in thread): > Now, I think a first step towards havinginstall.packages()to be able install Bioconductor out of the box, would be for Bioconductor to move away fromBiocManager::install(). If the Bioconductor project itself asks users to use another installation methods than what comes with R itself, I don’t think we can ask R andinstall.packages()to magically do it for us.
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2021-12-15
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2021-12-16
Levi Waldron (08:01:39): > I’d like to invite any interested members of the community to get involved in organizing BioC2022, planned to be in a hybrid format in Seattle July 27-29, 2022. There is lots to be done, including sponsorship and funding, outreach, website, workshop technical organization, program development, code of conduct communication and enforcement, and local organization. It is a great way to get to know other passionate Bioconductor users and developers, and to support the project. Please fill out this form if you’d like to get involved:https://forms.gle/cbjHww7uHJFRzwVx5 - Attachment (Google Docs): BioC2022 Committee Application > The organizing committee for BioC2022, to be held in Seattle on July 27-29 2022, needs organizers to help in planning the event. Participation involves attending approximately monthly remote meetings (more frequently as the conference approaches) plus taking on responsibilities in one or more of the areas listed below.
Andres Wokaty (15:59:43) (in thread): > Do you need to have experience in the committee you volunteer for?
2021-12-17
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2021-12-18
Kevin Blighe (04:32:45): > Is anybody aware of a package other thanoligo andaffy that can do RMA normalisation for Affymetrix arrays? Bothaffy andoligo , apparently, are written using outdated C libraries that cannot support very large studies.
Kevin Blighe (05:38:15): > ‘very large studies’ ==== long vectors
Vince Carey (06:05:22): > Hi@Kevin BligheI don’t know the answer to your question, but if you would like to add some facts about the problems you encountered athttps://github.com/Bioconductor/affy/issues , perhaps a project to enhance affy’s capabilities could be undertaken. Problem size, array class, error messages, etc. It is not hard to imagine a “bigrma” function that would work using new approaches to data representation, if such a solution is not already available. (I think asking at the support site would make sense too…)
Kevin Blighe (06:07:39): > Hey Vince, yes, let me replicate the exact error - it was previously reported on the Support Site and the conclusion was that the packages required code updates using modern C libraries. Let me get the exact error again, though
Vince Carey (06:54:48): > I see that Benilton has a github repo for oligo.https://github.com/benilton/oligo … which seems to get more endorsement on the support site. I will watch there for issues also.
Vince Carey (06:55:02): > @Benilton S Carvalho^^
Martin Morgan (07:01:38) (in thread): > I’m not@Levi Waldron:wink:or involved with BioC2022 organization, but I’m sure they would welcome all levels of experience!
Levi Waldron (07:05:10) (in thread): > Enthusiasm is the only necessary qualification! Although we can no doubt use your skills too :)
Kevin Blighe (09:40:50): > Error thrown byaffy::mas5()during background correction:* Error in matrix(.C(“affy_background_adjust_R”, as.double(as.vector(allintensities)), :** long vectors (argument 1) are not supported in .CError thrown byoligo::rma()during the same step is: Error in basicRMA(pms, pnVec, normalize, background) :** ERROR; return code from pthread_create() is 22*
Kevin Blighe (09:41:05): > This dataset has ~18000 CEL files. I will post on GitHub
Henrik Bengtsson (13:55:37) (in thread): > (Disclaimer: I’m the creator together with several past and current Bioconductor folks)aroma.affymetrix should do it for you. It was created already back in 2005 to handle large data sets on even small machines (< 1 GiB of RAM). It can process any number of samples - the only limit is your disk space. It replicates RMA, gcRMA, etc. for expression arrays, and SNPRMA of oligo + various CN methods for SNP arrays, e.g.https://aroma-project.org/replication/gcRMA/ andhttps://aroma-project.org/replication/SNPRMA/ . It’s very well tested and validated. Although up-to-date (I think), the documentation/website could be better organized. > > The package relies onaffxparser for parsing Affymetrix CDF and CEL files. So, as long asaffxparser aroma.affymetrix
Kevin Blighe (14:02:14) (in thread): > Thanks Henrik, I will take a look. I had previously used the Aroma suite of functions during my PhD 10 years ago for processing the Affy SNP 6.0 for SNP / CN. Was unaware that it caters also for expression arrays
2021-12-19
Vince Carey (10:00:32): > For the mas5 attempt can you try with a simple modification available via > > BiocManager::install("Bioconductor/affy", ref="try-Call") > > You’ll have to restart R after this installation. I don’t see any obvious regressions with this substitution of .Call for .C. It may take us deeper into the code to find other limitations. Also, can you point me to the support site entry where this was discussed? Perhaps further discussion should be athttps://github.com/Bioconductor/affy/issues .
2021-12-23
Mikhail Dozmorov (10:08:14): > GenomicFeatures::makeTxDbFromUCSCseems broken, posted an issue on the support sitehttps://support.bioconductor.org/p/9141300/ . It seems like UCSC changed their data format? I wonder if anyone has a quick fix other than manually building the TxDb objects?
Mikhail Dozmorov (11:02:54) (in thread): > A workaround: > > library(TxDb.Hsapiens.UCSC.hg38.knownGene) > txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene > # transcripts grouped by gene: GRangesList > transcriptsByGene <- transcriptsBy(txdb, by = "gene") > transcriptsByGene > > HopeGenomicFeatureswill be fixed.
2021-12-30
Vince Carey (09:41:31) (in thread): > @Kevin Blighei’ve lost track of this. Any progress?
Kevin Blighe (13:41:02) (in thread): > Hey@Vince Carey, I tried this fix for affy, but ran into the same problem. I also tried Henrik’s solution via aroma.affymetrix, but ran into version issues and gave up.
Kevin Blighe (13:41:20) (in thread): > In the end, I stratified the dataset by tissue, and this allowed me to use oligo::rma to get it done
Kevin Blighe (13:41:33) (in thread): > Dataset was just over 18000 CEL files; so, quite large
Vince Carey (16:58:19) (in thread): > Thanks for the info. I think we should try to get the code to work at scale. What class of Affy array were you working on? Do you have a sense of the threshold – how many arrays could be handled before it broke? Understood if this is a low priority for you, but if you have the facts we might be able to reproduce the error and establish a solution.
Kevin Blighe (17:00:04) (in thread): > Unsure of the exact threshold, but a dataset of ~8000 CEL files works AOK
Kevin Blighe (17:00:13) (in thread): > Even that is impressive, to be honest. That is a lot of data
Kevin Blighe (17:00:46) (in thread): > The dataset being used in available publicly, TG-GATEs
2022-01-02
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Rosalina Tincopa Marca (21:08:23): > Hi everybody :).I run an script in R, in a server and i got this error
Rosalina Tincopa Marca (21:08:48): > bash command.sh > ARGUMENT ‘Rscript’ ignored ignored
Rosalina Tincopa Marca (21:28:17): > in command.sh is:
Rosalina Tincopa Marca (21:28:21): > R Rscript pingpong_for1.R
Rosalina Tincopa Marca (21:29:00): > i also puth the pathway of tge R version as well
2022-01-09
Dirk Eddelbuettel (00:14:07): > Drop the R – just use Rscript as inRscript pingpong_for1.R.
2022-01-10
Jenny Drnevich (09:59:26): > Thought some BioC people might be interested in this: > The call for tutorials for useR! 2022 is open until Monday, January 31, 2022. One more time the conference is looking for proposals to teach in English, Spanish and French and the organization will pay USD $500 for tutorials that are selected. + info:https://user2022.r-project.org/participate/call-for-tutorials/ - Attachment (user2022.r-project.org): Call for Tutorials > Speaking and Presenting
Rosalina Tincopa Marca (11:13:31) (in thread): > Thank you! I also found this online. “The error message indicates that it is the R executable and not the Rscript executable that was run. You can verify this by using a terminal: > > R /home/path/to/file/helloworld.R # produces above error > Rscript /home/path/to/file/helloworld.R # should work > /home/path/to/file/helloworld.R # should work if file is executable”
Dirk Eddelbuettel (11:14:57) (in thread): > Yes, very close. Option 3 needsboth the correct mode to permit execution,and the shebang#!/usr/bin/env Rscript(or equivalent) to tell the shellwhat to run.
Dirk Eddelbuettel (11:32:20) (in thread): > Oh, and as we are so esoteric now,R -q < /home/path/to/file/helloworld.Ralso works and, if you add flag--interactiveeven gets a plot window. I happened to need that yesterday ;-)
Rosalina Tincopa Marca (11:35:35) (in thread): > Thank you, I will try in another run:+1:
Rosalina Tincopa Marca (12:18:54): > Hi everybody:slightly_smiling_face:Please, can somebody give a hint how to solve this.I run the code > pingpong_for1.R > after running a lot hours I got this error****[1] “plotPP”*******Error: $ operator is invalid for atomic vectors******Execution haltedI google (https://www.statology.org/r-error-operator-is-invalid-for-atomic-vectors/ ) and what I understood is that I am trying to get the element of a vector in wrong way but I do not understand with respect to the code I am using: > p3<- How to Handle R Error: $ operator is invalid for atomic vectors > This tutorial explains how to handle the following error in R: $ operator is invalid for atomic vectors.
Rosalina Tincopa Marca (12:23:14): > here the code - File (R): pingpong_for1.R
Lluís Revilla (12:41:31) (in thread): > Hi, this seems better suited for the support site:support.bioconductor.org . If you open there a question tag with the appropriate package and the maintainer might be able to help. Sorry I can’t help more
2022-01-11
Koustav Pal (04:55:20): > @Koustav Pal has joined the channel
Koustav Pal (04:58:08): > Hi, I am the maintainer of HiCBricks and would like to change my maintainer email address. Unfortunately, since moving institutions I’ve lost access to the original email address. How do I go about changing the email address?
Lori Shepherd (07:51:38): > The git credentials app the handles the ssh keys for access is using your gmail address already. You should be able to push/pull to thegit.bioconductor.org repository and be able to change the DESCRIPTION file yourself.
Lori Shepherd (07:54:46): > If you continue to have issues please send an email tomaintainer@bioconductor.org where we can discuss in more detail with information about emails and usernames
Kurt Showmaker (08:42:49): > Sharing an opportunity to contribute to theTrends in Computational Methods and Cyberinfrastructure for Translational Medicine and Sciencespecial issue of theInternational Journal of Translational Medicinedesigned to highlight the fellow computational and cyberinfrastructure community members work in translational medicine and science. > > Topics covered in the special issue include: > 1) institutional/multi-institutional/national cyberinfrastructure facilitating translational medicine and science with an emphasis on researchers use of cyberinfrastructure for research and innovation > 2) manuscripts concerning the adaptation of computer/software platforms or multiple software into “best practices”, workflows, or services to tackle complex or computationally challenging analysis (e.g., image analysis, genomics, proteomics, transcriptomics, protein structure prediction) > 3) software development and maintenance in translational medicine and science > 4) educational programs and training for non-programmers > 5) reproducible research in computational biology. > > For more details, please see the link below, and feel free to reach out if you have any questions.https://www.mdpi.com/journal/ijtm/special_issues/Computational_Translational_Medicine
Nils Hoffmann (10:37:00): > @Nils Hoffmann has joined the channel
2022-01-13
rohitsatyam102 (11:28:44): > Hello Everyone!! I am learning shiny app development by myself and I hope I will be able to find some help here regarding an issue. Since, I am not aware if their is a separate channel to discuss shiny issues, I am posting it here. I was trying to add a dropdown in the data tables in shiny and plan for the rows (with the dropdowns) to appear progressively as I click on a graph. This is to get x and Y coordinate from the image interactively save them in data table. Something like shown in the figure. However, I am facing two issues: > 1. These values are not getting updated in the actual data.table and when I download it in .csv format the fields are not populated with anything but a html code. > 2. Also, as I add new rows, the older selection of the dropdowns are reset to deault values. - File (PNG): image.png - File (PNG): image.png
rohitsatyam102 (11:31:31) (in thread): > Here are the files for the reproducibility. - File (PNG): img.png - File (Pascal): temp2.R
Hervé Pagès (12:42:22) (in thread): > Have you checked the RStudio Community (shiny category)?https://community.rstudio.com/c/shiny/8 - Attachment (RStudio Community): shiny > Shiny issues, features, and best practices.
Meriem Bahda (12:57:12): > @Meriem Bahda has joined the channel
Alan O’C (14:18:00) (in thread): > I’m not a shiny person, but SID and RID will be HTML code because you’re adding them asselectInputs I guessSID=as.character(selectInput("scid","",unique(seobj$Species), width = "100px", selected=unique(seobj$Species)[1])))
Alan O’C (14:20:06) (in thread): > Also not totally relevant but I enjoy making interactive apps in javascript/php a lot more than I have enjoyed my few experiments with Shiny. Shiny really shines (haha) when you’re using a lot of stat functionality that would be difficult/tedious to implement in JS
2022-01-14
rohitsatyam102 (00:32:22) (in thread): > Thanks@Hervé PagèsI will post my query there.
Heather Turner (05:45:10): > :bell:The deadline for outline proposals to host a hybrid useR! 2023 conference closes on Friday 28 January 2022:https://www.r-project.org/conferences/useR_2023_call.html .
rohitsatyam102 (07:27:06) (in thread): > @Alan O’CI have yet to get started in JS. Thanks for pointing out the SID and RID inputs but I am unable to understand how else can I add dropdown and save the choices made by user in data table. Perhaps, I will post this query on the shiny link provided. Thanks both of you for the time you took out to reply.
Alan O’C (07:31:19) (in thread): > Right, maybe you’d need to handle parsing the values of the selectInput in the document write handler function > > content = function(file) { > write.csv(values$DT, file, row.names = FALSE) > } >
Jared Andrews (09:01:03) (in thread): > This is kind of funny because my experience has been almost the complete opposite - shiny felt much more friendly than JS when doing any actual manipulation of inputs.
Alan O’C (09:03:35) (in thread): > It may be that I’ve broken my brain by learning JS first, but I found the handling of interactive elements to be totally opaque
2022-01-15
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2022-01-18
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2022-01-19
Matt Ritchie (05:41:29): > I came across this in another slack group,and thought I’d share in case anyone in the Bioconductor community has project ideas that might fit the callhttps://github.com/PlaintextGroup/oss-virtual-incubator
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2022-01-20
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hillel brukental (03:19:18): > Hi everyone, I have a genotypic data on some trees population (5000 snp’s), i would like to perform analysis like structure, PCA, phylogenetic tree etc. could someone recommend on an R package?
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Jenny Drnevich (10:18:39) (in thread): > Not a BioC package but Adegenet is a good one to start with.https://cran.r-project.org/web/packages/adegenet/index.html - Attachment (cran.r-project.org): adegenet: Exploratory Analysis of Genetic and Genomic Data > Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure (‘genind’ class), alleles counts by populations (‘genpop’), and genome-wide SNP data (‘genlight’). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
Rosalina Tincopa Marca (13:12:01) (in thread): > Thank you:+1:. I will do it!
2022-01-21
Kevin Rue-Albrecht (07:15:01): > Hi all, a corner case spotted during debugging ofiSEEuon devel. > On release: > > > intersect(NULL, LETTERS) > character(0) > > But on R-trunk: > > > intersect(NULL, LETTERS) > NULL > > Just in case that discrete update was driving anyone else insane:slightly_smiling_face:
Lluís Revilla (09:28:15) (in thread): > Weird, it is not documented on NEWS even if it is user facing…
2022-01-23
hillel brukental (05:48:28) (in thread): > thank you!
Kevin Rue-Albrecht (15:04:30) (in thread): > yup - not a nice surprise, being bitten by that one ^^
2022-01-24
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2022-01-25
Hervé Pagès (15:08:40) (in thread): > Well, the good news is thatintersect()is now symmetrical. On release: > > > intersect(1:3, letters) > character(0) > > intersect(letters, 1:3) > integer(0) > > intersect(NULL, letters) > character(0) > > intersect(letters, NULL) > NULL > > On R-trunk: > > > intersect(1:3, letters) > character(0) > > intersect(letters, 1:3) > character(0) > > intersect(NULL, letters) > NULL > > intersect(letters, NULL) > NULL > > But yeah, this change should be mentioned in the NEWS file.
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2022-01-27
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2022-01-31
Lori Shepherd (07:57:57): > The community advisory board is seeking nominations for new members. Please seehttps://support.bioconductor.org/p/9141753/ for more information and a link to the nomination form. The deadline for submission is February 25 2022. New members will be elected from the list of submitted nominees by the current community board members.
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2022-02-01
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2022-02-03
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2022-02-04
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Wes W (14:35:19): > Good afternoon everyone, quickest of questions about data sharing after a publication. Let me know if my assumptions are incorrect. I was under the impression that Nature publications had to make their data publicly available. I have requested access to the raw data of 2020 Nature paper and the authors have essentially said no. We basically have a different understanding of the nature reporting standards for making the “availability” of the data “to interpret, verify and extend the research in the article”. They feel the count matrix is all that is required, and we feel we need the raw data. While I feel I am not in a position to push harder than I have, I would love to hear the communities thoughts and if, regardless of outcome if I was wrong to request the raw data or think they should be sharing it after over a year since publication. > > I have heard that some groups or journals give researchers some time to embargo the release of the data they generated to give them more time to use it. I do not believe Nature is one of those journals from what I have researched, and in cases where it is done it seems to be limited to 1 year post-publication which this paper most certainly is. > > thanks in advance
Dario Strbenac (15:00:14): > I think the reviewers working for Nature journals are typically molecular biologists and they often don’t even know what type of data would be important to make available for a reanalysis. The reads would be important to reproduce the figures and ensure the reference genome alignment was done well.
Jenny Drnevich (15:03:08): > If you think they are improperly withholding the raw data, you can contact the Nature Editor for the paper. Especially if they did not give a reproducible description of exactly how they generated the counts.
Alan O’C (15:18:22): > I think you should be entitled to obtain the raw data (given normal access controls, eg for human data). As Dario said probably some loose enforcement of data availability by reviewers/editors. Hopefully you don’t have to push the editor to chase them
Sean Davis (15:58:09) (in thread): > If this study is NIH-funded, the data are likely subject to this policy.https://osp.od.nih.gov/wp-content/uploads/Supplemental_Info_GDS_Policy.pdf
Sean Davis (15:59:45) (in thread): > There is no embargo period after publication under this policy; in many cases of large-scale studies, the data are “supposed” to be made public soon after production (and before publication).
Sean Davis (16:00:55) (in thread): > What exactly constitutes Level 2 data or higher is going to be open for discussion, but in my experience, NIH has asked for RNA-seq to include RNA-seq reads, including unmapped reads.
Wes W (16:32:47) (in thread): > Thanks@Sean Davis
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2022-02-05
Jonathan Griffiths (04:04:04) (in thread): > Bear in mind that what youshould be able to access can sometimes be very different from the reality of what you will actually be able to access. I would imagine that the chance of the editor being able/willing to help you recolve this is <5%. Where I am working at the moment, we have considerable experience chasing down public datasets, and if the authors aren’t immediately helpful then odds are very heavily against us making any progress with it.
2022-02-06
Lluís Revilla (06:43:57) (in thread): > I was about to raise this to R-devel mailing list but it is documented on the value section of the functions. On R-devel: > > For ‘union’, a vector of a common mode. > > > > For ‘intersect’, a vector of a common mode, or ‘NULL’ if ‘x’ or > > ‘y’ is ‘NULL’. > > > > For ‘setdiff’, a vector of the same ‘mode’ as ‘x’. > > > > A logical scalar for ‘setequal’ and a logical of the same length > > as ‘x’ for ‘is.element’.
2022-02-07
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Wes W (11:17:43) (in thread): > Thanks@Jonathan Griffiths, shame to hear, but good to know im not alone
Lindsay Clark (13:04:51) (in thread): > Yeah, I think your expectations are spot on in principle, but in practice, data are very often not adequately shared. Some combination of “the student graduated and we don’t know where the data are/don’t have time to deal with it” and “there’s some non-zero chance that we’ll do something else with the data, and we don’t want to be scooped”.
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2022-02-09
Kasper D. Hansen (08:51:58) (in thread): > Should still be mentioned in NWS
2022-02-10
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2022-02-11
Kozo Nishida (04:02:22): > We (CAB) wrote a short blog post about what the CAB looks like.https://bioconductor.github.io/biocblog/posts/2022-01-31-join-the-bioconductor-community-advisory-board/ If you are interested in CAB and would like to ask a question, feel free to contact us (#community-advisory-board). - Attachment: Attachment > The community advisory board is seeking nominations for new members. Please see https://support.bioconductor.org/p/9141753/ for more information and a link to the nomination form. The deadline for submission is February 25 2022. New members will be elected from the list of submitted nominees by the current community board members. - Attachment (Bioconductor community blog): Bioconductor community blog: Join the Bioconductor Community Advisory Board > Each year the Bioconductor Community Advisory Board (CAB) puts out a public call for new board members. This post tells you more about what the CAB does and how you can apply to become a member.
Kozo Nishida (04:03:02) (in thread): > This blog is still tentative, but we don’t have enough time before the CAB nomination deadline, so we made it public for everyone to see.
Nour El kazwini (10:25:24): > @Nour El kazwini has joined the channel
2022-02-13
Jeroen Ooms (10:47:31): > I have a question about S4, about the use ofsetOldClass(). Any S4 experts want to chime in here?https://github.com/jeroen/jsonlite/issues/378
Xin Fang (15:02:38): > @Xin Fang has joined the channel
2022-02-15
Alvaro Sanchez (07:16:02): > I have a question regarding the packageSTRINGdb: how to store the output plot as a variable? > > library(STRINGdb) > > string_db <- STRINGdb$new(version = "11.5", species=9606, score_threshold = 200, input_directory="") > > diffExpressGenes <- data.frame(gene = c('AAAS', 'AACS', 'AAMP', 'AASS', 'ABCB7', 'ABCD4')) > > mapped <- string_db$map(diffExpressGenes, 'gene', removeUnmappedRows = TRUE) > > plot <- string_db$plot_network(mapped$STRING_id) > > Even though this returns the plot that I want, the variableplotisNULL: > > > plot > NULL >
Kasper D. Hansen (07:38:35): > You can only expect stuff like this to work if it uses ggplot2.
Federico Marini (07:53:14): > Probably your best shot is to store the resulting graph object - I think that should be possible?
Federico Marini (07:53:38): > and then, have a function that feeds exactly on said graph objects and do the plotting for you
Federico Marini (07:53:49): > I wish that would actually be the default behavior
Federico Marini (07:54:30): > just my 2:coin:on this:wink:
Spencer Nystrom (08:13:53): > I think it’sp <- grid::grabExpr(<your plotting function>)
Spencer Nystrom (08:14:16): > That will capture these. (but I might’ve got the function name off from memory)
Alvaro Sanchez (08:34:36) (in thread): > This doesn’t seem to work:confused:
Alan O’C (08:34:56): > grid.grab probably won’t work with base plots either? since they’re not grid-based
Alan O’C (08:35:31): > > r$> g <- grid.grabExpr(plot(1:10)) > r$> g > NULL >
Spencer Nystrom (08:36:17) (in thread): > Ah think it’sgrid::grid.grabExpr
Alvaro Sanchez (08:38:40) (in thread): > Thanks for trying, though it is stillNULL: > > p <- grid::grid.grabExpr(string_db$plot_network(mapped$STRING_id)) > > > p > NULL >
Helena L. Crowell (09:04:21): > If it is a base R plot, I did this … a while back to prevent a function from rendering plots by itself (not sure if there’s a better way, but this one’s all base R): > *works with anything btw, sopcould also be aggplot… it just captures anything that’d be displayed in the plots pane otherwise > > .p <- \() { > pdf(NULL) > dev.control(displaylist = "enable") > plot(1, 1) > # 'recordPlot' is from 'grDevices' > p <- recordPlot() > invisible(dev.off()) > return(p) > } > > # nothing happens > p <- .p() > # this gives 'recordedplot' > class(p) > # this renders the plot > p >
Spencer Nystrom (09:09:01) (in thread): > I think Helena’srecordPlotssuggestion should work then. I’ve done that for base graphics before. Wasn’t sure if the snpdb plot was base or grid.
Alvaro Sanchez (09:30:03) (in thread): > It is a ggplot, so not sure if this will work.
Alvaro Sanchez (09:30:19) (in thread): > WIll try later
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2022-02-18
David Dittmar (02:23:11) (in thread): > Hi! As part of my thesis writing process I had to capture various plots that were not ggplot or grob objects. A general approach that worked for me even with customized plots (including additional calls to par()) after the actual plot, plotting onto the plot device active at that time) was using the pryr package with the %<a-% syntax which basically stores the whole plot in a single plot call that can be fed to multiplanelfigure::capture_base_plot() as expression for grob conversion. Maybe a look at the attached example helps you. > > library(pryr) > library(multipanelfigure) > # Example for capturing a plot > bc.hypox.pryr %<a-% {barcodeplot(avp.ivt.tr.res$table$logFC, > index=H.ind[["HALLMARK_HYPOXIA"]], > col.lab="white", > labels=c("up in poly","up in allo"), > col.bars = "orange" > ) > par(new=TRUE) > plot.new( ) > plot.window( xlim=c(-5,5), ylim=c(-5,5) ) > text(-5,5,"Orange bars: Genes up in expanded allo Treg", adj = c(0,.5)) > text(-5,3.5,expression(italic(P)[adj.] **"<"** ~0.012), adj = c(0,.5)) > } > bc.hypox.base<-capture_base_plot(bc.hypox.pryr) >
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Alvaro Sanchez (07:36:29) (in thread): > Thanks David, luckily I found a workaround my problem. Thanks for your answer!
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2022-02-19
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2022-02-24
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Gene Cutler (18:04:17): > Anybody have recommendations for a parsimony tree-building package that can handle thousands of sequences?
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2022-03-01
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2022-03-02
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2022-03-03
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Steffen Neumann (08:16:04): > https://biohackathon-europe.org/projects.html The call for project proposals for BioHackathon Europe 2022 is now open. - Attachment (biohackathon-europe.org): Projects > Paris 7-11 November 2022
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2022-03-04
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2022-03-05
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2022-03-07
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2022-03-08
Charlotte Soneson (14:26:21): > The abstract submission deadline for BioC2022 has been extended until March 29. Conference website with more information and link to submission form:https://bioc2022.bioconductor.org/ . Slack channel:#bioc2022
Mike Smith (15:58:34) (in thread): > Maybe I’m being blind, but does it say anywhere if the conference is virtual or in-person? And if it’s the latter, what city it’s in? All I can see is the “venue to be decided” message.
Charlotte Soneson (16:05:52) (in thread): > Sorry, the website is still in the process of being updated. The conference is planned as a hybrid event (in Seattle/online).
2022-03-09
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2022-03-11
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2022-03-12
Jianhai Zhang (22:29:44): > Hello, when building a package if the only code relevant to package Matrix isis(dat0, 'dgCMatrix')in a function, how should I write@importFrom Matrix?
2022-03-13
Fabricio Almeida-Silva (04:20:21): > Hi,@Jianhai Zhang. The function is() belongs to the {methods} package. If you simply want to check the object’s class, you can simply write @importFrom methods is. Don’t forget to add methods to the “Imports” field of your DESCRIPTION file.
Jianhai Zhang (18:25:49): > Got it, thank you!@Fabricio Almeida-Silva
2022-03-14
Hervé Pagès (02:40:46): > Plus of course: > > importClassFrom(Matrix, dgCMatrix) > > which inroxygen > @importFrom Matrix dgCMatrix > > As for importing stuff from themethods strongly suggest importing the whole package namespace rather than importing selectively. So just: > > import(methods) > > There are no penalties in doing this and it will make any package that makes use of S4 much easier to maintain in the long run.
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Alan O’C (04:53:48): > You wouldn’t need the class definition to useis, though? It just checks the class attribute
Hervé Pagès (12:55:21): > I’m not really sure about that. Maybe, maybe not, but it shouldn’t matter. Whatis()does exactly internally isis()’s business and its implementation could change any time. I don’t know whatsetClass("Foo", contains="dgCMatrix")does internally either but we got into the habits of importing the parent class in that case, probably for good reasons. I would approachis(x, "dgCMatrix")the same way. I think it’s a case where trying to be too smart can backfire in unexpected ways.
Alan O’C (13:37:38): > I’d rather be clear on what’s necessary and what’s not as it reduces the scope when bug hunting:slightly_smiling_face:
Hervé Pagès (13:42:40): > Yes, I agree in general, but in this particular case it introduces the risk of subtle bugs that I never want to have to hunt for:slightly_smiling_face:
Kasper D. Hansen (14:32:50): > I sense a lot of hard-earned frustration behind@Hervé Pagès’s recommendation
Alan O’C (14:39:45): > Yeah, I think for S4 classes you need to at least require the package with the class definition is installed to check for subclasses actually
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Jianhai Zhang (15:18:10) (in thread): > Thank you for the answers!@Hervé Pagès
2022-03-15
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Lori Shepherd (10:38:11): > BiocAwards 2022 nomination is now open. Please seehttp://bioconductor.org/about/awards/
2022-03-18
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2022-03-20
Wadschma (11:26:23): > @Wadschma has joined the channel
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2022-03-21
Alison Merikangas (15:48:21): > @Alison Merikangas has joined the channel
2022-03-22
Natalie Kucher (12:20:09): > Hi all, the annual Galaxy Community Conference will be held July 17-23 in Minneapolis, MN, and it’s a great venue to talk about data intensive science. The abstract submission deadline is April 12. Registration is now open2022 Galaxy Community Conference (GCC2022) > All about Galaxy and its community.
2022-03-23
Matteo Tiberti (02:39:26): > @Matteo Tiberti has joined the channel
Doortje Theunissen (04:35:35): > @Doortje Theunissen has joined the channel
Leonardo Collado Torres (09:26:31): > Hmmhttps://twitter.com/raphaels101/status/1506321623250571265?s=21 - Attachment (twitter): Attachment > This just in from Brian Ripley (developer of #rstats, maintainer of CRAN): “you have far exceeded your fair share of CRAN time for 2022 already, indeed your fair share for the 2020s.” > > Let’s talk about threatening platforms, visibility, and equity shall we? > > Thread 1/7.
Alan O’C (09:33:46) (in thread): > CRAN isn’t fit for purpose IMHO. If you don’t fix problems promptly, you’ll be kicked off CRAN within weeks. But apparently fixing things as they arise is also not allowed. Bizarre.
Lluís Revilla (09:54:10) (in thread): > There is a working group to help CRAN and address these and other issues. See the minutes of what’s been discussed. If anyone wants to contribute they are welcomehttps://github.com/RConsortium/r-repositories-wg
Alan O’C (10:38:14) (in thread): > It is not terribly reassuring to me that “to win the trust of CRAN” is a major objective in the recent minutes
Lluís Revilla (10:58:42) (in thread): > Sadly it isn’t but this is the state of the R community, CRAN and R core relationships.
Spencer Nystrom (12:00:25) (in thread): > So frustrating that everyone seems to have a story about getting “Ripley-ed”. That kind of behavior spreads in an org and I feel the snark creep into other non-Ripley interactions I have with CRAN, too. Thankful Bioc takes pride in fostering it’s community.
Friederike Dündar (16:13:58) (in thread): > seems hard to reconcile with the person described here:https://dirk.eddelbuettel.com/blog/2007/08/11/ - Attachment (dirk.eddelbuettel.com): Thinking inside the box > Dirk Eddelbuettel, R, C++, Rcpp
Friederike Dündar (16:14:11) (in thread): > But maybe Raphael was destroying the power-law?
2022-03-24
Aedin Culhane (22:18:45): > The May Institute on Computation and Statistics for Mass Spectrometry and Proteomics, taking place on May 9 – May 20, 2022 on the Boston campus of Northeastern University (online), is now accepting applications. > > The program includes tutorials and practical hands-on sessions, presenting open-access data processing tools (Skyline, FragPipe), programming languages (R, Python), statistical analysis tools (MSstats), and data repositories (MassIVE, PRIDE and Panorama). Instructors are leading experts, who contributed numerous computational methods and software. The presentations are integrated to focus on analyses of several well-chosen datasets. Together we will take an in-depth look into case studies of design and analysis of mass spectrometry-based experiments. > > > Week 1: > * Intro and hands-on, Sue Abbatiello: targeted MS-based proteomics with Skyline > * Intro and hands-on, Lindsay Pino: targeted MS-based proteomics with Skyline > * Hands-on, Brendan MacLean: Part 1: Skyline processing of proteome-wide DIA of a controlled mixture > * Hands-on, Brendan MacLean: Part 2: Skyline-based comparison of refined versus proteome-wide queries of DIA experiments > * Keynote, Alexey Nesvizhskii: Quantification workflows in FragPipe computational pipeline > * Hands-on, Felipe Leprevost: Quantification workflows in FragPipe computational pipeline > * Hands-on, Ryan Benz: Part 1: Introduction to R for beginners > * Hands-on, Ryan Benz: Part 2: Introduction to R for beginners > > Week 2: > * Tutorial, Kylie Bemis: Intermediate R crash course for MS practitioners > * TutTutorial, Olga Vitek: Introduction to statistical methods and MSstats for label-free proteomics > * Hands-on, Meena Choi and Brendan MacLean: Analysis of data in Skyline Part 1 and Part 2 in MSstats, and comparison of the results > * Tutorial, Olga Vitek: Introduction to statistical methods and MSstatsTMT for label-based proteomics. > * Hands-on, Ting Huang: Analysis of data in the FragPipe tutorial with MSstatsTMT. > * Tutorial, Nuno Bandeira: Reproducible quantitative MS-based proteomics with MassIVE > * Tutorial, Meena Choi: Reproducible quantitative MS-based proteomics with MassIVE.quant > * Tutorial, Yasset Perez-Riverol: Reproducible quantitative MS-based proteomics with PRIDE > * Tutorial, Vagisha Sharma: Reproducible quantitative MS-based proteomics with Panorama > * Hands-on, Charles Tapley Hoyt: Modern software development practice with Python > > More information is athttps://secure-web.cisco.com/1ceBKtYDkcCig_liKg8AnJCsnzpbYSIiK1SuPxzGwIxRXdEefcw7Dm1or0BuGC_NwoAywqyiyljCIDwQ49qhZyBpYCbLUqVsSFUHfGIN6FidvD9XjgX1FEc5Rx6UTJyEyeyvx_ozEFMvyNQU48jHEaGHlwCboEdGiZFMurux_LcApDik-TILBFIMa6bXrOpuj3yTnBxa65piacpHj_r1WVoydVh70uzs9InUbvP-uarVJ__0vXZfzJbWgj4s10LfUF11DG5CdhsCNgH0pyadQzkCogO-PAJ8a9DgP0oyeIbgjBVR04HhOpAdththdnDPf/https%3A%2F%2Fcomputationalproteomics.khoury.northeastern.edu%2F Please share this widely. > > — > Olga Vitek > Professor > Khoury College of Computer Sciences, Northeastern University > URL:olga-vitek-lab.ccis.northeastern.edu Twitter: @olgavitek
2022-03-28
Jovan Isma (08:17:58): > @Jovan Isma has joined the channel
Jonathan Carroll (18:56:31): > I have anedgeRquestion: should I expect identical results fromcpm(x[, samples])andcpm(x)[, samples]? I (perhaps naively) expected that the results would not depend on the number of samples, but that doesn’t seem to be the case, ever so slightly. This has an impact if I split the cpm values at the median - some samples jump to the other side depending on how I perform this calculation. > > Using an example from the docs > > ## prior.count = 2, auto lib.size > set.seed(1) > pc <- 2 > ls <- NULL > y <- matrix(rnbinom(200, size=1, mu=10), 10, 20) > full <- edgeR:::cpm.default(y, log = TRUE, prior.count = pc, shrunk = FALSE, lib.size = ls) > sub <- edgeR:::cpm.default(y[, 1:5], log = TRUE, prior.count = pc, shrunk = FALSE, lib.size = ls) > identical(sub, full[, 1:5]) > #> [1] FALSE > > (continued in thread…)
Jonathan Carroll (18:56:55) (in thread): > Comparison:
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 16.11348 17.34539 15.89775 14.44614 16.97110
#> [2,] 15.23309 14.93545 17.53681 15.11920 17.50207
#> [3,] 16.65626 15.83300 14.44614 18.89277 17.06000
#> [4,] 15.23309 16.99341 17.20823 16.81382 17.43717
#> [5,] 16.41024 15.30018 17.32627 14.44614 17.78888
#> [6,] 17.35856 17.49367 16.60650 17.66682 16.77496
#> [7,] 15.23309 16.52686 15.10458 16.63728 14.89590
#> [8,] 18.01677 17.26512 14.44614 16.43609 14.44614
#> [9,] 16.86637 16.99341 18.44955 15.11920 14.44614
#> [10,] 17.92588 17.49367 16.17450 15.92296 17.06000
full[, 1:5]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 16.07710 17.33346 15.85444 14.31318 16.95383
#> [2,] 15.16016 14.84383 17.52711 15.03959 17.49199
#> [3,] 16.63328 15.78739 14.31318 18.89260 17.04412
#> [4,] 15.16016 16.97651 17.19450 16.79386 17.42635
#> [5,] 16.38182 15.23092 17.31410 14.31318 17.78169
#> [6,] 17.34679 17.48349 16.58250 17.65847 16.75428
#> [7,] 15.16016 16.50114 15.02408 16.61392 14.80147
#> [8,] 18.01151 17.25215 14.31318 16.40829 14.31318
#> [9,] 16.84734 16.97651 18.44719 15.03959 14.31318
#> [10,] 17.91989 17.48349 16.13990 15.88051 17.04412
Jonathan Carroll (18:57:18) (in thread): > my guess is it has something to do withhttps://code.bioconductor.org/browse/edgeR/blob/master/src/add_prior.cpp?branch=master&file=src/add_prior.cpp#L35 where the adjusted prior count for each library is added to every element - Attachment (code.bioconductor.org): Bioconductor Code: Browse > Browse the content of Bioconductor software packages.
Jonathan Carroll (18:58:04) (in thread): > These approaches work, but the inputs don’t (?) make any sense - setting prior.count to 0 > > ## prior.count = 0, auto lib.size - works, occasional NaN where y == 0 > set.seed(1) > pc <- 0 > ls <- NULL > y <- matrix(rnbinom(200, size=1, mu=10), 10, 20) > full <- edgeR:::cpm.default(y, log = TRUE, prior.count = pc, shrunk = FALSE, lib.size = ls) > sub <- edgeR:::cpm.default(y[, 1:5], log = TRUE, prior.count = pc, shrunk = FALSE, lib.size = ls) > identical(sub, full[, 1:5]) > #> [1] TRUE >
Jonathan Carroll (18:58:42) (in thread): > or fixing thelib.size > > ## prior.count = 2, fixed lib.size - works, but y == 0 leads to result =~ 1 > set.seed(1) > pc <- 2 > ls <- 1e6 > y <- matrix(rnbinom(200, size=1, mu=10), 10, 20) > full <- edgeR:::cpm.default(y, log = TRUE, prior.count = pc, shrunk = FALSE, lib.size = ls) > sub <- edgeR:::cpm.default(y[, 1:5], log = TRUE, prior.count = pc, shrunk = FALSE, lib.size = ls) > identical(sub, full[, 1:5]) > #> [1] TRUE >
Jonathan Carroll (18:58:51) (in thread): > Any guidance would be greatly appreciated
Xueyi Dong (23:09:49) (in thread): > > Whenlog=TRUE, thecpmfunction adds an offset to the CPM values before converting to the log2-scale. By default, the offset is 2/L where 2 is the “prior count” andL is the average library size in millions, so the log-CPM values are related to the CPM values by log2(CPM + 2/L ).
Xueyi Dong (23:10:13) (in thread): > It has something to do with the library size. See here:https://www.bioconductor.org/packages/devel/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html
2022-03-29
Jonathan Carroll (00:13:21) (in thread): > Thank you@Xueyi Dong- that clears up my confusion. My initial expectation was indeed naive and I should not expectcpmto be independent of the average library size. > > A contrived example where an excluded sample does not alter the average count shows this effect nicely > > pc <- 2 > y <- matrix(c(2, 3, 3, 3, 2, 3, 4, 4, 3), 3, 3, byrow = TRUE) > y > #> [,1] [,2] [,3] > #> [1,] 2 3 3 > #> [2,] 3 2 3 > #> [3,] 4 4 3 > full <- edgeR:::cpm.default(y, log = TRUE, prior.count = pc, shrunk = FALSE, lib.size = NULL) > sub <- edgeR:::cpm.default(y[, 1:2], log = TRUE, prior.count = pc, shrunk = FALSE, lib.size = NULL) > identical(sub, full[, 1:2]) > #> [1] TRUE > > It seems I was very close with my guess at the code source, which is also nice to see.
Oby Egeolu (12:11:33): > @Oby Egeolu has joined the channel
2022-03-30
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2022-04-01
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Lukas Weber (19:01:45) (in thread): > Hi Julia, just saw this message. I checked and seems the error is gone now. I think there have been some temporary glitches with the builders in the last few days, so hopefully it was unrelated to SpatialExperiment. Could you please let me know again if it is still not working / there is still a problem with SpatialExperiment? Thanks!
Julia Wrobel (22:50:54) (in thread): > Thanks Lukas! Yeah I think it was just a glitch in the builders. I re built my package with no changes and it went through the second time
2022-04-02
Vince Carey (06:40:42): > Any jupyterlab whizzes out there? I am wondering if it is possible to configure vertical extent of widget presentation. With jupyterlab a map or datatable rendering is very squished: - File (JPEG): narrowPresentation.jpg
Vince Carey (06:41:35): > With a stock jupyter notebook the default presentation is: - File (JPEG): jnb.jpg
2022-04-04
Garth Kong (13:20:24): > Just putting this out there, are there any price estimates for the bioC 2022 conference registration?
2022-04-05
Erica Feick (08:41:23) (in thread): > We are hoping to have this information very soon, and open registration for both in person and virtual!
Gene Cutler (13:41:45): > Anyone have a recommendation for a package for aligning protein sequences to the genome?
Hervé Pagès (14:21:28) (in thread): > Assuming that your protein sequences come from known CDS regions, you could extract the CDS sequences, translate them, and align to that. > See the “4. TRANSLATE THE CDS SEQUENCES” example in?GenomicFeatures::extractTranscriptSeqsfor translating the CDS sequences (will produce an AAStringSet object), andmatchPattern/vmatchPatterninBiostrings DECIPHER
Gene Cutler (19:09:44) (in thread): > Thanks. It turns out that not all my sequences come from canonical CDSes, so that didn’t work. > I’ve been using DECIPHER for other alignments, but it didn’t seem to be able to do this protein -> discontinuous DNA alignment either. > > In the end, I used theexoneratecommand line tool. Unfortunately, the chromosomal coordinates in the output CIGAR strings had (as it appeared to me) unpredictable off-by-one shifts that made a simple parsing of the output unreliable. I had to write a perl script to do a slightly arduous parsing of the full exonerate alignments to get accurate mapping positions.
Jared Andrews (21:20:32): > Any good solutions for showing a basic interactive genome browser, using local files, that can be plugged into a Shiny app?
Jared Andrews (21:21:22): > JBrowseR has looked the best, but it requires URL to files and the basic webserver that ships with it doesn’t work with RStudio Connect/shinyapp.io.
Frederick Tan (22:40:15) (in thread): > Perhapshttps://github.com/paul-shannon/igvShiny
Jared Andrews (22:44:42) (in thread): > I saw that, I am expecting the same webserver issues as JBrowseR had when deployed, but will give it a shot tomorrow. Thanks for the suggestion.
Sridhar N (22:51:55): > how many files are we talking? To be viewed that is..
Sridhar N (22:52:16): > just use igv.js?
2022-04-06
Jayaram Kancherla (00:53:01) (in thread): > self marketing -https://bioconductor.org/packages/release/bioc/html/epivizrChart.html
Jared Andrews (07:36:48) (in thread): > The igv viz from that gets close but being unable (that I can tell) to remove the alignment track for a bam file is kind of a deal breaker.
Jared Andrews (07:38:46): > Contemplating it. Max of like five bam files with bed files (signal plus peaks)
Jared Andrews (07:40:28): > It’s a hackathon project so I was hoping for something that’d just work out of the box without taking too much time to figure out.
Gene Cutler (12:01:07): > What about igvR:https://bioconductor.org/packages/release/bioc/html/igvR.html - Attachment (Bioconductor): igvR > Access to igv.js, the Integrative Genomics Viewer running in a web browser.
Jared Andrews (12:16:49): > Gviz appears to be my answer, thanks for all the suggestions!
Eric Davis (14:22:38): > Maybe plotgardener will work for you?https://phanstiellab.github.io/plotgardener/index.html - Attachment (phanstiellab.github.io): Coordinate-Based Genomic Visualization Package for R > Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.
Jared Andrews (15:26:41): > Oh that looks even easier, thanks for the rec.
Martin Rodriguez Nuñez (16:24:36): > @Martin Rodriguez Nuñez has joined the channel
2022-04-07
Babette Jakobi (06:39:32): > Hey everyone, I am working on a meta-analysis of the gut-microbiome in ADHD. I am having some troubles -conceptually- if it would make sense to do a meta analysis of beta-diversity,(e.g. permanova), did someone already think about this or do you guys have some strong feelings against it? Im not sure if the concept allows to compare effect sizes …Would greatly appreciate your input
Himel Mallick (06:52:57) (in thread): > Do you have access to the full data for all the studies? If yes, you can check out the MMUPHin package (https://www.bioconductor.org/packages/release/bioc/html/MMUPHin.html ) which is exactly built for the same purpose. - Attachment (Bioconductor): MMUPHin > MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery.
Alvaro Sanchez (08:18:54): > For those of you interested in Shiny:https://www.linkedin.com/events/appsilonshinyconference20226904379041910980608 - Attachment (linkedin.com): Appsilon Shiny Conference 2022 | LinkedIn > We are proud to announce the First Annual Appsilon Shiny Conference, hosted by Appsilon with support from RStudio PBC. The conference will take place virtually on 27-29 April, 2022. Early Bird Tickets are FREE until March 15th. There are a limited number of early bird tickets available, so reserve your spot as soon as possible. 𝗔𝗯𝗼𝘂𝘁 The Appsilon Shiny Conference has three goals: 1. Showcase recent advancements in R Shiny technology such as open source packages, Shiny interoperability, and commercial applications. 2. Create a shared space for the diverse global community of Shiny developers to learn, network, and collaborate. 3. Provide a platform for Shiny community members to share their open source packages and Shiny applications. 𝗦𝗽𝗲𝗮𝗸𝗲𝗿𝘀 * Diane Beldame (ThinkR) * Joe Cheng (RStudio) * Winston Chang (RStudio) * Michael C. Rubin (ODAPES) * Barret Schloerke (RStudio) * Marek Rogala (Appsilon) * Maya Gans (Atorus Research) * Eric Nantz (The R Podcast, R-Weekly) * Jacqueline Nolis (Saturn Cloud) * Pedro Silva (Appsilon) * Marcin Dubel (Appsilon) * Anna Skrzydło (Appsilon) * Filip Stachura (Appsilon) * Damian Rodziewicz (Appsilon) * Samantha Toet (RStudio) * Curtis Kephart (RStudio) * David Granjon (Novartis) 𝗔𝗯𝗼𝘂𝘁 𝗔𝗽𝗽𝘀𝗶𝗹𝗼𝗻 Appsilon builds the world’s most advanced R Shiny applications, with a specialization in enterprise Shiny dashboards. Global 2000 companies trust Appsilon to build custom Shiny apps, scale PoCs, improve Shiny app performance, and enhance dashboard UI. To find out for yourself what’s special about Appsilon, visit our Shiny Demo Gallery or try out our Shiny open-source tools. 𝗔𝗱𝗱𝗶𝘁𝗶𝗼𝗻𝗮𝗹 𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗼𝗻 If you have questions about the Shiny Conference or would like to be considered for the Program Committee, email us at mailto:shinyconf@appsilon.com|shinyconf@appsilon.com .
Sarath Kumar Murugan (10:41:09): > @Sarath Kumar Murugan has joined the channel
2022-04-10
Henrik Bengtsson (13:00:59): > Hi. Lots of R users follow thehttps://rweekly.org/ feed. It’s a weekly feed that summarize news in R, new packages and updated packages, blog posts, other news, upcoming conferences, etc. > > Contributing to it is as easy as doing a pull request forhttps://github.com/rweekly/rweekly.org/blob/gh-pages/draft.md . Adding Bioconductor conferences would be beneficial, but also other Bioconductor news, and calls for participation. Bioconductor package maintainers could also add their updates.
2022-04-11
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2022-04-12
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2022-04-13
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2022-04-15
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2022-04-20
Charlotte Soneson (04:49:34): > Abstract submission for the European Bioconductor Conference 2022 is open (deadline May 31)! The conference is currently planned to take place as a mainly in-person event in Heidelberg, Germany, on September 14-16. Seehttps://eurobioc2022.bioconductor.org/submissions/ for more information. - Attachment (eurobioc2022.bioconductor.org): Submissions > Submissions
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2022-04-21
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2022-04-22
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2022-04-25
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2022-04-26
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2022-04-27
Lori Shepherd (17:32:13): > Bioconductor 3.15 is released! See full release announcement:https://bioconductor.org/news/bioc_3_15_release/
Lori Shepherd (17:32:54) (in thread): > Thanks to all developers and community members for contributing to the project!
Peter Hickey (19:31:25) (in thread): > Thank you Lori and the rest of the team!
2022-04-28
Luke Zappia (03:25:08) (in thread): > Congrats to the core team and all the developers:tada:! > > Just a small note. Could we please have more detail for times when deadlines are announced? Something like “1 pm ET” isn’t really clear for non-US people. Adding UTC time or even just a city in the time zone you are using would be great. Thanks!
Lori Shepherd (06:40:04) (in thread): > Thanks for the suggestion we will try to accommodate in the future releases
2022-04-29
Leonardo Collado Torres (12:20:30) (in thread): > thanks to you and the BioC Core team for putting it all together:smiley:
2022-05-01
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2022-05-04
Laura Marcos-Zambrano (11:50:40): > @Laura Marcos-Zambrano has joined the channel
Krithika Bhuvanesh (18:57:28): > I’m looking to pick someone’s brain on how to factor strand information . Backstory : I have some processed genotype data from a very old SNP array. I’m trying to make it into a VCF file. Example in image. Should I simply get the rsID anno from the SNPlocs.Hsapiens.dbSNP144.GRCh37 BioC package , and factor in the strand information into the INFO column ? - File (PNG): Screen Shot 2022-05-04 at 6.38.59 PM.png
2022-05-05
Laurent Gatto (05:39:16): > I just saw a new package submission,goSorensen, and I first thought it was a tribute to@Charlotte Soneson.
Lori Shepherd (10:46:08): > :warning:The search onbioconductor.org is currently unavailable. we are investigating the issue.
Roberto Bullitta (10:52:24): > @Roberto Bullitta has joined the channel
Kasper D. Hansen (10:54:02): > Not really sure where to put it but the multi sample chapter in the OSCA book is missing in the new release:http://bioconductor.org/books/3.15/OSCA.multisample/
Vince Carey (11:45:10) (in thread): > Thanks Kasper – this could be a manifestation of general propagation problems owing to a full disk.@Lori Shepherd?
Lori Shepherd (11:48:09) (in thread): > No – its because its failinghttp://bioconductor.org/checkResults/3.15/books-LATEST/
Kasper D. Hansen (12:34:43) (in thread): > But the basic chapter is also failing but the webpage is there
Kasper D. Hansen (12:34:59) (in thread): > That was just an observation
Lori Shepherd (12:42:43) (in thread): > could be the space issue. lets see if it populates after the next build
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2022-05-06
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Charlotte Soneson (11:07:16): > Do you want to join the Bioconductor Technical Advisory Board, or do you know someone who would be a great fit? Then fillthis short form (if you’re nominating someone else, please first confirm that they are interested) beforeMay 31 https://bioconductor.org/about/technical-advisory-board/ , and if you have questions, feel free to post them in the#tech-advisory-boardchannel. Please help spread the word!
Peter Hickey (18:16:23) (in thread): > What time are the meetings usually?
2022-05-07
Charlotte Soneson (01:43:32) (in thread): > Meetings are currently on the first Thursday of the month at noon US Eastern time.
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2022-05-08
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2022-05-09
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2022-05-10
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Lori Shepherd (12:35:27): > Some deadlines to be aware of are fast approaching: > 1. The in-person Bioc2022 conference lottery begins this Sunday May 15. Please see thebioc2022 registration page for more details > 2. The Bioc2022 Award nomination deadline is next Friday May 20. Please nominate up to 3 qualified individuals. More information onBiocAwards page
2022-05-11
Jan Stanstrup (04:34:34): > I have a curious problem and I am wondering if it has a known solution. I was hoping someone would know if the problem has an established name. Suppose you make a mixture of compounds, but you make a mistake. You added the wrong amount of something. To not throw the mixture away you could add more of some compounds to get to the desired concentration of all the compounds. The problem is that it is not straight forward to calculate how much to add of each ingredients, since every time you add something you lower the concentration of everything else. > It sounds like a common problem that should have a known solution. So far I managed to write an numeric optimization in R that seems to work well, but I wonder if there is a more elegant way to do it.
Alvaro Sanchez (04:45:39) (in thread): > The name you’re looking for is dilution problems.
Jan Stanstrup (04:51:59) (in thread): > thanks. but if I look for that I only find classical things where the components are neglectable in weight/volume compared to the solvent. Here there is no “solvent” as such. Also the school examples that come up are things with just a single component to dilute.
Jan Stanstrup (05:04:17) (in thread): > suppose you are supposed to make a 40:60 mix of A and B. By mistake you did 60:40. So now you can fix it by adding more B. But how much to achieve the 40:60 mix? It gets very complicated with many components. I am wondering if there is a known general solution.
Moritz E. Beber (05:44:08) (in thread): > There are various dilution calculators our there, have you tried any of those?
Jan Stanstrup (05:47:03) (in thread): > seems to all be for a single solute/solvent.
Jan Stanstrup (05:47:38) (in thread): > Anyway, thanks for the answers. I just wanted to be sure this wasn’t a well-known problem.
Moritz E. Beber (05:50:06) (in thread): > http://lukaszmentel.com/batchcalculator/ maybe? - Attachment (lukaszmentel.com): Batch Calculator > batch calculator homepage
Moritz E. Beber (05:50:42) (in thread): > orhttps://pyeql.readthedocs.io/en/latest/index.html
Gavin Rhys Lloyd (10:43:55) (in thread): > I did it like this:
Gavin Rhys Lloyd (10:43:58) (in thread): > > fcn = function(current=c(60,40),target=c(40,60)) { > > # current is the existing mixture you want to adjust e.g. 60:40 collect = c(60,40). Must sum to 100. > # target is the mixture you are aiming for e.g. 40:60 target = c(40,60). Must sum to 100. > > if (sum(current)!=100){ > warning('sum(current) != 100') > } > if (sum(target)!=100){ > warning('sum(target) != 100') > } > > # keep original input > orig=current > > # ensure only adding to mixture; smallest ratio first means all others will > # be an increase > x = order(target/orig,decreasing = FALSE) > > # loop over all unique pairs > for (k in 1:(length(current)-1)) { > for (j in (k+1):(length(current))) { > > # desired ratio between j and k based on target > rat=target[x[j]]/target[x[k]] > > # if k is fixed, what value for j gives correct ratio? > val = rat*current[x[k]] > > # update current with corrected value for this ratio so it gets used > # next time its needed > current[x[j]]=val > > } > > } > > # amount to add of each is difference between input and updated > toAdd=current-orig > > # report > print(paste0('To adjust a mixture from ',paste0(orig,collapse=':'), > ' to ', paste0(target,collapse=':'), > ' make the solution up to ',paste0(current,collapse=':'), > ' by adding ', paste0(toAdd,collapse=':'))) > print(paste0("The final volume will be ", sum(current)/sum(orig), 'x larger.')) > > # return amount to add of each substance > return(toAdd) > } >
Gavin Rhys Lloyd (10:44:10) (in thread): > not sure if its exactly what you want though
Jan Stanstrup (11:30:08) (in thread): > shit that is brilliant. Exactly what I was after. Thanks! I am not sure I understand right now how it works but I will study it. It gives the correct result for my problem, is more generalized and avoids the uncomfortable use of numeric optimization.
Jan Stanstrup (11:33:56) (in thread): > for kicks and giggles here is my solution: > > library(tidyverse) > > > input <- structure(list( > cmp = c("a", "b", "c", "d", "e", "f"), > start = c(1.931094620003,9.167703668716, 15.558664038586, 73.185397800042, 0.15623154969, 0.000908322963), > target = c(2.126, 7.036, 10.093, 80.572, 0.172, 0.001) > ), > class = c("tbl_df", "tbl", "data.frame"), > row.names = c(NA, -6L) > ) %>% as.data.frame() %>% column_to_rownames("cmp") > > > > # get limits > input <- input %>% > mutate(rel_off = (start-target)/start, > lower = 0, > upper = (1/max(rel_off))*sum(target)-sum(start) # not sure about this > ) %>% > mutate(upper = if_else( max(rel_off)==rel_off, 0, upper)) > > > > > fun_mix <- function(add, > a_s, b_s, c_s, d_s, e_s, f_s, > a_t, b_t, c_t, d_t, e_t, f_t > ){ > > a_a <- add[1] > b_a <- add[2] > c_a <- add[3] > d_a <- add[4] > e_a <- add[5] > f_a <- add[6] > > S <- a_s+a_a+b_s+b_a+c_s+c_a+d_s+d_a+e_s+e_a+f_s+f_a > > e <- (((a_s+a_a)*100/(S)-a_t)/a_t)^2 + > (((b_s+b_a)*100/(S)-b_t)/b_t)^2 + > (((c_s+c_a)*100/(S)-c_t)/c_t)^2 + > (((d_s+d_a)*100/(S)-d_t)/d_t)^2 + > (((e_s+e_a)*100/(S)-e_t)/e_t)^2 + > (((f_s+f_a)*100/(S)-f_t)/f_t)^2 > > > return(e) > > } > > > # par_manual <- c(1.35, 1.7, 0, 51, 0.109, 0.000632) > > result <- nlminb(start = rep(0, nrow(input)), > objective = fun_mix, > lower = input$lower, > upper = input$upper, > > a_s = input["a", "start"], b_s = input["b", "start"], c_s = input["c", "start"], d_s = input["d", "start"], e_s = input["e", "start"], f_s = input["f", "start"], > a_t = input["a", "target"], b_t = input["b", "target"], c_t = input["c", "target"], d_t = input["d", "target"], e_t = input["e", "target"], f_t = input["f", "target"] > ) > > > out <- input %>% bind_cols(tibble(add = result$par)) > > out <- out %>% mutate(final_amount = start+add, > final_conc = (final_amount/sum(final_amount))*100, > error = ((final_conc-target)/target)*100 > ) > > out %>% as_tibble >
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2022-05-12
Hervé Pagès (17:32:00) (in thread): > Sounds like in some cases these adjustments will actually require to add a lot of compounds so if you’re not going to use all the final mixture, you’ll end up throwing away some of it (which could be a lot of it). There are even situations where you’ll need to add more amount of compounds than what it would have taken to make the mixture again from scratch. > > If the goal is to minimize cost of the “reparation”, you’ll probably want to introduce the cost of each compound in the equation. There are situations where minimal cost would be achieved by throwing awaypart of the initial mixture. For example with your 40:60 A/B mix, if you’ve already made the exact amount of mixture that you need, but unfortunately with the wrong proportions (you’ve switched them), you’ll achieve minimal cost by throwing 1/3 of the initial mixturebefore doing the adjustment.
Kristen Steenbergen (22:53:54): > @Kristen Steenbergen has joined the channel
2022-05-13
Babette Jakobi (06:14:26): > Hey every one quick question, does it make sense to to clr transformations on prevalence thresholded data or does the prevalence filtering skew the “reference” or the geometric mean too much? > And if that’s the case, if we choose prevalence filtering within methods such as ancom2, aldex2 do they perform the prevalence thresholding after transformation and how?
Danique Mulder (06:14:55): > @Danique Mulder has joined the channel
2022-05-15
Antonija Kolobaric (15:22:13): > @Antonija Kolobaric has joined the channel
2022-05-16
Jan Stanstrup (08:08:08) (in thread): > thanks. that is right. I am grateful for all the help.
Kasper D. Hansen (14:16:50): > https://sfconservancy.org/news/2022/may/16/vizio-remand-win/ - Attachment (Software Freedom Conservancy): Software Freedom Conservancy right-to-repair lawsuit against California TV manufacturer Vizio, Inc. remanded to California State Court > For Immediate Release — IRVINE, CA, USA — Software Freedom Conservancy announces it has succeeded in federal court with its motion to have its lawsuit against Vizio, Inc. remanded back to Superior Court in Orange County, California. Vizio, Inc. previously filed a request to “remove” the case from California State Court into U.S. Federal Court.
Kasper D. Hansen (14:17:03): > Ruling on GPL
Kasper D. Hansen (14:17:17): > > Court Ruling shows that the GPL agreements function both as copyright licenses and as contractual agreements, says nonprofit organization
Henrik Bengtsson (20:29:37): > “[Sandler] explains that in past litigation, the plaintiffs have always been copyright holders of the specific GPL code. In this case, Software Freedom Conservancy hopes to demonstrate that it’s not just the copyright holders, but also the receivers of the licensed code who are entitled to rights.”
2022-05-17
Monica Coelho (03:37:49): > @Monica Coelho has joined the channel
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Kristian Ullrich (16:46:57): > Hi, > I am porting existing C++ code into Rcpp. > So far everything is working, butR CMD checkfails with the following warnings, which is related to thestd::chdirandstd::getcwdfunction. > > Found the following significant warnings: > mcscanxr.cpp:1041:14: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] > mcscanxr.cpp:1103:11: warning: ignoring return value of 'char* getcwd(char*, size_t)', declared with attribute warn_unused_result [-Wunused-result] > mcscanxr.cpp:1141:18: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] > mcscanxr.cpp:1162:14: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] > mcscanxr.cpp:1178:10: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] > > The problem is that the original C++ code usesstd::chdirto first check if a directory exists and then changes into it to write some files. > > if (outdir!=""){ > const char *outdir_fn = outdir.c_str(); > if (chdir(outdir_fn)<0){ > mkdir(outdir_fn,S_IRWXU|S_IRGRP|S_IXGRP); > chdir(outdir_fn); > } > } > > After the process I need to change back into the original working directory before exiting the rcpp function. > My initial fix, first usingstd::getcwdand at the end of the rcpp function to get back into the original working directory with thestd::chdirnow seems to be part of the same problem. > > char curwd[256]; > getcwd(curwd, 256); > > Any ideas how to circumvent these warnings are highly appreciated?
Dirk Eddelbuettel (17:24:03): > Hi Kristian.#generalis a pretty broad channel so maybe best not to spam it. Team Rcpp sits on a mailing list we usually recommend, you have me here by chance too. We could probably spin off a channel… > > In short, what you have there is more recent warnings from more recent compilers. Thestd::chdir()and alike functions have been around since forever, have always returned an error code, and it is was common to just ignore it. Now under picky compiler settings it warns. So you either assign:auto res = chdir(somearg);and do something withres, or you add-Wno-unused-resultto your compiler flags. (One think I have done is a simple wrapper as inif (std::chdir(somearg) != 0) Rcpp::stop("Error from chdir");which should be enough to quieten the compiler … but adds tedium to editing.
Martin Morgan (17:32:07) (in thread): > If this warning is from@Kristian Ullrich’s code re-setting the working directory around a wrapped function, maybe it’s better to do this at the R level with > > fun = function(...) { > pwd <- getwd() > on.exit(setwd(pwd), add = TRUE) > ... # call C++ code > } > > so that one is sure to reset the directory regardless of problems occurring in C++. Otherwise this idiom would need to be implemented in C++.
Lori Shepherd (20:23:13): > <!channel>please remember to nominate qualified individuals for bioc2022 awards by this Friday!!! More information and nomination form found on awards home pagehttps://www.bioconductor.org/about/awards/
Kristian Ullrich (23:48:09) (in thread): > Thank you for your suggestions and the nice explanation why thestd::chdirthrough warnings with more recent compilers. I like the idea of a dedicated Rcpp user channnel.
Dirk Eddelbuettel (23:50:38) (in thread): > About to call it a night here in Central time but I just created#cpp(assuming that is ok with those in charge). See you there?
2022-05-18
Santiago Thibaud (13:53:51): > @Santiago Thibaud has joined the channel
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2022-05-19
Tyrone Lee (09:10:54): > @Tyrone Lee has joined the channel
Aidan Lakshman (10:39:46): > Hi everyone, I’m having issues catching a small memory leaking in some C code I wrote for R…I posted the question on stackoverflow, but I figured I’d link it here too since this community is more likely have experience with this issue than the average SO viewer:https://stackoverflow.com/questions/72306204/heap-corruption-error-when-calling-c-from-r-cant-find-the-memory-leak Thanks! - Attachment (Stack Overflow): Heap Corruption error when calling C from R, can’t find the memory leak > I’m at my wits end trying to debug this issue, and I figured I’d turn to SO for help. I’m writing a function in C to optimize some parts of my R code, and I’m getting a Heap Corruption Error when r…
Martin Morgan (10:59:59) (in thread): > have you considered using therocker/r-devel-san image? There might be a learning curve if unfamiliar with docker, but worth it. ‘Advanced’ use would likely involve mapping a local folder to the image with-v /local/folder:/docker/mount/location.
Aidan Lakshman (11:05:16) (in thread): > Oh, I have not! I didn’t even know that was a thing, I’ll check it out later today. Thanks a bunch!
Mike Smith (13:05:12) (in thread): > Similarly, could you use a docker container to run R with Valgrind?
Aidan Lakshman (13:19:02) (in thread): > Yeah, definitely also an option. I was hoping to be able to debug it without needing to spin up VMs/docker containers, but it’s increasingly seeming like that’s the route I’ll have to go. > > Part of me is worried this is an Apple silicon issue, running it on Linux could just solve the problem.
rebecca jaszczak (13:53:51): > @rebecca jaszczak has joined the channel
Hervé Pagès (13:57:29) (in thread): > Shouldn’t you walk backward on your linked list here? > > while (corrs != NULL){ > ptr = corrs; > corrs = corrs->next; > free(ptr); > } > free(corrs); > > Also isn’tcorrsguaranteed to be NULL when you exit the loop? Callingfree()on NULL is not good.
Aidan Lakshman (14:01:44) (in thread): > Yes, I’ve subsequently fixed the latter part of that (calling free on NULL).I’m not sure how to walk backward through it, like via a recursive function? Typically this is how I’ve seen it done to free an LL, by moving the head forward and freeing the previous head.I did just refactor it to useR_allocinstead ofcallocso that R could handle the allocated memory, but unfortunately that didn’t fix the problem either. That refactor renders this section of code unnecessary, but maybe that’s introducing errors with R making mistakes allocating the memory.
Hervé Pagès (14:06:15) (in thread): > Yes usingR_allocinstead ofcallocis definitely the way to go. Especially since you were not checking the pointer returned by yourcalloccalls. Usingcalloc/freeproperly is tricky e.g. if you get a NULL then you have to free whatever was allocated before callingerror()which is hard to get right. By usingR_allocyou bypass all that difficulty: if allocation fails, it will return an error and all the memory that was previously allocated viaR_allocwill get automatically released.
Hervé Pagès (14:08:43) (in thread): > I don’t see the updated code on SO
Aidan Lakshman (14:08:59) (in thread): > Just updated, sorry for the delay—was trying to make sure it matched up with what I have locally
Aidan Lakshman (14:14:06) (in thread): > Makes sense regardingcallocversusR_alloc, thanks for the insight :)
Hervé Pagès (14:16:53) (in thread): > > int *firstSeqPos = INTEGER(coerceVector(fSP, INTSXP)); > int *secondSeqPos = INTEGER(coerceVector(sSP, INTSXP)); > > This is not good. The SEXP returned bycoerceVector()need to be protected. But it’s usually considered better practice to do this at the R level right before entering the .Call entry point. Note that iffSPandsSPare integer matrices, there’s no need to coerce them to integer as they are already seen as integer vectors at the C level.
Aidan Lakshman (14:51:26) (in thread): > Wow you are a life saver, thank you! It works now. I didn’t realize it returned an SEXP, and I think the background garbage collector was cleaning it up too early. Thanks so much for looking through this and helping debug.
Aidan Lakshman (15:17:12) (in thread): > Thanks everyone!! - File (PNG): PNG image.png
Hervé Pagès (16:06:04) (in thread): > That’s a nice speed improvement. I realize now that having switched fromcalloctoR_allocprevents you from freeing the nodes that you skip so you end up allocating memory forlength(fSP) *length(sSP)nodes instead ofNVnodes only. I assume that in typical situationsNVis going to bemuch smaller thanlength(fSP) *length(sSP). So this might be a case where usingcalloc/freeis maybe more appropriate. If that reduces memory footprint by 10x or 100x then it’s going to make a huge difference, especially iffSPandsSPare big matrices!
Aidan Lakshman (16:09:53) (in thread): > Hmmm, that’s a good point—the vector sets come fromXStringSetobjects, so in the future it would probably be a good idea to be as careful with memory as possible so it can support large alignments. That should be a fairly easy refactor though to revert tocalloc, I’ll just be a little more careful with ensuring I’m not callingfree(NULL)anywhere:sweat_smile:
Hervé Pagès (18:03:11) (in thread): > A few more things: > > It seems that right now your C code will crash ifnvis >length(fSP) *length(sSP)because your lastforloop will try to walk beyond the linked list. > > It should not be too hard to revert tocallocbut don’t underestimate the amount of effort and cautiousness that is needed to get this right. It’svery easy to introduce memory leaks if one is not careful. For example, it’s great that you support user interrupts (viaR_CheckUserInterrupt) but you want to make sure that memory is properly released upon interruption. Since a user interrupt immediately takes you back to R without giving you the opportunity to release resources, you need to introduce a 2nd .Call entry point (e.g.trimCovar_cleanup) that takes care of that, and do something like this at the R level: > > .trimCovar <- function(...) { > on.exit(.Call("trimCovar_cleanup")) > .Call("trimCovar", ...) > } > > This will ensure that, whatever happens, resources are released. Note that this means that yourtrimCovar_cleanupentry point is able to find the resources allocated by thetrimCovarentry point. An easy way to achieve this is to use global static variables to point at resources e.g. place this: > > static node *corrs = NULL; > > early in the C file (before the definitions of thetrimCovarandtrimCovar_cleanupfunctions). > > I think there are ways to keep usingR_allocwhile allocating onlyNVnodes but that is another story for another day.
Martin Morgan (18:19:26) (in thread): > For what it’s worth, I posted a C++ solution in our new#cppchannelhttps://community-bioc.slack.com/archives/C03G97XF1LZ/p1652998672173449 . The use of cpp11 (or Rcpp) makes these protection imbalances more-or-less a thing of the past. The use of C++ Standard Template Library means that we don’t have to re-implement a priority queue from scratch. - Attachment: Attachment > @Aidan Lakshman posted in the #general channel about debugging a memory corruption problem in C code. It turns out this was due to a protection stack imbalance. Since these are very tricky to spot, and since C++ abstractions in R provide a straight-forward way around this, and because I’d like to explore the {cpp11} package a bit, and because I seem to know only one STL data structure (the priority queue, which happens to be appropriate for the problem) I thought I’d post an alternative implementation here. > > My re-implementation is > #include <tuple> > #include <queue> > #include <iostream> > > #include "cpp11.hpp" > using namespace cpp11; > > [[cpp11::register]] > integers trimCovar_cpp(doubles fm, integers firstSeqPos, integers secondSeqPos, > int nv, int nr) > { > // Use a Standard Template Library (STL) 'priority queue' > // to store triples of score / row index / column index values. > // The comparator uses first score, then row, then column index to > // order, so 'ties' go to the lowest row / column indexs > typedef std::tuple<double, int, int> triple; // score, row, column > std::priority_queue< triple, std::vector<triple>, std::greater<triple> > > corrs; // priority queue of largest scores > > // Note that we do not have to worry about coercion, argument type, > // or allocation, cpp11 takes care of all of this for us > int sp1l = firstSeqPos.size(); > int sp2l = secondSeqPos.size(); > > int colv1, colv2; > int cv1, cv2; > double p1, p2, score=0; > > // original C code > for (int i=0; i [corrs.top]( sp1l; i++){ > cv1 = firstSeqPos[i]; > colv1 = (cv1 - 1) * nr; > for ( int j=0; j<sp2l; j++ ){ > cv2 = secondSeqPos[j]; > colv2 = (cv2 - 1) * nr; > > // KL Divergence > score = 0; > for ( int k=0; k<nr; k++){ > std::cout << "i, j, k: " > << i << ", " << j << ", " << k > << std::endl; > p1 = fm[colv1 + k]; > p2 = fm[colv2 + k]; > if (p1 != 0 && p2 != 0){ > score += p1 * log(p1 / p2); > } > } > > // save in priority queue > triple elt(score, i, j); > if (corrs.size() < nv) { > // always push if fewer than required values > corrs.push(elt); > } else { > // push if current element is larger than smallest element > if ([http://corrs.top)() [corrs.top]( elt) { > corrs.pop(); > corrs.push(elt); > } > } } > R_CheckUserInterrupt(); > } > > // create integer vector from ordered scores > writable::integers ans; > while (!corrs.empty()) { > triple value = <http://corrs.top)(); > ans.push_back(std::get<1](http://corrs.top)() [corrs.top]( elt) { > corrs.pop(); > corrs.push(elt); > } > } } > R_CheckUserInterrupt(); > } > > // create integer vector from ordered scores > writable::integers ans; > while (!corrs.empty()) { > triple value = <http://corrs.top)(); > ans.push_back(std::get<1)(value)); > ans.push_back(std::get<2>(value)); > corrs.pop(); > } > > return ans;; > } > Use from R (better to make a package, of course…) is > fm [vignette](- matrix( > c(0.5, 0.5, 0.0, 0.0, 0.0, 0.5, > 0.5, 0.5, 1.0, 1.0, 1.0, 0.5), > nrow = 2, > byrow = TRUE > ) > firstSeqPos <- 1:3 > secondSeqPos <- 4:6 > nv <- 3 > nr <- nrow(fm) > > cpp11::cpp_source("stackoverflow_72306204.cpp") > trimCovar_cpp(fm, firstSeqPos, secondSeqPos, nv, nr) > (I’m not really sure whether I’ve got the arguments correct; the StackOverflow post didn’t include a fully reproducible example). > > For reference: > 1. The {cpp11} <https://cran.r-project.org/web/packages/cpp11/vignettes/cpp11.html). > 2. C++ reference pages for priority_queue and tuple > 3. A very useful post on using Rcpp for identifying largest N values using a priority queue, generalize a StackOverflow answer I provided.
Aidan Lakshman (18:37:15) (in thread): > Thanks so much for all these tips@Hervé Pagès, it’s really difficult getting started with developing C extensions for R, and your advice is making a world of a difference. I’m looking forward to (hopefully) having the chance to talk with you more at Bioc2022. > > on your notes: > * it will indeed crash if nv > that product, though I’m checking for this scenario prior to calling the code in the R script > * this is a great tipon freeing memory in case of interrupts—I hadn’t thought about this case. I did have a mysterious crash earlier and I suspect it’s due to not correctly handling this case. I’ll incorporate that change into the code asap
Aidan Lakshman (18:38:54) (in thread): > @Martin Morganthanks for the solution, and thanks for creating a channel for C/++ help! Unfortunately my advisor doesn’t allow us to use external packages for development so I’m stuck with base C:sweat_smile:but I agree that the C++ implementations are often much easier to work with and avoid many of these issues
Aidan Lakshman (18:39:35) (in thread): > I appreciate all the discussion from everyone—thanks for all the input!
Hervé Pagès (18:40:23) (in thread): > The use of astd::priority_queueis awesome and saves a lot of work! My “other story for another day” was basically re-implementing something like that in C:sweat_smile:
2022-05-20
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2022-05-21
Dirk Eddelbuettel (08:20:10) (in thread): > > Unfortunately my advisor doesn’t allow us to use external packages for development so I’m stuck with base C > That’s a basic human rights violation you can bring up with the campus ethics board:stuck_out_tongue_winking_eye:Kidding aside you can actually do what@Martin Morgandoes and use a priority queueinside a C++ function and “simply” use the clunky C API of R to access it – which you already know how to. Saves you from manually dealing with your linked list. (And for completeness, I have a micro-package that is just a handful of header-only re-declarations which wrap a IMHO nice minimal C++ layer around the C API. You could copy from those what you need for a more hybrid C/C++ approach without external packages. Mentioning it mostly for completeness…)
Aidan Lakshman (08:25:39) (in thread): > Oh that’s a good idea! I more or less gave up on the hybrid C/++ approach because the docs were hard to understand haha and I was having a hard enough time using just base C. Could you link me to the repo for that package so I can take a look at the code?
Dirk Eddelbuettel (08:31:05) (in thread): > Sure. I’d actually love feedback, and you with your ethics-board case are a good potential user:wink:so I’d love to head from you. Repo ishttps://github.com/eddelbuettel/tidycpp and a set of examples are inhttps://github.com/eddelbuettel/tidycpp/tree/master/inst/snippets (and most of them are also in the simple vignette).
Dirk Eddelbuettel (08:34:51) (in thread): > Now I use that currently viaRcpp::sourceCpp()because that frees me from the issue R creates and which you have whereR CMD SHLIBcreate anOS-dependent filename you need to adjust for indyn.load(). Wrapping something like that in a function that picks .so or .dll is a simple extension but hasn’t happened yet. There is no actual use of Rcpp headers or code, it is just an execution helper you can work around and skip if you prefer that (or are “required to”).
Aidan Lakshman (08:42:26) (in thread): > Thank you!!
Charlotte Soneson (13:42:25): > Bumping this - deadline for (self-)nominations to the Bioconductor TAB onMay 31. https://community-bioc.slack.com/archives/C35G93GJH/p1651849636404109 - Attachment: Attachment > Do you want to join the Bioconductor Technical Advisory Board, or do you know someone who would be a great fit? Then fill this short form (if you’re nominating someone else, please first confirm that they are interested) before May 31 (at midnight in a time zone of your choice). For more information about the current board and the election process, see https://bioconductor.org/about/technical-advisory-board/ , and if you have questions, feel free to post them in the #tech-advisory-board channel. Please help spread the word!
2022-05-22
Erica Feick (07:23:39): > There are still in-person tickets available for BioC2022 in Seattle, WA! Enter your name here and you will be contacted.https://forms.gle/MU4dXYSjkqa4uVJ59 - Attachment (Google Docs): BioC22 In-Person Ticket Wait List > Due to the limited amount of in-person tickets available for the July 2022 conference, we have established a wait list. As additional tickets become available, you will be notified to register.
2022-05-23
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2022-05-24
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2022-05-25
Fabricio Almeida-Silva (05:48:12): > Hello, everyone. Can anyone confirm that the deadline for software demo/talk submission to EuroBioc22 is May 31st? The schedule is still under development, so I was wondering if the deadline will be postponed.
Charlotte Soneson (06:52:44) (in thread): > Yes, at least at the moment the deadline is still May 31. The schedule will be constructed after reviewing the submissions and selecting the ones that will be accepted for the different types of submissions.
Fabricio Almeida-Silva (06:54:00) (in thread): > Thank you!
Brian Hanratty (14:51:19): > @Brian Hanratty has joined the channel
2022-05-26
Cindy Fang (14:50:59): > @Cindy Fang has joined the channel
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2022-05-27
이상호 (00:43:13): > @이상호 has joined the channel
Brian Hanratty (13:22:53): > Does anyone have any idea if there is a timeline for bioconductor to support apple silicon arm64 architecture?
Andres Wokaty (13:38:54): > That’s something I am working on. There’s a bit of a delay getting it going right now. The first part of this is just doing a few tests and then if that goes well, we’ll add them to the build system and make the packages available.
Hervé Pagès (17:10:06): > Just to clarify, we’re targeting BioC 3.16 for those binaries i.e. if every goes well we should be able to produce them and make them available anytime between now and the 3.16 release in October.
2022-05-28
Leonardo Collado Torres (10:48:43): > Interesting!Thanksfortheinfo:)
2022-05-31
Fabricio Almeida-Silva (01:55:43) (in thread): > Hi,@Charlotte Soneson. Do you know if we’re getting a decision on our submission before the registration deadline?
Charlotte Soneson (02:43:28) (in thread): > We’re hoping to send out the decisions in the week of July 4.
Fabricio Almeida-Silva (02:50:08) (in thread): > Good to know! Thanks a million!:wink:
2022-06-01
Andrew Abrams (07:50:34): > @Andrew Abrams has joined the channel
Vince Carey (08:33:03): > Looking for Bioconductor users interested in the zarr format. Reply in thread please.
Erica Feick (10:51:43): > We have more in-person tickets available for BioC2022 in Seattle! You can register athttps://bioc2022.eventbrite.com . Registration is $400 for faculty, staff, government and industry; $250 for students and postdocs. - Attachment (Eventbrite): BioC2022 Annual Conference > Registration is now open. Please read below for the types of tickets available and how to register.
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2022-06-03
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2022-06-04
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rohitsatyam102 (23:02:05): > Am looking for some packages that can perform Integration/ combinatorial analysis using scRNAseq, bulkRNAseq, Bulk HiC and Bulk/sc ATACseq. Any suggestions??
2022-06-07
Charlotte Soneson (03:09:54) (in thread): > Out of curiosity - did you already try/succeed to build and use the newRhtslibin Bioc 3.16 on the m1? We’re having trouble getting it to work (while all other packages so far seem to build fine), and we are trying to figure out if it’s a local issue or a more general one, so I thought it was worth reaching out to see if you had already tried it out:slightly_smiling_face:. For context, we’re trying to reproduce/debug the current macbuild error for QuasR in devel.
Robert Castelo (09:17:04) (in thread): > The Bioconductor MOFA2package should do at least the integration of bulk data, but maybe works also with scRNAseq, ask the authors. The maintainer should at least answer you on the support site, although I think they give most of the support through a dedicatedSlack Workspace .
Andres Wokaty (10:01:43) (in thread): > I haven’t run it yet. I’m still setting up the build. I bookmarked your message and will get back to you about it.
Charlotte Soneson (10:04:54) (in thread): > :gratitude-thank-you:
2022-06-08
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Aedin Culhane (23:00:56) (in thread): > Mogsaalsodoesintergrations. It’s designedforbulkbutweareadaptingforScRNAseq
rohitsatyam102 (23:25:03) (in thread): > Thanks.@Aedin Culhaneand@Robert Castelo. Will check them out.
2022-06-09
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2022-06-10
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2022-06-12
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2022-06-14
Andres Wokaty (17:22:59) (in thread): > I was able to install/build Rhtslib on the M1 I’m trying.
2022-06-15
Charlotte Soneson (01:38:10) (in thread): > Great,thanksalotforchecking!Ithinkwehaveidentifiedtheissueonourside:slightly_smiling_face:
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2022-06-17
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2022-06-20
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2022-06-21
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2022-06-24
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2022-06-25
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2022-06-26
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2022-06-27
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2022-06-28
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Fabricio Almeida-Silva (08:08:25): > Hi, everyone. > > I’ve had my 4th Bioconductor package accepted last week (June 20,https://github.com/Bioconductor/Contributions/issues/2682 ), and what I always do after one of my packages is accepted is to keep checkingbioconductor.org/packages/ every now and then to see if the landing page was created. > > Because I keep checking if the landing page was created every day, I was wondering: what happens under the hood when a package is accepted? Is there a deadline for the landing page to be created? I don’t remember reading anything about this part of the process.
Lori Shepherd (08:13:51): > once a package is accepted – we run a script to add the accepted packages to the daily builder and close the issue (normally done once or twice a week) – once the package builds on the daily builder a package landing page is generated (after the build finishes) – also updates to the landing pages (ie. description info or citations, new version of package etc) won’t appear until after the subsequent build (normally a 1-2 hours after completion)
Lori Shepherd (08:20:41) (in thread): > yours has not been created because it looks like it was closed manually instead of when running the script for accepted packages. I’ll remind the reviewers not to close the issue
Lori Shepherd (08:22:34) (in thread): > I’ll correct this now.
Fabricio Almeida-Silva (09:59:01) (in thread): > Thanks for the detailed explanation and for fixing the issue,@Lori Shepherd:grinning:
2022-06-29
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2022-06-30
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2022-07-02
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2022-07-03
rohitsatyam102 (06:08:50): > Hi Everyone!! > > Any package suggestion for Differential Network analysis in Bulk RNASeq data between control and knockout samples (each with 3 biological replicates)?? I was checking outwTOandCoDINapackages but couldn’t find proper documentation.csdRis for large sample sizes.
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2022-07-04
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2022-07-05
benedek.danko (10:29:04) (in thread): > Hi, I don’t know if it fits your purposes but once I used MOGAMUN for searching differentially activated subnetworks between two conditions using bulk RNA-seq data.https://www.bioconductor.org/packages/release/bioc/html/MOGAMUN.html - Attachment (Bioconductor): MOGAMUN > MOGAMUN is a multi-objective genetic algorithm that identifies active modules in a multiplex biological network. This allows analyzing different biological networks at the same time. MOGAMUN is based on NSGA-II (Non-Dominated Sorting Genetic Algorithm, version II), which we adapted to work on networks.
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2022-07-07
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2022-07-08
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2022-07-09
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2022-07-10
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2022-07-11
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2022-07-14
Michael Love (08:13:40) (in thread): > Another similar case — we had a packageedsaccepted on July 8 and I’ve been doing this thing similar to Fabricio — checking the packages/ each day but it’s not added yet. More curious what’s going on in the background, no rushhttps://github.com/Bioconductor/Contributions/issues/2680#issuecomment-1178910697 https://bioconductor.org/packages/eds
Lori Shepherd (08:57:44) (in thread): > sorry about this. I will run the script for accepted packages over the weekend or on monday as I’m on holiday today and tomorrow. they should appear by monday / tuesday at the latest. i apologize for the delay
Michael Love (09:07:24) (in thread): > no problem! i understand that there are humans behind the wheel
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2022-07-15
rohitsatyam102 (20:09:08): > Can anyone suggest me to a workflow (or step by step guide) to analyse .gpr files. Actually there are a lot of tutorials on how to handle CEL files but rarely on how to handle microarray .GPR files. Using GEOquery I am able to generate the expressionSet objects, but I am not sure how to proceed from here!!
2022-07-16
Sean Davis (12:24:55) (in thread): > Your best bet is to ask on the support site:https://support.bioconductor.org if you want the highest chance of having someone see and answer your questions. That said, what is it that you are asking above? About .GPR files or what to do after you have an ExpressionSet? If the latter, we’d need to know what your goal is.
2022-07-17
rohitsatyam102 (10:21:48) (in thread): > Thanks@Sean Davis. Since this wasn’t any package related query, I thought asking it here. The ultimate goal is to carry out differential expression analysis. I could actually use GEOQuery package to get the ExpressionSet object. But now I don’t know way forward!!
2022-07-18
Filip Stachura (06:39:33): > @Filip Stachura has joined the channel
Sean Davis (09:23:00) (in thread): > If these are microarray data, consider looking at the excellent Limma User Guide and using limma.
Steffen Neumann (11:00:26): > Hi, I am trying to help the IPO team fix their package, that is on BioC for 5 yrs now, and the PhD has moved on … . Can I somewhere check who has access to git@git.bioconductor.org:packages/IPO ?
Alan O’C (11:03:49) (in thread): > Maintainer: Thomas Riebenbauer <Thomas.Riebenbauer atjoanneum.at > at least
Lori Shepherd (11:09:26) (in thread): > This would be better asked onbioc-devel@r-project.org mailing list – > but@Alan O’Cis correctthomas.riebenbauer@joanneum.at is the registered email in the git credentials account to manage keys associated with the username with access
Steffen Neumann (11:10:44) (in thread): > Main question was the git credentials, so thanks both !
Lori Shepherd (11:11:15) (in thread): > the git credentials account hasn’t been activated it seems – so if login doesn’t work try activating the account first
2022-07-19
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Aidan Lakshman (15:33:14): > Can anyone help me troubleshoot a build failure? I can’t get my package to build on bioconductor, and I can’t reproduce the error locally. For some reason the compilation of source files always fails, and I’m not completely sure from the Writing R Extensions page what I’m supposed to be including insrc/. Error message is in thread below, but it’s essentially failing with “file format not recognized” on my*.ofiles. Should I be excluding these so they get compiled at runtime?
Aidan Lakshman (15:33:24) (in thread): > Error: > > ############################################################################## > ############################################################################## > ### > ### Running command: > ### > ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL SynExtend > ### > ############################################################################## > ############################################################################## > > > * installing to library '/home/biocbuild/bbs-3.16-bioc/R/library' > * installing **source** package 'SynExtend' ... > **** using staged installation > **** libs > gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o SynExtend.so R_init_synextend.o calcMIR2C.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR > R_init_synextend.o: file not recognized: file format not recognized > collect2: error: ld returned 1 exit status > make: ***** [/home/biocbuild/bbs-3.16-bioc/R/share/make/shlib.mk:10: SynExtend.so] Error 1 > ERROR: compilation failed for package 'SynExtend' > * removing '/home/biocbuild/bbs-3.16-bioc/R/library/SynExtend' >
Aidan Lakshman (15:36:43) (in thread): > I should add that this builds fine on my local machine, as well as on other machines I have access to (ARM and intel Macs)
Kasper D. Hansen (15:37:47): > Wait what, you’re having.ofiles in git? You shouldn’t do that; those are architectur specific
Aidan Lakshman (15:38:22): > :confused:I knew that was the answer, thanks….it’s been a while since I worked with C. Lesson learned haha
Kasper D. Hansen (15:40:08): > You should only have text files, apart from possibleRdata/Rdsfiles. Certainly nothing but text in/src
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2022-07-21
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Andres Wokaty (13:46:02): > Hi, I just made#queer-bioc. Maybe we can meet up at Bioc2022 in person or virtually?:slightly_smiling_face:
2022-07-22
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2022-07-25
saskia (18:14:03): > <!channel>The CoC committee has updatedthe Code of Conduct . The new CoC refers to our incident procedures and introduces our independent Ombudsperson, who will oversee conflict resolution when required. For each CoC committee member, we disclose further affiliations with the Bioconductor project. > > Ahead of Bioconductor conference season, we want to remind everyone to adhere to the CoC at all times. We strive to maintain a kind and welcoming environment that is free of harassment for all. Do not hesitate toreport behaviour that makes you feel unsafe or unwelcome. - Attachment (Google Docs): Bioconductor Code of Conduct Reporting Form > To report on any potential violation of our Code of Conduct (http://www.bioconductor.org/about/code-of-conduct/ ), please fill out this form to the best of your ability. The results of this form are shared only with the Bioconductor Code of Conduct Committee - Saskia Freytag (mailto:sas.freytag@gmail.com|sas.freytag@gmail.com ), Yagoub Adam (mailto:yagoub@alumni.usp.br|yagoub@alumni.usp.br ), Leonardo Collado-Torres (mailto:lcolladotor@gmail.com|lcolladotor@gmail.com ), Laurent Gatto (mailto:laurent.gatto@gmail.com|laurent.gatto@gmail.com ), Stephanie Hicks (mailto:shicks19@jhu.edu|shicks19@jhu.edu ), Michael Love (mailto:michaelisaiahlove@gmail.com|michaelisaiahlove@gmail.com ), Federico Marini (mailto:fede.maro@gmail.com|fede.maro@gmail.com ), Sowmya Parthiban (mailto:sowmyaparthiban@gmail.com|sowmyaparthiban@gmail.com ), Anna Quaglieri (mailto:anna.quaglieri16@gmail.com|anna.quaglieri16@gmail.com ), Johannes Rainer (mailto:johannes.rainer@eurac.edu|johannes.rainer@eurac.edu ), Lluís Revilla (mailto:lluis.revilla@gmail.com|lluis.revilla@gmail.com ), Federico Marini (mailto:fede.maro@gmail.com|fede.maro@gmail.com ), and Charlotte Soneson (mailto:charlottesoneson@gmail.com|charlottesoneson@gmail.com ). You may also make a report directly to one member of the Committee by contacting them directly. If any member of the Committee has a conflict of interest with a report, they will be recused and will not have access to the content or process of the report followup. Upon submitting your report, you should receive a separate acknowledgement of receipt via email from the Code of Conduct Committee within 24 hours on weekdays, or within 48 hours for an event that takes place on a weekend. Please email mailto:code-of-conduct@bioconductor.org|code-of-conduct@bioconductor.org if you have not received this acknowledgement. The Committee will investigate your report and follow up according to our Code of Conduct with the aim of making a decision and implementing enforcement as soon as is reasonably possible. We can’t follow up an anonymous report with you directly, but we will fully investigate it and take whatever action is necessary to prevent a recurrence.
2022-07-26
Alvaro Sanchez (07:40:42): > Will the talks and workshops at BioC2022 be recorded?
Leonardo Collado Torres (10:16:58) (in thread): > You might want to join#bioc2022. > > And from the website, it says that talks will be uploaded to YouTube.
Leonardo Collado Torres (10:17:27) (in thread): > https://bioc2022.bioconductor.org/schedule/ has a “YouTube” column already - Attachment (bioc2022.bioconductor.org): Schedule > Schedule
Erica Feick (10:45:55) (in thread): > We anticipate that videos will be available starting August 15th.
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2022-07-27
Ya-Feng Wen (01:09:02): > @Ya-Feng Wen has joined the channel
Yuri Kotliarov (08:36:38): > Is live BioC2022 video stream available? I’m at the app but cannot view the stream.
Rumeysa Fayetörbay (08:59:40): > @Rumeysa Fayetörbay has joined the channel
Wes W (09:15:20): > @Yuri Kotliarovthe schedule is in Pacific Time zone. I believe the keynote wont start for another 2 hours if I am correct in my math
Yuri Kotliarov (09:21:33) (in thread): > That’s it.:slightly_smiling_face:Thanks!
Nicholas Cooley (10:01:10): > the best way to access the streams is thestream videobutton on the agenda section of the web app right? does that button not become accessible till the stream starts?
Erica Feick (10:44:29): > That is correct - hopefully you are in the opening session!
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Michael Love (10:57:29): > ok good, they just cut the microphone
Michael Love (10:57:36): > Just a reminder that the virtual audience can sometimes hear in between sessions
Michael Love (10:57:56): > so don’t say anything you wouldn’t want 107 people to hear
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Ana Ferreira (12:00:33) (in thread): > I don’t see that button anywhere? Have you been able to join the conference?
Ana Ferreira (12:01:12): > How do I access the conference?
Kevin Rue-Albrecht (12:04:37) (in thread): > try this link :https://app.socio.events/MTc1NjA/overview
Kevin Rue-Albrecht (12:04:52) (in thread): > and log in using the email that you registered with
Ana Ferreira (12:06:03) (in thread): > Thank you so much Kevin, I looked everywhere and couldn’t find this link. I appreciate your help
Kevin Rue-Albrecht (12:06:23) (in thread): > I had the same issue an hour ago:wink:
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Nicholas Cooley (12:39:22) (in thread): > in the agenda tab of the socio website thing each session in the agenda has it’s small description and a blue join live stream button
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Ana Ferreira (14:47:35) (in thread): > thank you. I cleaned up my spam the other day. probably the link to access the conference ended up there.
Hena Ramay (14:49:48): > Hi , Is it possible to register for bioc2022 today? Sorry, I was on vacation and totally forgot to register ahead of time!
Erica Feick (14:52:19): > I just reopened virtual registration for the next couple of hours athttps://bioc2022.eventbrite.com/ . - Attachment (Eventbrite): BioC2022 Annual Conference > Registration is now open. Please read below for the types of tickets available and how to register.
Hena Ramay (14:58:20) (in thread): > Thanks Erica! I was able to register.
Hena Ramay (15:46:54) (in thread): > @Erica FeickI am trying to access the conference but it is telling me that the email is not registered. Can you please check.henaramay@gmail.com
Hena Ramay (15:54:15) (in thread): > I was trying to login tohttps://app.socio.events/MTc1NjA/auth as mentioned in a previous thread.
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Jacopo Umberto Verga (16:38:41): > Hi, I am having problems logging in Orchestra for the workshops, how can I get the credentials/register? > Thanks
Alex Mahmoud (16:41:58) (in thread): > If you go tohttp://app.orchestra.cancerdatasci.org/1 , you can login with Google or an email, then search for your workshop name, and launch an RStudio afterwards for that workshop. You will get a URL, but have to wait a little bit until a “Launch Workshop” button appears, after which you login to RStudio at your personal URL withrstudiousername andrstudiopassword
Sean Davis (16:43:28) (in thread): > In addition to the instructions from Alex, here is a bit more detail. > 1. Navigate tohttp://orchestra.cancerdatasci.org/ > 2. Click “Login to get started” > 3. Choose either to login with google or email. > 4. If you choose login with email, you be asked to provide your name and a password. > 5. If login with email and are asked for a password, but you don’t remember it, just click “trouble with logging in” and you’ll get email telling you how to reset your password.
Jacopo Umberto Verga (16:44:24) (in thread): > I have tried to reset the password a pair of time but the new password isn’t accepted
Jacopo Umberto Verga (16:46:40) (in thread): > Solved, I used a shorter password and now works. > Thank for the help
Sean Davis (16:47:16) (in thread): > Good to know,@Jacopo Umberto Verga. I’ll have to check on that.
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2022-07-28
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Anirban Shaw (13:15:53): > :wave:Hi everyone!
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Zhilong Jia (23:47:27): > could the Bioconductor package webpage show a total number of downloads for every package? Sometimes, the developer may need to get the number easier, instead of summing all the downloads per year. Thank you.https://support.bioconductor.org/p/9145357/
2022-07-29
Marcel Ramos Pérez (00:17:47): > We usually report statistics by year to funding agencies. You can check theBiocPkgToolspackage for those stats. I think the sum of all of the downloads across years isn’t too onerous.
Zhilong Jia (00:27:49): > Exactly. couldBiocPkgToolsmake a webpage for this? Or show the number on the stat download page of Bioconductor webpage (for examplehttp://bioconductor.org/packages/stats/bioc/DESeq2/ ). summing is easy but unnecessary. Thank Marcel.
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Leonardo Collado Torres (16:35:30): > Seehttps://github.com/lcolladotor/cv/blob/fb0274c0896ffd0596c04dc65ccd881b9550263a/index.Rmd#L275-L308 andhttps://github.com/lcolladotor/cv/blob/fb0274c0896ffd0596c04dc65ccd881b9550263a/index.Rmd#L313
Marcel Ramos Pérez (16:46:04) (in thread): > Thanks Leo, we can useBiocPkgToolsas well: > > library(BiocPkgTools) > library(dplyr) > biocDownloadStats(pkgType="software") |> filter(Package == "recount3") |> summarize(tot_dl = sum(Nb_of_downloads)) > # A tibble: 1 × 1 > tot_dl > <int> > 1 4357 >
Stephanie Hicks (16:58:00): > If anyone is interested in working at the intersection (and supporting) of Bioconductor and R-Ladies (https://rladies.org ), feel free to join the#r-ladieschannel!:rladies::wave::gratitude-thank-you:(h/t@Daniela Cassol)
Leonardo Collado Torres (18:36:47) (in thread): > Awesome! Thanks@Marcel Ramos Pérez:)
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2022-07-30
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2022-08-01
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2022-08-03
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2022-08-04
Amarinder Singh Thind (02:28:28): > Anyone working/worked on 850k EPIC array? I have few queries related to cross-reactive probes
Jared Andrews (10:11:49): > Yes. There are a few lists of cross reactive probes published - we usually throw them out.
Jared Andrews (10:12:25): > If we’re worried about that. Which we usually are given a nice chunk of our samples are xenografts.
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rohitsatyam102 (15:57:43): > I have a package development idea and I am not sure whom to contact for guidance? Any pointers? I know R package development but don’t know how to make a package for accessing public database resources. Is there a guidebook specifically for that.
Andrew J. Rech (16:19:37) (in thread): > if there are existing people whose package structure is similar that you admire, you could reaach out to them for advice. most people are happy to respond with some direction.
Amarinder Singh Thind (20:04:41) (in thread): > I got this list of cross reactive probes for EPIC array , to me 135885 unique probes to be removed seems very high. Is it normal practice? However for 450k Array cross reactive probe number is ~30k .https://github.com/sirselim/illumina450k_filtering
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2022-08-06
Federico Marini (18:00:13) (in thread): > https://contributions.bioconductor.org/ - Attachment (contributions.bioconductor.org): Welcome | Bioconductor Packages: Development, Maintenance, and Peer Review > This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook.
Federico Marini (18:00:52) (in thread): > this is pretty much a biocbible on the whole topic of making a package bioc-ready
Federico Marini (18:02:12) (in thread): > as for the topics: it might be specific on what you have in mind- do you have a repo with some code in it?
2022-08-08
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2022-08-09
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2022-08-10
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Aidan Lakshman (12:31:43): > any chance someone could help me with a quick problem i’m having with S3 dispatch? i’m writing a low level class similar todist, and I’m trying to implement a newdiag()function. The class is calledsimand I wrote adiag.sim()function, but for some reason callingdiag(s)(withsan object of classsim) instead callsbase::diag()everytime. > > Am I missing something? I tried addingregisterS3method('diag', 'sim', diag.sim)but it didn’t work either. > > I can add code too if necessary, internally the class just holds a vector that’s essentially the upper triangle of a matrix.
Aidan Lakshman (12:33:21) (in thread): > for reference: > > > is(s) > [1] "sim" > > class(s) > [1] "sim" >
Alan O’C (12:36:14) (in thread): > Probably easiest to link to code
Sean Davis (12:39:29) (in thread): > It would be useful to see how you constructed your class and method (agreeing with@Alan O’C).
Aidan Lakshman (12:39:50) (in thread): > sounds good, one sec I’ll try to format it in a way that’s easy to read
Aidan Lakshman (12:45:08) (in thread): > I’m subsetting to just the relevant parts, there are some other constructors but the.vectorcase is the simplest i think. I’m also removing some of the error checking just to make it a little simpler for this message. > > constructor: > > as.sim.vector <- function(x, NAMES=NULL, DIAG=TRUE){ > # We can just solve quadratic formula if input a vector > # n^2 - n - 2*length(x) = 0 > # a=1, b=-1, c=-2*length(x) > > b <- ifelse(DIAG, -1, 1) > l <- 2*length(x) > deter <- 1 + 4*l > > # Has to be the positive case to be valid > val <- (sqrt(deter) + b) / 2 > > if (is.null(NAMES)){ > NAMES <- as.character(seq_len(val)) > } > > structure(x, > DIAG=DIAG, > nrow=val, > NAMES=NAMES, > class='sim') > } > > example: > > > s <- as.sim(1:10) > > s > 1 2 3 4 > 1 1.00 2.00 3.00 4.00 > 2 5.00 6.00 7.00 > 3 8.00 9.00 > 4 10.00 > > Similarity matrix with 4 members. > > > unclass(s) > > unclass(s) > [1] 1 2 3 4 5 6 7 8 9 10 > attr(,"DIAG") > [1] TRUE > attr(,"nrow") > [1] 4 > attr(,"NAMES") > [1] "1" "2" "3" "4" > > diag function (nrow, ncol, nameswere included to try to be consistent withbase::diag): > > diag.sim <- function(x, nrow, ncol, names=TRUE){ > nr <- attr(x, 'nrow') > svals <- c(0, cumsum(nr:1)) + 1 > v <- as.vector(x) > return(v[svals[1:nr]]) > } > > I can also include how the[.simand[<-.simare written if necessary, but they shouldn’t apply to this case
Aidan Lakshman (12:49:45) (in thread): > Expected output: > > > diag(s) > [1] 1 5 8 10 > > Actual output is equivalent to callingdiag(1:10), so it’s basically just dropping through to callbase::diagon the internal vector
Alan O’C (12:50:44) (in thread): > Did you also definediagas an s3 generic, probably with a default method?
Aidan Lakshman (12:53:44) (in thread): > i didn’t because I thought it was already a generic–I tried to do this: > > registerS3method('diag', 'sim', diag.sim) > > and that did not work. > > I also tried registering it as an S3 generic: > > diag <- function(x, ...) UseMethod('diag') > > diag.sim <- function(x, ...) { ... } > > but this broke the standarddiag(m), wherema matrix. > > I quickly tried to add in a default method: > > diag <- function(x, ...) UseMethod('diag) > > diag.default <- function(x, ...) { diag(x, ...) } > > diag.sim <- function(x, ...) { ... } > > but as you can expect this breaks due to a recursive function call indiag.default -> diag.default
Alan O’C (12:54:16) (in thread): > You’re better off doingdiag.default <- base::diag
Aidan Lakshman (12:54:54) (in thread): > oh! that works!
Aidan Lakshman (12:54:59) (in thread): > just tried that too haha, thank you!
Alan O’C (12:55:01) (in thread): > (ordiag.default <- function(x, ...) base::diag(x, ...)may be better if you’re handling arguments weirdly; certainly there are some situations I have used that over the other example)
Aidan Lakshman (12:55:48) (in thread): > i diddiag.default <- function(x, …) base::diag(x, …)but I think thediag.default <- base::diagis cleaner
Aidan Lakshman (12:55:57) (in thread): > thanks for the help!
Aidan Lakshman (12:59:37) (in thread): > ah sorry, one more question–is there a different syntax for doing the same thing withdiag<-? > > I tried the same way: > > `diag<-` <- function(x, value, ...) UseMethod('`diag<-`') > > `diag<-` <- base::`diag<-` > > `diag<-.sim` <- function(x, value, ...){ ... } > > but I got: > > > diag(s) <- 1:4 > Error in `diag<-`(`**tmp**`, value = 1:4) : > only matrix diagonals can be replaced > > the functions that have to be escaped with...always confuse me
Alan O’C (13:00:55) (in thread): > > `diag<-.default` <- `base::diag<-` >
Aidan Lakshman (13:01:03) (in thread): > oh…duh
Aidan Lakshman (13:01:06) (in thread): > thank you!
Alan O’C (13:01:36) (in thread): > All good, assignment functions are v confusing
Aidan Lakshman (13:04:26) (in thread): > all working now, thanks again for the quick help!
Marcel Ramos Pérez (17:09:51) (in thread): > Note.UniProt.ws functionality has been restored based on UniProt’s API changes. Feel free to test it out and let us know if you have questions via the support site or GitHub for devel version bug reports. See package version2.36.2or2.37.2(in devel).
2022-08-11
António Domingues (02:59:59): > Hi all, a bit of side question but does anyone know of online code editors that are R/BioC-friendly? Something like google colab, but that feel more like Rstudio. It can be either free or paid. I am asking because I am thinking about ways of setting an environment for someone (e.g.) job candidates to easily come in and do some live coding without having them thinking too much about the set-up. I noticed orchestra was used for the BioC workshops but that’s for academic use only (I believe)
Jonathan Carroll (03:23:07) (in thread): > https://rstudio.cloud/ ? - Attachment (rstudio.cloud): RStudio Cloud - Do, share, teach, and learn data science
António Domingues (03:26:04) (in thread): > Actually, yes! I forgot that Rstudio had a cloud offering. Cheers.
Jeroen Gilis (03:56:41): > @eurobioc2022 : For printed posters, only portrait or landscape allowed as well?
Laurent Gatto (04:06:03) (in thread): > I can confirm that portrait A0 will work, but landscape haven’t been mentioned at all.@Simone Bell, could you confirm about the latter?
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2022-08-15
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2022-08-17
Laurent Gatto (10:01:24): > Join us during theBioconductor Teaching Week https://support.bioconductor.org/p/9146055/
2022-08-22
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2022-08-24
Chris Chiu (05:47:46): > Is there a way to annotate clusters for scRNA-seq by combining two gene sets: i) highly expressed, and ii) lowly expressed (not negative)?
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2022-08-26
Fabricio Almeida-Silva (03:12:13): > Hi, everyone. Does anyone have examples of pretty pkgdown documentation websites for Bioc packages? > > All of my Bioc packages have documentation websites that I create and automatically update thanks to the GHA workflow provided by {biocthis}. However, I think the default UI could be better. > > I am looking for inspirational examples and suggestions (e.g., themes, fonts, etc). An example of a documentation website I find pretty is the pkgdown website:https://pkgdown.r-lib.org/
hillel brukental (03:51:37): > hi everyone, need your help in two subjects: > 1. i have genotyping data (5000 snps) of some almond germplasm (150 samples), i would like to identify and visualized the conserved and polymorphic regions of this core. does anyone know about some package for this? > 2. can someone recommended on a package and workflow for the de novo assembly of HIFI reads? also for compering between genomes (pan-genomes analysis). take into account i have no early experience. > thank you!
Leonardo Collado Torres (08:16:12) (in thread): > I haven’t customized any pkgdown website. I guess that you could use Bioconductor’s colors if you wanted. Anyways, I think that you’ll be the first to do this level of customization as pkgdown websites. Let me know how it goes :)
Fabricio Almeida-Silva (08:45:56) (in thread): > That’s exactly what I was thinking: a pkgdown website with Bioc flavors. Ideally, this should be a in a format that the whole community could use, perhaps as part of BiocStyle or biocthis. This could solve some inconsistencies between pkgdown and BiocStyle, such as pkgdown’s inability to handle multiple author affiliations in vignettes. > > Anyway, I will try to play with some customizations. If something good comes out of it, maybe I can submit a PR to {biocthis} with a helper function (e.g.,biocthis::use_bioc_pkgdown()).:wink:
Leonardo Collado Torres (08:51:23) (in thread): > Sounds good :) and feel free to bounce ideas off me. As for BiocStyle, maybe reach out to Mike Smith
Fabricio Almeida-Silva (09:02:43) (in thread): > Great! Thank you!
Artem Sokolov (09:46:35) (in thread): > I’ll have to dig out which theme this was, but here is what I put together for one of my papers a while ago:https://labsyspharm.github.io/ABCmonster/index.html
Artem Sokolov (09:50:07) (in thread): > This was the template:https://github.com/labsyspharm/ABCmonster/blob/cc3633e755d9c332b67d3b5f02cc41e480126de4/inst/_pkgdown.yml#L15-L17
Fabricio Almeida-Silva (09:51:32) (in thread): > Thanks a million, Artem!
Kevin Rue-Albrecht (10:27:11) (in thread): > It’s more than you asked for, you’ll need to trim some of it down, but I did that for a workshop package in 2020https://isee.github.io/iSEEWorkshopEuroBioc2020/ - Attachment (isee.github.io): iSEEWorkshopEuroBioc2020 > This workshop covers basic usage of iSEE for interactive visualization of SummarizedExperiment objects.
Fabricio Almeida-Silva (10:31:41) (in thread): > Amazing,@Kevin Rue-Albrecht! The home page is the most creative thing I’ve seen for a pkgdown website! It feels Christmassy now.
Kevin Rue-Albrecht (10:34:21) (in thread): > Most of the pkgdown magic happens in that file:https://github.com/iSEE/iSEEWorkshopEuroBioc2020/blob/main/pkgdown/extra.css
Fabricio Almeida-Silva (10:37:10) (in thread): > Great! Thanks a lot!
Kevin Rue-Albrecht (10:46:01) (in thread): > Trying it out now it seems like the pkgdown template has updated a bit, and the css needs tweaks as a result. I could swear I started a GitHub gist for that file, but I cannot find it. Updating, testing and I’ll share the link to a new Gist here soon
Fabricio Almeida-Silva (10:54:02) (in thread): > I just realized that one simply needs to add a _pkgdown.yml file to inst/ to change the default UI. Adding that has already enhanced a lot: > > template: > bootstrap: 5 >
Kevin Rue-Albrecht (10:55:01) (in thread): > ah yeah, there are a lot of ‘hidden’ gems all over the pkgdown docs
Kevin Rue-Albrecht (10:55:45) (in thread): > (and by the time you get used to one fancy new thing, they’ll have implemented two new ones:wink:)
Fabricio Almeida-Silva (10:56:56) (in thread): > Fonts are bigger with Bootstrap 5 and the navbar looks better as well. Now I just need to change font colors to match Bioc colors. Using bslib seems to be easier. I will experiment a bit and keep you posted.
Kevin Rue-Albrecht (10:57:33) (in thread): > here’s my updated css file:https://gist.github.com/kevinrue/4e0de8bc0635009e7e6bc3ddfe7ddaa9
Fabricio Almeida-Silva (10:59:22) (in thread): > It is a bit like this quotation from Through the Looking Glass, by Lewis Caroll: “Now, here, you see, it takes all the running you can do to keep in the same place.” It’s very hard to keep up with all the updates.:sweat_smile:
Fabricio Almeida-Silva (11:00:12) (in thread): > Thank you!
Kevin Rue-Albrecht (11:01:29) (in thread): > I’m testing the css on my current submission here:https://github.com/iSEE/iSEEhub/pull/23 Once I merge it, it will become visible here:isee.github.io/iseehub/
Fabricio Almeida-Silva (11:02:39) (in thread): > Great. Bookmarked.
Leonardo Collado Torres (12:06:45) (in thread): > So, if I’m following correctly, usinghttps://community-bioc.slack.com/archives/C35G93GJH/p1661525642930339?thread_ts=1661497933.425919&cid=C35G93GJH +https://gist.github.com/kevinrue/4e0de8bc0635009e7e6bc3ddfe7ddaa9 is all that’s needed? - Attachment: Attachment > I just realized that one simply needs to add a _pkgdown.yml file to inst/ to change the default UI. Adding that has already enhanced a lot: > > template: > bootstrap: 5
Leonardo Collado Torres (12:07:14) (in thread): > once someone like Kevin figures out all thecssmagic hehe
Fabricio Almeida-Silva (12:09:37) (in thread): > I’m trying to add bootstrap variables directly to the _pkgdown.yml file that goes inside inst/, so I don’t need to push a .css file to the gh-pages branch. As far as I understood, the .css file must go inside the pkgdown/ directory, which cannot exist in the master/main branch.
Kevin Rue-Albrecht (12:12:08) (in thread): > well, i was actually about to dig up that long-running discussion again, the core team is not particularly keen to have a lot of “non-standard” files on the master/main branch (e.g., pkgdown and other config files), but i believe that the discussion is relaxing a bit, and IMHO “non-standard” files have a tendency to become fairly standard once they become popular enough
Kevin Rue-Albrecht (12:13:08) (in thread): > See ->https://github.com/lcolladotor/biocthis/issues/21
Fabricio Almeida-Silva (12:16:48) (in thread): > Agreed. The core team could accept a pkgdown/ directory in the future. I saw that you had to create another branch (kra-css) for your ISEEhub repo just to have the .css configs for pkgdown, right?
Kevin Rue-Albrecht (12:20:08) (in thread): > Ah no, don’t worry about thekra-cssbranch, that’s just what i do on github, when I experiment with new code. I work on a branch, and when I’m happy with the new code, I merge it to master/main
Kevin Rue-Albrecht (12:21:27) (in thread): > The code only really takes effect when it arrives on the master/main branch. The GitHub Action workflow uses the main branch to compile the pkgdown website. All other branches are only drafts. Well, except thegh-pagesbranch which contains the HTML pages of the compiled website
Fabricio Almeida-Silva (12:22:05) (in thread): > Got it. So are you planning to merge it with master and leave the pkgdown/ directory on master?
Kevin Rue-Albrecht (12:23:28) (in thread): > It is merged (it took me a bit of extra time because a github check failed for a transient web issue) > The github action workflow checking the package and compiling the website is running here:https://github.com/iSEE/iSEEhub/runs/8040278589?check_suite_focus=true
Kevin Rue-Albrecht (12:24:31) (in thread): > and to answer: yes, this has added thepkgdowndirectory on master/main, so we’ll see whether my reviewer accepts it this time or not
Fabricio Almeida-Silva (12:25:51) (in thread): > Oh yes, I just saw it. Let’s see if the pkgdown directory will be accepted. I don’t remember ifBiocCheck()returns an error or warning for this.
Kevin Rue-Albrecht (12:41:59) (in thread): > there we go, workflow completed, and pkgdown website up:https://isee.github.io/iSEEhub/ - Attachment (isee.github.io): iSEE for the Bioconductor ExperimentHub > This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app.
Leonardo Collado Torres (12:42:32) (in thread): > Nice!
Leonardo Collado Torres (12:42:56) (in thread): > Would you mind opening a PR atbiocthisfor this? Or if I copy your styling files?
Fabricio Almeida-Silva (12:46:40) (in thread): > Very nice! One thing I also tried to handle but couldn’t: do you know if it’s possible to use the Bioc green only in the title and leave h1 blue, as Bioc vignettes? It seems that titles on pkgdown pages also have h1 tags.
Kevin Rue-Albrecht (12:51:23) (in thread): > In theory everything’s possible in css, as long as the class (title, h1) or context (class of parent elements) uniquely identifies the things that needs a different styling.I’m juggling other things right now but I think your description is clear enough that I can look at it later
Kevin Rue-Albrecht (12:52:52) (in thread): > @Leonardo Collado Torresfeel free to take the styling file as it is now (use the gist link above), but be aware that I will likely update it soon based on@Fabricio Almeida-Silva‘s suggestion.I don’t really want to maintain a PR and the gist simultaneously myself until it stabilizes
Leonardo Collado Torres (13:00:10) (in thread): > I’ll wait then:smiley:
Leonardo Collado Torres (13:00:15) (in thread): > no need to do it today
Leonardo Collado Torres (13:00:23) (in thread): > just ping me whenever you think I should take a look
Kevin Rue-Albrecht (16:02:03) (in thread): > @Leonardo Collado TorresI think you can take it from here now:https://github.com/iSEE/iSEEhub/blob/main/pkgdown/extra.css Feel free to edit the header, that was just in case someone took the file from my workshop, for a minimum of traceability.
Connor Higgins (21:00:18): > @Connor Higgins has joined the channel
2022-08-29
Yu Zhang (13:41:59): > @Yu Zhang has joined the channel
Jianhai Zhang (23:06:00): > Hello, I developed my own class “coord”. When I type an object of this class, all slot contents are shown in the R console. How can I hide these contents from the screen? - File (PNG): Screenshot from 2022-08-29 20-05-34.png
Lambda Moses (23:11:42) (in thread): > You can write your own method ofprintfor your S3 class orshowfor your S4 class to determine how the object will be shown in the console.
Steve Lianoglou (23:12:36) (in thread): > You need to create ashowmethod for yourcoordclass, something like > > setMethod("show", "coord", function(object) { > print("Length of x is: ", length(object@coordinate$x)) > }) > > … or something like that. > > You can find some more helphere .
Jianhai Zhang (23:26:58) (in thread): > Got it, thank you.
2022-08-30
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2022-09-01
Jianhai Zhang (06:32:06): > I want to set replace method for usage:names(myObject)[i] <- value. Does anyone know how to correct the following design?@export ``setGeneric("names[<-", function(x, i, value) standardGeneric("names[<-"))``@export ``setReplaceMethod("names[<-", "myClass", function(x, i, value) { # do sth })
Lluís Revilla (06:40:24) (in thread): > I think you need two (replace) methods for that to work:names<-and[<-for the class of your object.
Alan O’C (07:15:52) (in thread): > I think you just need anames<-function for that as long as the names are just a character vector
Alan O’C (07:20:28) (in thread): > A very silly example but demonstrates the point: > > f <- structure(1:10, class="foo", nom = list(names = letters[1:10])) > f > #> [1] 1 2 3 4 5 6 7 8 9 10 > #> attr(,"class") > #> [1] "foo" > #> attr(,"nom") > #> attr(,"nom")$names > #> [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" > names.foo <- function(x) attr(x, "nom")$names > names(f) > #> [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" > `names<-.foo` <- function(x, value) { > attr(x, "nom")$names <- value > x > } > names(f)[1:5] <- LETTERS[1:5] > names(f) > #> [1] "A" "B" "C" "D" "E" "f" "g" "h" "i" "j" >
Kasper D. Hansen (08:33:52) (in thread): > You absolute do not need to set the generic unless roxygen2 does something weird
Jianhai Zhang (18:15:11) (in thread): > I only usednames<-, and it works out. Thank you all guys.
2022-09-02
Kevin Rue-Albrecht (06:19:28) (in thread): > @Leonardo Collado TorresI just remembered to open an issue on {biocthis}, sorry if I wasn’t clear when you could have taken a look yourself
Jiansi Gao (17:42:58): > @Jiansi Gao has joined the channel
Jianhai Zhang (20:08:34): > I am trying to document multiple functions in the same Rd file. I found the solutions (@rdname ) here:https://stackoverflow.com/questions/15932585/multiple-functions-in-one-rd-file . But when I querysum1by?sum1, there is no help file opened. I also tried @describeeIn , and it does not help either. Does anyone have suggestions?
Jianhai Zhang (20:32:13) (in thread): > When I start a new R session, it works.
2022-09-06
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2022-09-08
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2022-09-12
Harshita Ojha bs17b012 (11:48:26): > Hi Everyone, > > I, Harshita Ojha, the undersigned, recently completed my Integrated Dual Degree from the Indian Institute of Technology, Madras, India in July 2022. > > I am currently working as a Software Engineer at an EdTech company(also a Unicorn). > > I am looking forward to expand my knowledge and hence this message is to enquire about a part-time(full time on weekends) opportunity in the field of Software Engineering or Data Science. > > PFA the resume for your reference. > > > > > > Thanks and regards, > Harshita - File (PDF): Harshita_Ojha_Resume_2022-1.pdf
Ana Cristina Guerra de Souza (16:52:10): > @Ana Cristina Guerra de Souza has joined the channel
ALAKANSE OLUWASEUN (17:35:56): > @ALAKANSE OLUWASEUN has joined the channel
2022-09-13
Vince Carey (07:03:12): > Would like to hear from anyone who is using Apache Spark in bioinformatics applications. There is a channel on spark but it is currently invitation only….
Ludwig Geistlinger (16:10:14) (in thread): > We have played a little bit around with it for BioPlexhere throughsparklyrand the unfortunately abandonedgraphframespackage
Vince Carey (16:11:26) (in thread): > thanks!
Alex Schrader (17:15:02): > @Alex Schrader has joined the channel
2022-09-14
Ali Quidwai (10:47:31): > Hey Everyone , > While working with annotation dbi for my current project , I encountered few problems and would like to know to know if there is a equivalent version of annotation dbi in python , if not is there a group which is currently working on such a kind of project , where I can contribute ?
Michael Lawrence (10:57:06) (in thread): > Which problems did you encounter?
Ali Quidwai (13:24:45) (in thread): > I code in python and have recently started coding in R , I was doing semantic segmentation using annotation dbi package .I know i can do that using pytorch
Ali Quidwai (13:25:47) (in thread): > I want to know if there is a platform where a equivalent package in python is availabl e
2022-09-15
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Luke Zappia (02:21:08) (in thread): > I’m not sure whether there is a Python annotation dbi or not but in general access to genomic annotations is lacking in Python. There is however an R torch library which has a lot of the same functionality as PyTorch so maybe that would be another optionhttps://cran.r-project.org/web/packages/torch/index.html . - Attachment (cran.r-project.org): torch: Tensors and Neural Networks with ‘GPU’ Acceleration > Provides functionality to define and train neural networks similar to ‘PyTorch’ by Paszke et al (2019) arXiv:1912.01703 ](https://arxiv.org/abs/1912.01703)) but written entirely in R using the ‘libtorch’ library. Also supports low-level tensor operations and ‘GPU’ acceleration.
Shila Ghazanfar (11:21:45): > hi everyone who’s attending EuroBioc2022 reminder to submit a birds of a feather session via the github:https://github.com/Bioconductor/EuroBioC2022/issues in addition i’d like to flag that we have a#shinychannel related to all things to do with interactive apps in bioconductor, if you’re interested do join:slightly_smiling_face:thanks and best wishes, shila
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Ali Quidwai (12:35:55) (in thread): > Thanks a lot Luke , for sharing this
2022-09-16
Aedin Culhane (04:20:29): > There is a new#industrychannel and new industry working group
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2022-09-18
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2022-09-19
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2022-09-20
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2022-09-21
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2022-09-22
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2022-09-23
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Krithika Bhuvanesh (14:17:50) (in thread): > Does this mean there is already a channel for academia ?
2022-09-26
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Andres Wokaty (16:31:50): > Bioconductor is partnering withOutreachy , an internship program in open source and open science for those “subject to systemic bias and impacted by underrepresentation in the technical industry where they are living”. As part of the selection process for the Dec-Mar 2023 internships, Outreachy applicants will have the month of October to contribute to Bioconductor and from these contributions, we’ll select 2 interns. I wanted to ask community members to consider joining#outreachyto help field Bioconductor-related questions. One of our current projects is to make the creation of a new BSgenome data package easier. If you make these packages, please consider joining. Thanks for your support!
2022-09-27
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2022-09-28
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2022-10-02
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2022-10-03
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2022-10-05
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Henrik Bengtsson (22:45:07): > :warning:Just a friendly reminder that someR CMD checkNOTEs report on possibly serious pitfalls that, if not fixed, might result in silent errors and non-reproducible results. Forgetting to import everything in the NAMESPACE file is one such example, e.g. > > * checking R code for possible problems ... NOTE > ... > findRegions : <anonymous>: no visible global function definition for > 'median' > ... > Consider adding > importFrom("graphics", "abline", "axis", "par") > importFrom("stats", "median", "pchisq", "quantile") > importFrom("utils", "download.file", "read.delim", "write.table") > to your NAMESPACE file. > > Why is this a potential problem? Consider running the following in a fresh R session: > > library(ACME) > data(example.agff) > example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9) > foundregions <- findRegions(example.agffcalc,thresh=0.001) > head(foundregions)[, 6:10] > #> Chromosome Start End Median Mean > #> testsamp1.chr1.1 chr1 18370933 160502834 3.778240e-01 0.4516588005 > #> testsamp1.chr1.2 chr1 160504242 160511031 1.941371e-04 0.0001449863 > #> testsamp1.chr1.3 chr1 160512520 161743150 4.560643e-01 0.4888990295 > #> testsamp1.chr1.4 chr1 161743296 161743722 3.221346e-05 0.0000860163 > #> testsamp1.chr1.5 chr1 161744293 161866348 3.778240e-01 0.4200206198 > #> testsamp1.chr1.6 chr1 161866419 161866419 5.729070e-04 0.0005729070 > > We can corrupt these results silently by doing: > > median <- function(x) 99999 > foundregions_boom <- findRegions(example.agffcalc,thresh=0.001) > head(foundregions_boom)[, 6:10] > #> Chromosome Start End Median Mean > #> testsamp1.chr1.1 chr1 18370933 160502834 99999 0.4516588005 > #> testsamp1.chr1.2 chr1 160504242 160511031 99999 0.0001449863 > #> testsamp1.chr1.3 chr1 160512520 161743150 99999 0.4888990295 > #> testsamp1.chr1.4 chr1 161743296 161743722 99999 0.0000860163 > #> testsamp1.chr1.5 chr1 161744293 161866348 99999 0.4200206198 > #> testsamp1.chr1.6 chr1 161866419 161866419 99999 0.0005729070 > > This is becausemedian()is a non-declared import and will therefore be searched for in the global environment, and if not found there, eventually in thesearch()path. Note that attaching a third-party package that exports its ownmedian()function can also corrupt the results, if it gives different results than the intendedstats::median(). AddingimportFrom("stats", "median")prevents this. > > PS. I only usedACME https://bioconductor.org/checkResults/devel/bioc-LATEST/index.html >. When I runrevdep checks on matrixStats and other packages, I often find NOTEs on missing imports in Bioconductor packages. This is much less common on CRAN, because CRAN won’t allow NOTEs when submitting a new or an updated package (so it’s only very old CRAN packages that have this mistake).
Kasper D. Hansen (23:10:05): > I am pretty surprised that we have packages with such notes in the project
Kasper D. Hansen (23:10:17): > I am not doubting you, I am just surprised
2022-10-06
Hervé Pagès (03:18:57): > They probably didn’t have them when they were accepted in Bioconductor. The thing is we don’t have a “no NOTE” policy after acceptance so anything can happen:disappointed:I agree that missing imports are a bad thing. Note that even with all the imports declared properly and anR CMD checkthat is 100% clean, it’s still very easy for a third-party package to corrupt the results produced by a package:wink:
Charlotte Hutchings (05:00:41): > @Charlotte Hutchings has joined the channel
Kasper D. Hansen (08:40:51): > I think this is something we need to put some thought into.The current state of affairs seems different from where we would want to be.
Henrik Bengtsson (13:12:40) (in thread): > Here are some quick thoughts: > > 1. Report also onNOTESas a package status, adding to the currentOK,WARNING,ERROR, andTIMEOUTonhttps://bioconductor.org/checkResults/devel/bioc-LATEST/index.html and package status badges > > 2. Set a goal in the devel community to strive forOK, i.e. withoutNOTEs. (I might be wrong, but I have the feeling that gettingR CMD check``NOTEs is considered okay and nothing much to worry about among Bioc developers) > > 3. AFAIU,WARNINGSis the level that alerts the project that a package needs attention. The too manyNOTEs that we currently have makes them too noise to consider an “needs-attention” indicator. > > 4. Use the leverage of the Bioconductor Project to work with R Core to makeR CMD checkmore customizable, so that Bioconductor can exclude someNOTEs that doesn’t fit the project. There are probably someNOTEs that you cannot get rid of this way. Ideally, all of them, so that any remainingNOTEis a true positive
Sean Davis (19:25:26): > For folks interested in clinically-related topics (Bioc and otherwise), there is a#clinicalchannel available.
saskia (21:02:35): > The Code of Conduct committee is seeking new members. If you are interested in serving on the committee with other dedicated and friendly faces, please apply. We particularly encourage applications from candidates identifying as belonging to minority groups.https://docs.google.com/forms/d/e/1FAIpQLSeTRs3m3-XNM7iGs0kyHfoaXNiwRVsgebmce10t0ieKfamaPg/viewform?usp=sf_link
saskia (21:02:55) (in thread): > For more information check out this presentation on what we do:https://docs.google.com/presentation/d/1VdcmY1bs0vIYQ2kegxDt0SqN7oaCeU5-gbkU_sTHD60/edit?usp=sharing
Kasper D. Hansen (23:17:58) (in thread): > 4. would be great. Alternatively, we need some way of parsing the notes
Kasper D. Hansen (23:18:22) (in thread): > We also need somee way (I think) of encoding exceptions we grant to specific packages
2022-10-07
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2022-10-08
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Chizi E (22:59:42): > Hola! Sorry if this is the wrong place to post this query. > > I am trying to install R-devel using bash/terminal. But when I run “make info”, I am stuck with the following error message:****“ERROR: ‘texi2any’ v5.1 or later needed but missing on your system.”****I would appreciate any advice on how to resolve this issue please. I have texi2any installed and a version check returns: (GNU texinfo) 6.5.
2022-10-09
Dike Victoria Chiemela (03:45:33): > @Dike Victoria Chiemela has joined the channel
Lluís Revilla (05:05:04) (in thread): > Which OS are you using? If you try to install it for testing Bioconductor packages I would recommend using the docker imageshttps://bioconductor.org/help/docker/
Karsten Rinas (10:41:05): > @Karsten Rinas has joined the channel
Andres Wokaty (12:55:35) (in thread): > Could I ask you to post more information about your OS, what steps you took, and a guide if any that you’re following? If this is for Outreachy, I would recommend asking on the#outreachychannel in the future.
Chizi E (13:24:44) (in thread): > My OS is Linux (Mint). Looking into docker images! Many thanks!!
Vince Carey (17:33:35) (in thread): > Hi@Chizi E… it would be nice to understand your situation. It is typically not necessary > to run “make info” manually. In my config.log from configuring R-devel, I have > > configure:5760: checking for texi2any > configure:5783: found /usr/bin/texi2any > > What does a search for texi2any in your config.log come up with? Was there a warning > that documentation could not be built, at the end of configure?
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Chizi E (20:50:29) (in thread): > Hola@Vince Carey, I searched for “texi2any” in config.log and found following output: > > configure:5764: checking for texi2any > > configure:5802: result: no > > configure:5892: WARNING: you cannot build info or HTML versions of the R manuals
Kasper D. Hansen (20:57:49) (in thread): > Well, is it in your PATH?
Chizi E (21:09:13) (in thread): > Sorry@Kasper D. Hansen, never done any compilation before now. Running “which texi2any” gives me a path: > > /path/to/texi2any > I take it that I can simply modify my config.log and set the path to texi2any, right?
Kasper D. Hansen (21:09:58) (in thread): > Not config.log
Kasper D. Hansen (21:10:32) (in thread): > That’s an output from configure
Chizi E (21:13:40) (in thread): > Hmmm…. could it be the config.site file I need to edit and set the path?
Kasper D. Hansen (21:49:13) (in thread): > You can set the path inconfig.site. I am confused why you need to do this, given that you say you havetexi2anyin yourPATH
Kasper D. Hansen (21:49:21) (in thread): > But it doesn’t hurt to try
Kasper D. Hansen (21:49:56) (in thread): > You can also search inconfig.statusto get the exact test that fails
Chizi E (22:12:35) (in thread): > Hmmm…. Thanks for all the help! I have learnt a lot through this process
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2022-10-10
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Dike Victoria Chiemela (08:23:12): > Hello > Please I am having a hard time setting up the R studio and R devel on my laptop. > Can anyone work me through how to set up it up on a Windows 10 computer?
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Lluís Revilla (11:00:42) (in thread): > I am attempting to provide instructions to install r-devel in windows for the r devel guidehttps://contributor.r-project.org/rdevguide/ . What have you tried and what are you having problems with? - Attachment (contributor.r-project.org): R Development Guide > A guide to R development.
Dike Victoria Chiemela (11:09:37) (in thread): > Thank you so much. > I have been able to download and set it up. > I found help from YouTube and Google.
Dike Victoria Chiemela (11:11:32) (in thread): > I am now trying to clone the Repository and rename it, but I don’t really understand what that entails. > Am I cloning into my github account or my local computer, please can you clarify me on that? > I will be glad.
Lluís Revilla (11:14:42) (in thread): > If you want to install R-devel in your windows you need to have a local copy. R source code uses svn so you will need to have SVNtortoise or some other program that allows you to make a local repository
Lluís Revilla (11:15:03) (in thread): > You will also need to install Rtools42 in order to install r-devel
Dike Victoria Chiemela (11:18:16) (in thread): > Okay, thank you so much.
Dike Victoria Chiemela (12:00:19) (in thread): > Hello > Thank you so much for your help, I successfully downloaded SVNtortoise and Rtools42
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Jianhai Zhang (22:43:44): > Hello, I have errors in running this codelibrary(BiocParallel); bplapply(1:3, BPPARAM=MulticoreParam(workers=2), FUN=function(j) { j })Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment > Does anyone know the reason?
2022-10-11
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Hervé Pagès (01:38:43) (in thread): > @Lluís Revilla@Dike Victoria ChiemelaInstalling R-devel on Windows is as simple as following the “r-devel snapshot build” link on this pagehttps://cran.r-project.org/bin/windows/base/ , downloading “R-Devel build for Windows”, and running the installer. Rtools42 is not needed for that. > But the real question@Dike Victoria Chiemelais why you’d want to install R-devel. Bioconductor does not support R-devel yet. The currentdevel version of Bioconductor (BioC 3.16) requires the latest Rrelease (R 4.2) so maybe you want to install that instead?
Lluís Revilla (02:47:13) (in thread): > I should have asked the purpose. You are right@Hervé Pagès, if you will modify R and test it, it will help installing from source if not use the daily snapshots@Dike Victoria Chiemela.
Martin Morgan (10:30:15) (in thread): > @Jianhai Zhangcan you open an issue athttps://github.com/Bioconductor/BiocParallel and be sure to include the output ofsessionInfo(). I believe that you are using an out-of-date installation;BiocManager::valid()may provide some additional relevant information.
Andres Wokaty (12:25:14) (in thread): > @Hervé Pagèsis correct. Please install as he suggested. Sorry for the confusion!
Dike Victoria Chiemela (12:35:32) (in thread): > @Hervé Pagès@Andres Wokaty@Lluís RevillaI have this 2 versions of R installed now R4.2.1 and R4.3.0, I downloaded them because it was a required app for me to make a contribution to the Bioconductor project. - File (JPEG): 20221011_173241.jpg
Dike Victoria Chiemela (12:37:23) (in thread): > @Andres Wokatythank you ma’am for clarifying me, I already cloned the package template repository to my github repo and renamed it, I look forward to other steps in the contribution stage.
Dike Victoria Chiemela (12:59:07): > Hello, > welcome@Chinweto the channel, if you have any issues downloading R, kindly check my previous comments, I tried to pin them too. > It is quite helpful.
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2022-10-12
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Jianhai Zhang (17:18:22): > Hello, I run code chunk1 and chunk2 in two separate R sessions. Whyidentical(sce1, sce2)is not TRUE? I want to reproduce the results using or not using bplapply/MulticoreParam > > Chunk1 in R session1library(scater) ``set.seed(20) ``example_sce <- mockSCE(ncells=3000, ngenes=7000) ``example_sce <- logNormCounts(example_sce) ``sce1 <- runUMAP(example_sce)Chunk2 in R session2library(BiocParallel); library(scater) ``bpparam <- MulticoreParam(workers=1, RNGseed=20) ``sce2 <- bplapply(1, FUN=function(i) { `` example_sce <- mockSCE(ncells=3000, ngenes=7000) `` example_sce <- logNormCounts(example_sce) `` example_sce <- runUMAP(example_sce) `` example_sce ``}, BPPARAM = bpparam)
Martin Morgan (17:32:55): > identical()is strongf = function() new.env(); identical(f(), f()); maybe you would likeall.equal().
Alan O’C (18:04:54): > There’s been discussion of this before, but it’s a general RNG seed difference with and without bplapply that doesn’t seem right to me: > > library(BiocParallel) > bp <- MulticoreParam(workers=1, RNGseed=42) > rn1 <- bplapply(1, function(i) rnorm(100), BPPARAM=bp)[[1]] > rn2 <- {set.seed(42); rnorm(100)} > all.equal(rn1, rn2) > # [1] "Mean relative difference: 1.433797" >
Alan O’C (18:05:15): > Or rather different RNG behaviour with ostensibly the same seed
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Henrik Bengtsson (20:09:39) (in thread): > The RNG stream from the default R RNG (RNGkind()[1] == "Mersenne-Twister") and in parallel processing (RNGkind()[1] == "L'Ecuyer-CMRG") will never be the same, although they’re both statistically sound. Parallel processing requires an RNG specially designed for parallel processing in order to get statically sound results. The one available among the built-in ones is L’Ecuyer-CMRG. So, to get the same RNG stream from regular R code, one would, at a minimum, have to setRNGkind("L'Ecuyer-CMRG"). But one would also have to generate the RNG substreams (usingparallel::nextRNGStream()and possibly alsoparallel::nextRNGSubStream()) the same way thatBiocParallel bplapply()for different parallel backends. Then you can obtain numerically identical random numbers, e.g. > > library(BiocParallel) > > bp <- SerialParam(RNGseed = 42) > rn1 <- bplapply(1:2, FUN = function(i) rnorm(100), BPPARAM = bp) > > bp <- MulticoreParam(workers = 2L, RNGseed = 42) > rn2 <- bplapply(1:2, FUN = function(i) rnorm(100), BPPARAM = bp) > > bp <- SnowParam(workers = 2L, RNGseed = 42) > rn3 <- bplapply(1:2, FUN = function(i) rnorm(100), BPPARAM = bp) > > identical(rn2, rn1) > #> [1] TRUE > > identical(rn3, rn1) > #> [1] TRUE >
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Kasper D. Hansen (20:13:46): > As Henrik is saying, what is hidden from the code is that the RNG is silently changed behind the scenes because the standard R RNGwon’twork well in paralllel processing.This is an important but unfortunate side effect.
Kasper D. Hansen (20:14:59): > Even thenI don’tthink you would get reproducibility if you change workers
Kasper D. Hansen (20:16:28): > Reproducibility purists will claim this is an issue but I will say that this is exactly as designed.
Kasper D. Hansen (20:17:28): > What you really want to do - but this is hard - is generate enough random samples for whatever precisionyou’rereporting and then make sure that number is reproducible.
Martin Morgan (22:11:45) (in thread): > and also > > > rn3 <- bplapply(1:11, FUN = function(i) rnorm(100), BPPARAM = MulticoreParam(3, RNGseed=42)) > > rn5 <- bplapply(1:11, FUN = function(i) rnorm(100), BPPARAM = MulticoreParam(5, RNGseed=42)) > > identical(rn3, rn5) > [1] TRUE > > independent of worker number, which actually takes quite a bit of work (a lot thanks to@Jiefei Wang) to get close to consistent. > > The BiocParallelrandom number vignette touches on a lot of these issues, e.g., section 2.6 and the relationship betweenbplapply()andlapply().
Henrik Bengtsson (22:52:01) (in thread): > Actually,BiocParallel reply in the other thread . > > To clarify for others who follow this discussion: In parallel processing, we can have two kinds of statistically sound parallel RNG approaches: (1) one parallel RNG stream per worker, and (2) one parallel RNG (sub)stream per element iterated over. Both a perfectly valid, but only Method (2) is invariant to the number of workers. > > FWIW, in the future ecosystem we’ve (e.g. future.apply, furrr, doFuture) supported Method (2) from day one. Since Method (2) comes with significant overhead when you have lots of elements to iterate over (because you need to set up one RNG substream per element), it’s on the list to support also Method (1), cf.https://github.com/HenrikBengtsson/future.apply/issues/20 . The only thing hold me back from adding that is my procrastination to come up with a nice syntax so the developer can specify it.
Kasper D. Hansen (22:55:44) (in thread): > thanks
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2022-10-13
Chinwe (01:52:10) (in thread): > Thank you so much, Victoria.
Alan O’C (03:59:55) (in thread): > So the RNG used in (eg) mclapply is not statistically sound? Because: > > library(parallel) > rn1 <- mclapply(1, function(i) {set.seed(42); rnorm(100)})[[1]] > rn2 <- {set.seed(42); rnorm(100)} > identical(rn1, rn2) > # TRUE >
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Martin Morgan (09:39:33) (in thread): > browseVignettes(package = "parallel")has section 6 on random numbers; also?mcparallelhas a section describing behavior. I think the short answer is that yes, using a vanilla R and the default random number generator the random number streams in the workers are not statistically independent and at least in principle very bad things can happen. > > Note that > > > RNGkind("L'Ecuyer-CMRG") > > set.seed(42); rnorm(1) > [1] -0.9390771 > > unlist(bplapply(1:2, function(i) { set.seed(42); rnorm(1) })) > [1] -0.9390771 -0.9390771 >
Alan O’C (14:17:18) (in thread): > Interesting, thanks. Have only dabbled very briefly in learning about RNG in parallel, and a lot of it goes over my head
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2022-10-14
Ji Hye Choi (04:19:26): > @Ji Hye Choi has joined the channel
saskia (19:55:10): > Please apply to become a new member of the Bioconductor Code of Conduct committee by the 31st of October. Students welcome
Jianhai Zhang (20:37:34): > Thank you all guys for providing explanations for MulticoreParam/set.seed.
2022-10-16
Jianhai Zhang (13:44:52): > I have “names<-” like the following:#' @rdname SVGMethods``#' @export``#' @importFrom methods new``setReplaceMethod("names", "SVG", function(x, value) { ... }Another method “dimension<-”:#' @rdname SVGMethods``#' @param value A value for replacement.``#' @export``setReplaceMethod("dimension", "SVG", function(x, value) {`` x@dimension <- value; x``})In the main help file:#' @name SVGMethods``#' @docType methods``#' @aliases names<- dimension<-However, I got the warning during check for “names<-” not “dimension<-”Undocumented S4 methods: `` generic 'names<-' and siglist 'SVG' `` All user-level objects in a package (including S4 classes and methods) `` should have documentation entries.Does anyone know the reason?
Alan O’C (16:29:27) (in thread): > You need matching@rdnameI think
Alan O’C (16:30:09) (in thread): > Some examples herehttps://roxygen2.r-lib.org/articles/reuse.html - Attachment (roxygen2.r-lib.org): Reusing documentation > Tools for reusing documentation across topics, and between documentation and vignettes.
Jianhai Zhang (16:35:45) (in thread): > I have another method “dimension<-” that does not induce a warning. See my edited message.
Alan O’C (16:36:39) (in thread): > yeah it has @rdname set, names<- has @name set
Alan O’C (16:38:19) (in thread): > ie try for main doc: > > #' @rdname SVGMethods > #' @docType methods > #' @aliases names<- dimension<- >
Jianhai Zhang (16:38:53) (in thread): > Ok.
Jianhai Zhang (16:54:36) (in thread): > I replaced#' @name SVGMethodswith#' @rdname SVGMethodsin the main doc, it gave: > 1: [svg_methods.R:68] Block must have a @name:information_source:Either document an existing object or manually specify with @name > > I added both#' @name SVGMethodsand#' @rdname SVGMethodsin the main doc. The same warning still exists.
Alan O’C (16:54:54) (in thread): > can you link the repo
Jianhai Zhang (20:11:52) (in thread): > I made a minimal example.roxygen2::roxygenize('testpkg'); devtools::build('testpkg', vignettes = F); rcmdcheck::rcmdcheck('testpkg_2.1.3.tar.gz'); - File (Tarball): testpkg.tar
rohitsatyam102 (20:41:19): > I have a list of ggplots (96 plots) and I was trying to automate their plotting such that no more than 4 plots are present in a row and the output is an html file. Is there a way to achieve that? Usingggarrangedoesn’t look to be a good idea and when given list tosubplotit prints plots one after the other, not side by side.
Alan O’C (20:46:01) (in thread): > I get warnings here about[and[<-not names. Seems to be because you can use missing arguments to[maybe? Either way adding[<-,SVG-method [,SVG-methodto@aliasesfixes it for me
Spencer Nystrom (21:04:11) (in thread): > You can usepatchwork::wrap_plotsfor this.https://patchwork.data-imaginist.com/reference/wrap_plots.html You can setncol = 4and pass your list of ggplots and it will render a single object with the plots in the layout you want. - Attachment (patchwork.data-imaginist.com): Wrap plots into a patchwork — wrap_plots > While the use of + is a natural way to add plots together, it can be difficult to string together multiple plots programmatically if the number of plots is not known beforehand. wrap_plots makes it easy to take a list of plots and add them into one composition, along with layout specifications.
rohitsatyam102 (21:07:24) (in thread): > Nice. This is faster and It worked
Jianhai Zhang (22:04:38) (in thread): > I usednames<-,SVG-method, and the warning is gone. Thank you so much.
2022-10-17
Alan O’C (03:50:17) (in thread): > aye no bother glad it worked
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rohitsatyam102 (07:26:55) (in thread): > Also, If you wish to save the patchwork object as html file, you can useR3port::html_plot()becausehtmltools::save_htmlandsaveWidgetdoesn’t work.@Spencer NystromDo you happen to know any other way of saving patchwork plot as HTML file?
Spencer Nystrom (07:55:10) (in thread): > Those would be what I suggested, but I don’t really do that often.
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Sergio Oller (14:33:02): > Hi all, > > I am the maintainer of the AlpsNMR package in Bioconductor. My package added recently the “archive” [1] CRAN package as a Suggests. > > I’m getting an error on netbiolo2 due to “archive” not being available:https://master.bioconductor.org/checkResults/3.16/bioc-LATEST/AlpsNMR/nebbiolo2-checksrc.html I’m surprised because archive is a CRAN package. I wonder if the issue happens because archive has a system dependency on libarchive and that package is not installed on the build machine. > > I have read [2] but I didn’t find a relevant case there. The current archive version has been on CRAN since May and it has packages built for all architectures. > > Does anyone know how should I proceed with this issue? Any piece of advice is very much appreciated. > > Thanks! > > [1][https://cran.r-project.org/web/packages/archive/index.html](https://cran.r-project.org/web/packages/archive/index.html)[2][https://contributions.bioconductor.org/troubleshooting-build-report.html#dep311](https://contributions.bioconductor.org/troubleshooting-build-report.html#dep311) - Attachment (cran.r-project.org): archive: Multi-Format Archive and Compression Support > Bindings to ‘libarchive’ http://www.libarchive.org ](http://www.libarchive.org)) the Multi-format archive and compression library. Offers R connections and direct extraction for many archive formats including ‘tar’, ‘ZIP’, ‘7-zip’, ‘RAR’, ‘CAB’ and compression formats including ‘gzip’, ‘bzip2’, ‘compress’, ‘lzma’ and ‘xz’. - Attachment (contributions.bioconductor.org): Chapter 23 Troubleshooting Build Report | Bioconductor Packages: Development, Maintenance, and Peer Review > 23.1 How and when does the BBS pull? When will my changes propagate? Please remember the daily builder pulls, installs, builds, and checks package only once per day. This process starts around…
Lori Shepherd (14:35:11) (in thread): > @Andres Wokaty
Andres Wokaty (14:36:29) (in thread): > Thanks. I’ll check on nebbiolo2/
Andres Wokaty (14:55:49) (in thread): > So we neededlibarchive-devon nebbiolo2 to install the CRAN packagearchive. My recommendation is to add it as aSystemRequirementto make it more explicit.
Sergio Oller (15:01:08) (in thread): > libarchive-dev is already listed as a system requirement for the archive package in CRAN. Should I add that system requirement to my Bioconductor package as well? I don’t usually do that
Henrik Bengtsson (15:01:40) (in thread): > > … My recommendation is to add it as aSystemRequirementto make it more explicit. > Though, should that really be added by all packages depending onarchive archive https://cran.r-project.org/package=archive . Ifarchive all reverse dependencies would have to drop that themselves. That is, I argue finding all requiredSystemRequirementis something that should be picked up by the build tool.
Andres Wokaty (15:03:15) (in thread): > Unfortunately, the build system currently doesn’t do that.
Andres Wokaty (15:03:41) (in thread): > I still recommend what I suggested, though I understand your points.
Sergio Oller (15:11:45) (in thread): > I agree with@Henrik BengtssonHowever if adding libarchive-dev as a System requirement is what I need to do, I will do that. > > I would be happy to look into your build system (if you have it in a repository somewhere) to contribute improving it so it can pick these system requirements transitively.
Sergio Oller (15:12:52) (in thread): > I’m happy to have a solution. Thank you for your time looking into this issue!
Jianhai Zhang (16:33:36): > I runroxygen2::roxygenize('~/spatialHeatmap_update'), and got those unwanted long outputs on the screen. What is the reason?ℹ Loading spatialHeatmap ``Creating a new generic function for 'svg' in package 'spatialHeatmap' ``<script type="text/javascript"> ``document.addEventListener("DOMContentLoaded", function() { `` document.querySelector("h1").className = "title"; ``}); ``</script> ``<script type="text/javascript"> ``document.addEventListener("DOMContentLoaded", function() { `` var links = document.links; `` for (var i = 0, linksLength = links.length; i < linksLength; i++) `` if (links[i].hostname != window.location.hostname)`` links[i].target = '_blank';``});``</script>``<style type="text/css" scoped>``body {`` margin: 0px auto;`` max-width: 1134px;`` font-family: sans-serif;`` font-size: 10pt;``}``/* Table of contents style */``div#TOC ul {`` padding: 0px 0px 0px 45px;`` list-style: none;`` background-image: none;`` background-repeat: none;…
Hervé Pagès (17:24:38) (in thread): > Questions about package development belong to the bioc-devel mailing list. Thank you!
Nishika Kapuruge (17:36:40): > @Nishika Kapuruge has joined the channel
Jianhai Zhang (21:02:04) (in thread): > Can I ask questions related to package checking in the bioc-builds channel?
Hervé Pagès (21:03:07) (in thread): > yes
2022-10-18
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Sergio Oller (04:33:31) (in thread): > Just for traceability, here is the BBS issue and it has two PR attached to it:https://github.com/Bioconductor/BBS/issues/220
Andres Wokaty (10:16:10) (in thread): > Thanks for this, especially the PR for bioconductor_docker.
Sergio Oller (11:52:38) (in thread): > You’re welcome. Thanks for merging those. > > To finish this thread I’ve submitted another pull request documenting this procedure:https://github.com/Bioconductor/pkgrevdocs/pull/74 Feel free to consider this as well
2022-10-19
Varsha Verma (17:26:17): > @Varsha Verma has joined the channel
2022-10-21
Charlotte Soneson (04:37:35): > Would you like to host the European Bioconductor Conference in 2023, or join the planning committee with the aim of gaining experience in order to perhaps host the conference in the future? Then please fill this form (which has much more information about what the host role entails)before November 6 https://forms.gle/CJuUjTrvjDACp8NSA - Attachment (Google Docs): Application to host the European Bioconductor Conference (EuroBioC) > Please fill the form below before November 6, 2022 if you are interested in hosting the European Bioconductor Conference in 2023, or if you think that you might be interested in hosting it in the future and would like to join the planning committee to gain more experience with the process. Hosting EuroBioC is a great way to increase the exposure of Bioconductor in your local community, increase the visibility of the computational biology research in your area, and influence the program of the conference, all in a supportive environment. The target dates (typically 3 days) for EuroBioC2023 would be in September or early October 2023. The responsibilities of the local organizer include: assembling a local organization committee (including a local contact for the Code of Conduct committee) planning the overall budget for the conference identifying and booking a suitable venue - typically a large conference room (~100-150 persons) and a few smaller rooms for workshops and discussion sessions, plus space for breaks/poster sessions organizing a conference dinner and catering for coffee/lunch breaks participating in approximately biweekly conference calls with the program committee identifying potential local sponsors organizing travel and accommodation for keynote speakers suggesting (regional) keynote speakers organizing internet access, power strips, badges etc for participants As a local organizer, you will join and be supported by the planning/program committee (which includes organizers of previous European Bioconductor conferences), whose responsibilities include: setting up and managing the abstract submission system reviewing submissions, notifying submitters, assembling the program suggesting (global) keynote speakers, deciding on and inviting keynote speakers (considering suggestions from local organizer) setting up registration system planning and managing scholarships identifying and contacting sponsors (in collaboration with the local organizer) setting up and managing the conference website managing financial transactions (this can potentially be done by the European Bioconductor Society, but will be discussed on a case-by-case basis) If you have any questions, feel free to send an email to the European Bioconductor Society at mailto:info@bioconductor.eu|info@bioconductor.eu . Please see https://eurobioc2022.bioconductor.org/ for more details about previous conferences.
Kevin Rue-Albrecht (05:04:21) (in thread): > Thanks for your interest@Haleema SadiaIt’s been pointed to me that I should seed the repo with suggestions. > While they’re not immediately visible as GitHub issues, I have brainstormed ideas in the Discussions tab here ->https://github.com/carpentries-incubator/bioc-project/discussions See the various threads called “Episode: …”
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2022-10-23
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2022-10-24
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2022-10-25
Maria Doyle (09:01:47) (in thread): > The Bioconductor Blog meetup for Hacktoberfest is on tomorrow Wednesday 9am ET, 2pm BST, 10pm JST. Drop by to write:writing_hand:or share your ideas:bulb:
2022-10-26
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2022-10-27
Sergio Oller (15:25:12): > Hi, > > I’m getting this error on the Bioconductor Build Server palomino4 (windows): > > * checking examples ... ERROR > Running examples in 'AlpsNMR-Ex.R' failed > Warning in file(con, "r") : > cannot open file 'AlpsNMR-Ex.Rout': Permission denied > Error in file(con, "r") : cannot open the connection > > Full log:http://bioconductor.org/checkResults/devel/bioc-LATEST/AlpsNMR/palomino4-checksrc.html I can’t reproduce it on my Ubuntu system nor in the Windows continuous integration on GitHub (there it succeeds):https://github.com/sipss/AlpsNMR/actions/runs/3330039892/jobs/5508011570#step:21:99 Has anyone seen this error before? > > Any help or hint is very much appreciated!
Andres Wokaty (15:44:54) (in thread): > I ran it manually on palomino4 and got the following: > > * checking examples ... ERROR > Running examples in 'AlpsNMR-Ex.R' failed > The error most likely occurred in: > > > ### Name: SummarizedExperiment_to_nmr_data_1r > > ### Title: Import SummarizedExperiment as 1D NMR data > > ### Aliases: SummarizedExperiment_to_nmr_data_1r > > > > ### **** Examples > > > > dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR") > > dataset <- nmr_read_samples_dir(dir_to_demo_dataset) > > dataset_1D <- nmr_interpolate_1D(dataset, axis = c(min = -0.5, max = 10, by = 2.3E-4)) > > se <- nmr_data_1r_to_SummarizedExperiment(dataset_1D) > Error in contrib.url(repos, type) : > trying to use CRAN without setting a mirror > Calls: nmr_data_1r_to_SummarizedExperiment ... require_pkgs -> rownames -> <Anonymous> -> contrib.url > Execution halted > * checking for unstated dependencies in 'tests' ... OK > * checking tests ... > Running 'testthat.R' > OK > * checking for unstated dependencies in vignettes ... OK > * checking package vignettes in 'inst/doc' ... OK > * checking running R code from vignettes ... SKIPPED > * checking re-building of vignette outputs ... SKIPPED > * checking PDF version of manual ... >
Sergio Oller (15:56:53) (in thread): > Thanks you so much! > > I now know where the problem is coming from. I was going crazy trying to figure it out. I’ll commit and push… Hopefully I’ll be in time for staying in the 3.16 release!
Sergio Oller (16:11:40) (in thread): > A utility function in my package was trying to useavailable.packages()to figure out the repository where a package should be installed from, to suggest “install.packages” or “BiocManager::install()”. > > That was unnecessary since BiocManager::install() handles both CRAN and Bioconductor packages without issues so the utility function can simply suggest to use BiocManager::install(). Besides, I did not consider the case where a mirror was not selected, giving an error on a corner-case setting, that BBS was hitting. > > Overengineering is bad. > > I’ve simplified the function and pushed an update on github and bioconductor. Crossing fingers:crossed_fingers:Thank you very much for your time.
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2022-10-28
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2022-10-31
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2022-11-01
Maria Doyle (05:58:24): > Bioconductor, supported by the Chan Zuckerberg Initiative’s EOSS program, has joined The Carpentries as a member organization to ensure excellence in instruction and to develop infrastructure to create and maintain high-quality, pedagogically-sound training with support for local languages.:mortar_board:Please apply in the form below if you are interested in becoming one of our 30 certified Carpentries instructors and contributing to the efforts of the Bioconductor teaching community! > > Applicants who teach in their local language are especially welcome:simple_smile:Apply here:https://forms.gle/TY5FdFckNosJB5x38
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2022-11-03
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2022-11-04
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Alexander Bender (18:48:19): > Hi, I have a rather old lock file from renv, trying to recreate the environment. It includes several Bioc packages, for example: > > "BiocGenerics": { > "Package": "BiocGenerics", > "Version": "0.36.0", > "Source": "Bioconductor", > "git_url": "[https://git.bioconductor.org/packages/BiocGenerics](https://git.bioconductor.org/packages/BiocGenerics)", > "git_branch": "RELEASE_3_12", > "git_last_commit": "0d5d169", > "git_last_commit_date": "2020-10-27", > "Hash": "1fe8a6250d04cfb040ebec87447770ba", > "Requirements": [] > } > > …which fails withWarning: failed to retrieve 'https://bioconductor.org/packages/3.12/bioc/src/contrib/BiocGenerics_0.36.0.tar.gz ' [error code 22]. Indeed, 0.36.0 does not exist (anymore?), but 0.36.1 does. Is there something I can do about that, still getting the exact locked version somehow? Should be an automated solution as there are many packages that fail with such an error.
Lori Shepherd (19:08:16): > If 0.31.1 existsfor a release than 0.36.0 would be in a subdirectory Archive…In the past we only kept whatever the updated version was butthenwe started keeping the intermediate versions but in a subdirectory
Lori Shepherd (19:11:20): > I’ll check the redirection links on Monday to check archive versions
Hervé Pagès (19:32:51) (in thread): > FWIW this works for 3.15https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/ but not for anything prior to that. I wonder if it’s not a problem with how past Bioconductor versions are hosted on xsede.
Spencer Nystrom (21:16:34): > This is a general problem with renv and Bioc packages. There’s a GitHub issue on the renv repo about it, but am on mobile so can’t dig it up just yet.
Lori Shepherd (21:20:42) (in thread): > I might have to put an extra redirect in for that folder
2022-11-05
Vince Carey (09:53:42): > @Alexander Benderit is interesting to see what we can do about a fallback that uses git. Can you provide the renv document that is causing problems? Presumably the tarball repositories that we provide wouldn’t get you exactly what is being asked for, but tooling that uses git/gert that would allow you to doinstallations from source on the desired source code should be possible – if not already available.
Alexander Bender (15:54:15) (in thread): > Sure, thanks for looking into it, here it is:https://gist.github.com/ATpoint/15c0bcab90270b9f55c8035e19b05236
2022-11-06
Yihun Zeleke (02:40:27): > @Yihun Zeleke has joined the channel
Vince Carey (08:54:08) (in thread): > https://gist.github.com/vjcitn/2ec74f495df23bce64e2e6521b92569c process_renv_lock()will operate on your lock file … needs refinement and will produce lots of folders so make sure you have space@Marcel Ramos Pérezmaybe something like this could go in BiocPkgTools
Sherine Khalafalla Saber (11:18:44): > @Sherine Khalafalla Saber has joined the channel
Aedin Culhane (18:24:15): > R in Pharma. Free online conference this weekhttps://hopin.com/events/r-pharma-2022/registration - Attachment (hopin.com): R/Pharma 2022 > Get tickets to R/Pharma 2022 virtual conference, taking place Nov 8-10, 2022.
Alexander Bender (20:03:10) (in thread): > I managed to get most of the Bioc tarballs with your solution and (inspired by this) all of the CRAN tarballs, now simply compiling everything from source. Thanks for your help.
2022-11-07
Peter Hickey (00:05:20): > :rotating_light:Win 1 of 50 free virtual registrations to attend BioC Asia 2022!:rotating_light:Register your interest athttps://forms.gle/brT6yhvP2mkLq4r1A Get in quick - winners will be selected at random and notified by next Monday! - Attachment (Google Docs): BioC Asia 2022: Free Virtual Registration Application > We’re offering up to 50 free virtual registrations to attend BioC Asia 2022 (https://biocasia2022.bioconductor.org/ )! Please enter your email address for your opportunity to win free virtual registration. We will select winners at random and notify them via email on Monday Nov 14, 2022.
Peter Hickey (00:48:56): > For those in China who cannot access Google Forms, we also have this registration link:https://wj.qq.com/s2/11107057/dd57/ - Attachment (wj.qq.com): 问卷系统 > 腾讯问卷提供多种问卷模板，帮助用户高效创建各类问卷。包含及调查模板、测试模板、满意度调查模板、疫情信息收集模板等。
Alexander Bender (07:11:35) (in thread): > Small caveat are annotation packages one need to fetch from a different URL and which does not seem to be on GitHubhttps://bioconductor.org/packages/ ", $bioc_version, "/data/annotation/src/contrib/", $pkg, "", $pkg_version, ".tar.gz")
Vince Carey (08:35:50) (in thread): > Right that would be an enhancement to the Gist let’s see if we are going to put something like this in biocpackage tools and then we can get some more code together
Lori Shepherd (10:03:38) (in thread): > 3.15 works only if you do the full path to the Archived version and not if you did say something similar to his example –https://bioconductor.org/packages/3.15/bioc/src/contrib/BiocCheck_1.32.0.tar.gz fails – so it would still not work properly unless the sub directories are specified —
Martin Morgan (10:47:10) (in thread): > SinceBioconductor version 3.6 , any release package version bump is archived. So you can find Bioconductor version 3.12 BiocGenerics version 0.36.0 athttps://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/BiocGenerics/BiocGenerics_0.36.0.tar.gz .@Spencer Nystromrenv should be doing this (looking first in the main repository, and if not found trying the archive); I believe it is following the same scheme as CRAN …
Alexander Bender (13:49:54) (in thread): > Thanks, I will open an issue at renv GitHub to suggest this.
2022-11-08
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2022-11-09
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2022-11-10
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Erica Feick (09:38:00): > We are pleased to announce that the dates for BioC2023 will be August 2-4 in Boston, MA! We are planning lots of exciting things, so stay tuned for information on invited speakers, scholarships, and registration info. We hope to see you there! - File (PNG): Save the Date! (1).png
2022-11-11
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2022-11-16
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2022-11-17
Marcel Ramos Pérez (15:54:12): > set the channel topic: Link to join the slack team - https://slack.bioconductor.org/
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2022-11-18
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2022-11-19
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2022-11-20
Mikaila Chetty (00:31:02): > Hi all. I am looking to learn new and develop current skills in transcriptomics, RNA-seq & also in structural bioinformatics (molecular docking, simulations & molecular modeling). > > Is there any mentor guided project that I can link up with? or maybe an experienced person in this field willing to work together?
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2022-11-21
Maria Doyle (06:00:39): > We have a new channel#social-mediafor Bioconductor social media discussions (Blog, Twitter, Mastodon, LinkedIn, YouTube, Bilibili, WeChat, Weibo etc) that anyone is welcome to join.
2022-11-22
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Michael Lee (00:18:31): > for the conference next week - any possibilities of late registration at this point even for online?
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Peter Hickey (03:20:57) (in thread): > are you asking about BioC Asia? If so, I’m afraid not. But the conference will be recorded and posted to YouTube following the event
Michael Lee (19:10:48) (in thread): > ok yes asking about BioC Asia
Michael Lee (19:10:57) (in thread): > can you please provide the links once available?
Peter Hickey (19:17:14) (in thread): > yep, we’ll post here when and to the mailing list when the recordings are available:slightly_smiling_face:
2022-11-23
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2022-11-24
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2022-12-05
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2022-12-13
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Ludwig Geistlinger (08:51:58): > Opportunities for discussing tools and packages for biomedical image analysis including segmentation, tiling, stitching, machine learning, image viewers, etc now in#image-analysis.
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2022-12-14
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Lori Shepherd (11:55:02): > CAB is seeking nominations for new members. If interested please fill out the following form by January 31:https://forms.gle/2nb2fJE4jgca3nqi7 - Attachment (Google Docs): Community Advisory Board Nomination Form > Information about the Community Advisory Board can be found at https://bioconductor.org/about/community-advisory-board/ . Yearly there are elections for new members to the board. Currently the board consists of 8-20 members. Members are elected to 3 year terms but may step down early at any time. Anyone from the community is welcome to run. We aim to have a diverse board from varying geographical and professional level stages in order to help Bioconductor be more inclusive to every background. The current advisory board will consider all nominees and vote to fill the limited number of vacant board positions. If interested please fill out the following form: asterisk questions are required, non asterisk are optional.
Bárbara Zita Peters Couto (14:08:32): > @Bárbara Zita Peters Couto has joined the channel
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2022-12-19
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saskia (17:29:22): > <!channel>: The CoC committee has updated theCode of Conduct . The new CoC explicitly includes packages and associated commits. We also have 4 new members@Gerry Tonkin-Hill,@Martin Davila,@Shixiang Wangand@Federica Gazzellonias well as a brand new ombudsperson from the Galaxy project. Please do not hesitate toreport any unwelcome behaviour to the CoC committee. > > The CoC committee wishes everyone happy holidays and a very happy new year! - Attachment (Google Docs): Bioconductor Code of Conduct Reporting Form > To report on any potential violation of our Code of Conduct (http://www.bioconductor.org/about/code-of-conduct/ ), please fill out this form to the best of your ability. The results of this form are shared only with the Bioconductor Code of Conduct Committee - Saskia Freytag (mailto:sas.freytag@gmail.com|sas.freytag@gmail.com ), Laurent Gatto (mailto:laurent.gatto@gmail.com|laurent.gatto@gmail.com ), Martín Dávila-Cervantes (mailto:aldntmi@gmail.com|aldntmi@gmail.com ), Federica Gazzelloni (mailto:fede.gazzelloni@gmail.com|fede.gazzelloni@gmail.com ), Gerry Tonkin-Hill (mailto:g.tonkinhill@gmail.com|g.tonkinhill@gmail.com ), Shixiang Wang (mailto:wangshx@shanghaitech.edu.cn|wangshx@shanghaitech.edu.cn ), Michael Love (mailto:michaelisaiahlove@gmail.com|michaelisaiahlove@gmail.com ), Federico Marini (mailto:fede.maro@gmail.com|fede.maro@gmail.com ), Sowmya Parthiban (mailto:sowmyaparthiban@gmail.com|sowmyaparthiban@gmail.com ), Anna Quaglieri (mailto:anna.quaglieri16@gmail.com|anna.quaglieri16@gmail.com ), Lluís Revilla (mailto:lluis.revilla@gmail.com|lluis.revilla@gmail.com ), and Federico Marini (mailto:fede.maro@gmail.com|fede.maro@gmail.com ). > > You may also make a report directly to one member of the Committee by contacting them directly. If any member of the Committee has a conflict of interest with a report, they will be recused and will not have access to the content or process of the report followup. > > Upon submitting your report, you should receive a separate acknowledgement of receipt via email from the Code of Conduct Committee within 24 hours on weekdays, or within 48 hours for an event that takes place on a weekend. Please email mailto:code-of-conduct@bioconductor.org|code-of-conduct@bioconductor.org if you have not received this acknowledgement. The Committee will investigate your report and follow up according to our Code of Conduct with the aim of making a decision and implementing enforcement as soon as is reasonably possible. > > We can’t follow up an anonymous report with you directly, but we will fully investigate it and take whatever action is necessary to prevent a recurrence.
2022-12-20
Camille Santistevan (09:36:24): > @Camille Santistevan has joined the channel
Sean Davis (11:28:14): > The#bioc-conference-everyoneslack channel is now available for discussion of the 2023 Bioconductor Conference to be held August 2-4, 2023 in Boston.
2022-12-21
Tim Triche (08:30:41) (in thread): > Is it accurate to summarize as “don’tbe a jerk to, exclude, or belittle people, in commits or anywhere else”?
2022-12-22
Martin Morgan (10:27:39) (in thread): > Probably no one should be called a ‘jerk’ under the Code of Conduct, so maybe the summary you’re looking for is just “don’t exclude or belittle people, in commits or anywhere else” !
2023-01-01
Federica Gazzelloni (13:55:19): > :christmas-parrot::dealwithit-parrot:HAPPY NEW YEAR!!!:reverse_conga_parrot:
2023-01-02
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2023-01-05
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2023-01-09
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2023-01-10
Shixiang Wang (04:32:18): > Hi, guys. Recently I found it is hard to install Bioconductor packages in linux server with native mirrors. Error reports that it cannot find a file called PACKAGE. After some explorations, I found the packages in Bioc before v3.15 are not available anymore in mirrors as they were removed from Bioc official http/https mirror. As the R version in server is older and not easy to update timely, is there a good way to handle this problem?
Alexander Bender (05:17:31) (in thread): > Can you add details? Maybe this helps, need to modify the Bioc version and package for what you need:https://community-bioc.slack.com/archives/C35G93GJH/p1667836030619569?thread_ts=1667656422.511209&channel=C35G93GJH&message_ts=1667836030.619569 - Attachment: Attachment > Since <https://support.bioconductor.org/p/102555/#102555|Bioconductor version 3.6>, any release package version bump is archived. So you can find Bioconductor version 3.12 BiocGenerics version 0.36.0 at https://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/BiocGenerics/BiocGenerics_0.36.0.tar.gz . @Spencer Nystrom renv should be doing this (looking first in the main repository, and if not found trying the archive); I believe it is following the same scheme as CRAN …
Alexander Bender (05:19:15) (in thread): > Alternatively use Docker/Podman/Singularity (Bioconductor image comes with rstudio-server and all dependencies to compile any Bioc package) or conda/mamba.
Shixiang Wang (05:19:38) (in thread): > > > options(BioC_mirror="[https://mirrors.tuna.tsinghua.edu.cn/bioconductor](https://mirrors.tuna.tsinghua.edu.cn/bioconductor)") > > BiocManager::install("ALL") > 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details > > replacement repositories: > CRAN:[https://mirror.lzu.edu.cn/CRAN/](https://mirror.lzu.edu.cn/CRAN/)Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib/PACKAGES)' > Bioconductor version 3.12 (BiocManager 1.30.19), R 4.0.3 (2020-10-10) > Installing package(s) 'ALL' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/bioc/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/annotation/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/data/experiment/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib): > cannot open URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib/PACKAGES](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.12/workflows/src/contrib/PACKAGES)' >
Shixiang Wang (05:19:48) (in thread): > > > BiocManager::version() > [1] '3.12' >
Shixiang Wang (05:22:06) (in thread): > @Alexander BenderThanks:slightly_smiling_face:. I typically use the R via RStudio-Server. As many people use the same RStudio-server, it is hard to update the basic R.
Tim Treis (05:44:24): > @Tim Treis has joined the channel
Andrzej Oleś (06:23:56): > @Andrzej Oleś has joined the channel
Vince Carey (06:28:12) (in thread): > I can confirm thatnone > Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.3 (2020-10-10) > Installing package(s) 'parody' > Warning: unable to access index for repository[https://ftp.gwdg.de/pub/misc/bioconductor/packages/3.12/bioc/src/contrib](https://ftp.gwdg.de/pub/misc/bioconductor/packages/3.12/bioc/src/contrib): > cannot open URL '[https://ftp.gwdg.de/pub/misc/bioconductor/packages/3.12/bioc/src/contrib/PACKAGES](https://ftp.gwdg.de/pub/misc/bioconductor/packages/3.12/bioc/src/contrib/PACKAGES)' >
Vince Carey (06:29:36) (in thread): > On the other hand, using 3.12 docker image, if I pick the worldwide mirror, it succeeds: > > 1: 0-Bioconductor (World-wide) [https] > 2: Germany (Gottingen) [https] > 3: Japan (Tachikawa) [https] > 4: Japan (Wako) [https] > 5: China (Peking) [https] > 6: China (Nanjing) [https] > 7: China (Hefei Anhui) [https] > 8: Norway (Bergen) [https] > 9: Denmark (Aalborg) [https] > 10: Sweden (Umea) [https] > 11: (other mirrors) > > Selection: 1 > > BiocManager::install("rtracklayer") > 'getOption("repos")' replaces Bioconductor standard repositories, see > '?repositories' for details > > replacement repositories: > CRAN:[https://packagemanager.rstudio.com/cran/__linux__/focal/2021-02-17](https://packagemanager.rstudio.com/cran/__linux__/focal/2021-02-17)Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.3 (2020-10-10) > Installing package(s) 'rtracklayer' > also installing the dependencies ‘formatR’, ‘lambda.r’, ‘futile.options’, ‘matrixStats’, ‘futile.logger’, ‘snow’, ‘MatrixGenerics’, ‘Biobase’, ‘DelayedArray’, ‘GenomeInfoDbData’, ‘bitops’, ‘BiocParallel’, ‘Rhtslib’, ‘SummarizedExperiment’, ‘GenomicRanges’, ‘XML’, ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’, ‘Biostrings’, ‘zlibbioc’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’ > > trying URL '[https://packagemanager.rstudio.com/cran/__linux__/focal/2021-02-17/src/contrib/formatR_1.7.tar.gz](https://packagemanager.rstudio.com/cran/__linux__/focal/2021-02-17/src/contrib/formatR_1.7.tar.gz)' > Content type 'binary/octet-stream' length 150208 bytes (146 KB) >
Vince Carey (06:42:42) (in thread): > I also tried with Bioc 3.10, only mirror option “1” works. I think it is fair to say that none of the mirrors except option 1 has a proper PACKAGES.gz file, and won’t work for source packages at this time. We’ll be working on this today.@Lori Shepherd@Alex Mahmoud
Vince Carey (06:50:34) (in thread): > Curiously, using a mac, the mirror works, suggesting that the setup for source mirroring is wrong but binary mirroring may work > > > chooseBioCmirror() > Secure BioC mirrors > > 1: 0-Bioconductor (World-wide) [https] 2: Germany (Gottingen) [https] 3: Japan (Tachikawa) [https] > 4: Japan (Wako) [https] 5: China (Peking) [https] 6: China (Nanjing) [https] > 7: China (Hefei Anhui) [https] 8: Norway (Bergen) [https] 9: Denmark (Aalborg) [https] > 10: Sweden (Umea) [https] 11: (other mirrors) > > Selection: 5 > > BiocManager::install("parody") > Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) > Installing package(s) 'parody' > trying URL '[https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/parody_1.56.0.tgz](https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/parody_1.56.0.tgz)' > Content type 'application/octet-stream' length 494313 bytes (482 KB) > ================================================== > downloaded 482 KB >
Lori Shepherd (07:30:05) (in thread): > I tried 5 with 3.17 on a linux and it works fine
Vince Carey (08:06:43) (in thread): > To wrap this up for now, the primary intent of the mirrors is to serve current version of software in an efficient way. For legacy software, please use option 1 in chooseBioCmirror() or communicate with your preferred mirror maintainer to take steps to have the frozen prior versions in place.
Martin Morgan (13:42:13) (in thread): > From theHow to mirror a Bioconductor repository page the recommended command is…. > > rsync -e "ssh -i ~/.ssh" -zrtlv --delete \ > bioc-rsync@master.bioconductor.org:3.16/bioc \ > ~/bioconductor_repositories/3.16/bioc > > so > > (a) when the CRAN-style directory structure for a Bioconductor version is physically removed frommaster.bioconductor.org it cannot be rsynced. I believe older versions were physically removed from master to another location.BiocManager::install()still works because ofhttp:// wget --recursiveor similar that retrieves the CRAN-style repository from the https location. > > Maybe the web page describing how to mirror a Bioconductor repository should be updated to reflect the hazard of thersync --delete, and to include an alternative (e.g.,wget --recursive) for old releases (and fix the title of the page…;))
Lori Shepherd (13:46:08) (in thread): > the hard part is don’t they need the delete during the release in order to not have multiple different versions of the package in the same location when a package does a version bump? would that have any bad effects if multiple are there? – again we actually ask people to disable the rsync to the old releases anyways and have been trying to track down offenders – rather harsh to delete everything on them but would help us enforce that better – but yes it would probably help to explain in more detail on the mirror page — and have some consistent time frame after release to move an archived version so we can enforce a time frame
Martin Morgan (13:52:11) (in thread): > yes,--deleteis probably the right thing to do while the release is active; I don’t know how you’d get around that.
Erica Feick (14:36:43): > The organizing committee for the 2023Bioconductor conference (BioC2023) is looking for organizers to help in planning the event. Participation involves attending approximately monthly remote meetings (more frequently as the conference approaches) plus taking on responsibilities in one or more of the areas listed in the google form.https://lnkd.in/egB88PEw . > > Come join our organizing committee - expand your network and meet like-minded people who share your passion! Also, join the#bioc-conference-everyonechannel for all conference-related news!
Alex Mahmoud (17:34:36) (in thread): > One idea could be to serve the mirrors from a Jetstream VM for both archive and newer versions for the purpose of rsync? (i.e. we have a cron job thatrsyncs current versions andrclone copys archived versions to a Jetstream VM from the AWS VM and OSN, and for those who want to mirror we encourage to go from the Jetstream VM. It will both reduce traffic on AWS, and solve the problem of end users having to be aware of what is archived what isn’t. (I still think keeping direct pull from OSN/AWS makes sense by default for package installation etc, but a mirror VM could serve as both a backup for OSN/AWS and a first target for rsync to not expect mirror maintainers to change behavior?)
Nick R. (18:38:40): > @Nick R. has joined the channel
2023-01-12
Davide Corso (09:12:14): > Hello everyone, just a quick question. > I need to change the maintainer of a bioc package. Where do I have to push the changes? upstream/master or upstream/RELEASE_X_Y or both ?
Lori Shepherd (10:00:21): > both so that auto notification would work for both branches – and the current maintainer should also post tobioc-devel@r-project.org mailing list with the name/email of the new maintainer to make sure we set push/git access correctly on the Bioconductor end.
Aedin Culhane (12:34:58): > I created a slack channel#elixirfor discussions on bioconductor and elixir
2023-01-16
yantong (00:31:14): > @yantong has joined the channel
Katariina Pärnänen (05:13:44): > @Katariina Pärnänen has joined the channel
Thomas Sandmann (23:34:30): > @Thomas Sandmann has joined the channel
2023-01-17
Zedias Chikwambi (05:51:23): > @Zedias Chikwambi has joined the channel
2023-01-20
Yikun Jiang (03:00:36): > @Yikun Jiang has joined the channel
Maria Doyle (08:28:38): > Seeking Outreachy interns and project proposals Outreachy Mar - Aug 2023 internship cycle. Outreachy offers internships for those underrepresented and impacted by systemic bias in the technology industry. Interns will work remotely with mentors from our community. > > We are seeking Outreachy interns who would like to work on a Bioconductor project and mentors within the Bioconductor community to propose projects for Outreachy interns to work on during their internship. > * Feb. 6, 2023 at 4pm UTC is the deadline for submitting an initial internship applicationhttps://www.outreachy.org/apply > * Feb. 24, 2023 at 4 pm UTC is the deadline to submit projectshttps://www.outreachy.org/communities/cfp/bioconductor/ > If you want help crafting your project proposal, please contact the Bioconductor coordinators: Jennifer Wokaty and Maria Doyle onslack.bioconductor.org #outreachychannel > > Mentors should read the mentor FAQ:https://www.outreachy.org/mentor/mentor-faq For mentors, full details about the Outreachy program and the internship timeline can be found on the Call for Participation page on the Outreachy website:https://www.outreachy.org/communities/cfp/
Madelyn Carlson (08:32:43) (in thread): > @Maria DoyleAmazing! Thank you for posting. @Fatima and I have prepping bugsigdb as a project for that 2/24 deadline, with help from@Andres Wokaty. I’ll make sure to loop you in as we’re further along:tada:
Maria Doyle (08:47:11) (in thread): > Great to hear!:grinning:
Ankita Murmu (10:29:49): > @Ankita Murmu has joined the channel
Florence Njeri (12:04:17): > @Florence Njeri has joined the channel
Taofeeqat (16:08:12): > @Taofeeqat has joined the channel
2023-01-21
Taofeeqat (07:07:54): > Hi… I’m new here and I need docs on how to get started with Open source.. Can someone help pls?
rohitsatyam102 (08:11:10): > Trying to add images to my github README and the image is inimg/imag.pngbutis not rendering the image. It was working previously!! Can someone help?
rohitsatyam102 (08:18:57) (in thread): > for example see this post. This guy mentions his github repo but if you go and see his welcome page you will see that the image is broken:https://daily.dev/blog/creating-a-killer-github-profile-readme-part-1 - Attachment (daily.dev): Creating a Killer GitHub Profile README Part 1 > README’s. You know, those markdown files that get created when you generate a new project or create a GitHub repository. Perhaps you’re a developer who updates the README file for each project you wor
Spencer Nystrom (08:29:17) (in thread): > Sometimes you have to put a tag in the []. So,
rohitsatyam102 (08:29:54) (in thread): > Tried that already.Not working
rohitsatyam102 (08:31:09) (in thread): - File (PNG): image.png
rohitsatyam102 (08:31:27) (in thread): > I get this when adding[img]tag
Spencer Nystrom (08:35:46) (in thread): > Can you post the markdown? Just a few lines above and below the image tag is probably enough
rohitsatyam102 (08:37:24) (in thread): > >  > <br> > > ## Nextflow tutorial >
Spencer Nystrom (08:38:09) (in thread): > Try putting an extra return before the
Spencer Nystrom (08:38:30) (in thread): > Oh. No it’s the leading /
Spencer Nystrom (08:38:56) (in thread): > Set the path asimg/img.pngnot/img/img.png
rohitsatyam102 (08:39:21) (in thread): > Yeah I tried that too. Didn’t work
Spencer Nystrom (08:39:22) (in thread): > GitHub needs the path relative to the markdown file.
rohitsatyam102 (08:39:36) (in thread): > yeah even the relative path didn’t work
Spencer Nystrom (08:39:41) (in thread): > Is your image actually namedimg.png?
rohitsatyam102 (08:39:51) (in thread): > yes
rohitsatyam102 (08:40:18) (in thread): > tried changing name. Still won’t work
rohitsatyam102 (08:41:49) (in thread): > Tried jpg format too
Alexander Bender (09:24:04) (in thread): > It’s the
rohitsatyam102 (09:24:49) (in thread): > Removing it doesn’t solve the issue either.
Alexander Bender (09:32:02) (in thread): > Is it this here?https://raw.githubusercontent.com/Rohit-Satyam/CancerPipe/main/README.md
rohitsatyam102 (09:32:19) (in thread): > Yes
Alexander Bender (09:32:37) (in thread): > Linked file name iscancerpipe2.pngbut image present in our base is calledcancerpipe.pngwithout “2”:slightly_smiling_face:
rohitsatyam102 (09:32:59) (in thread): > I was uploading the cancerpipe2.png
rohitsatyam102 (09:33:01) (in thread): > as we speak
rohitsatyam102 (09:33:58) (in thread): > Lol Idk what changed but it worked now!!
Alexander Bender (09:34:11) (in thread): > The file was simply not uploaded yet it seems.
rohitsatyam102 (09:35:00) (in thread): > No even when I was clicking on images they weren’t opening
rohitsatyam102 (09:35:34) (in thread): > Even This started showing up:https://github.com/braydoncoyer
Idowu Festus (10:28:23): > @Idowu Festus has joined the channel
Hien (15:58:48): > @Hien has joined the channel
Jared Andrews (16:07:01): > St. Jude is hosting a hackathon. If anyone here is interested, has trainees that might be interested, or knows anyone that might be interested, I’d appreciate the share. > > I’m one of the organizers, so feel free to point people my way with any questions. We’ll be offering a limited number of travels awards to bring some participants to St. Jude for the event, but virtual participation is also welcome.https://twitter.com/JMA_Data/status/1616903620884037632?t=9wNNIfN7a1GzHDBEnbJ-3Q&s=19 - Attachment (twitter): Attachment > Enjoy hackathons? Take a look at the @StJudeResearch https://www.stjude.org/research/why-st-jude/biohackathon.html > > Info :thread::
2023-01-22
Aarathi Sugathan (22:11:59): > @Aarathi Sugathan has joined the channel
2023-01-23
Mark Jens (07:54:38): > @Mark Jens has joined the channel
Gavin Rhys Lloyd (08:25:57): > Hi all, my GitHub actions for devel branch fail because a bioconductor packageroplsis missing. The build report forroplsis passing all checks, but has a red circles for all hostnames. When I hover over the red circle I get a message:NO, package depends on "MultiDataSet" which is not available"Will the maintainer have been notified of this if the build checks are passing? Should I contact them directly? Thanks
Lori Shepherd (08:29:21): > They will have been notified by auto notification as well as individual email but it can’t hurt to reach out yourself to add a little indication that their failure is affecting others. It might get them to act quicker:slightly_smiling_face:
Gavin Rhys Lloyd (08:37:19): > it seems thatMultiDataSetis also a Bioconductor package, and has build warnings, so I guess when those warnings are addressed theroplspackage will be included again (assuming it passes the checks)
Lori Shepherd (08:39:07): > MultiDataSet is in Warning in Release but ERRORing in devel – which is why it is not available in devel; packages with warnings are still included
Gavin Rhys Lloyd (08:53:21): > ok thanks, good to know
2023-01-24
Jennifer Gerbracht (08:30:21): > @Jennifer Gerbracht has joined the channel
Hervé Pagès (17:54:16): > @Gavin Rhys Lloyd@Lori ShepherdSince the package is only failing in devel, I’m actually not sure that the maintainers ofMultiDataSet
Lori Shepherd (18:17:24): > I thought we had auto notifications in devel once a week. Notifications only for release right now? > > The package triage/clinic working group should be notifing them at some point too
Hervé Pagès (22:24:50): > I don’t think auto notifications are enabled in devel yet. We usually turn them on when we enter “release mode” i.e. between 6-8 weeks before a release.
2023-01-25
Lori Shepherd (07:54:32): > I know we don’t necessarily want to confuse people but would it be helpful to have them once a week so developers know if it’s failing in devel to have more time to work on it?
Andres Wokaty (12:18:32) (in thread): > I see 2 thumbs up–should I turn this on?
2023-01-27
Krithika Bhuvanesh (14:01:54): > Does anyone know which are the best #galaxy servers for NGS analysis ? Looking to see if we can incorporate Galaxy NGS workflows in teaching. Thank you
Vince Carey (14:31:52): > @Alex Mahmoud^^
Alex Mahmoud (14:35:40): > By servers, do you meanusegalaxy.eu vsusegalaxy.org etc ? They should have pretty comparable tools,usegalaxy.eu is generally a little better, butusegalaxy.org has better support for workshops iirc. Did you have a particular workflow/tutorial in mind? We can also host a Galaxy instance via Bioconductor and try to make it more seamless to go between RStudio/Jupyter with Bioconductor tools and Galaxy tools, and there would be no wait time if we host it ourselves
David Puerta Martos (15:25:02): > @David Puerta Martos has joined the channel
Krithika Bhuvanesh (15:35:36) (in thread): > Thank you@Alex Mahmoud! This is very helpful. I wenthttps://galaxyproject.org/use/ and saw a big list of public servers and got completely lost. I see thatusegalaxy.org has 250GB quota. Are you saying that there is a wait time to use the main galaxy servers ? Do you already have this “Galaxy instance via Bioconductor” offering ? That would be interesting too. We want to teach our students RNA-seq quantification, DNA-seq and WES variant calling pipelines mainly. Bonus if there are image segmentation pipelines (that handle NIFTI images). - Attachment (galaxyproject.org): Galaxy Platform Directory: Servers, Clouds, and Deployable Resources - Galaxy Community Hub > All about Galaxy and its community.
Krithika Bhuvanesh (15:36:51) (in thread): > Also I want to add, I have used Galaxy and Globus Genomics about 10 years ago when they were babies. Now they have all grown up , lot of information out there, trying to weed through it.
Alex Mahmoud (15:46:54) (in thread): > When using the public servers, jobs get queued in a public queue. They generally run fast, but there are times of high load, so it’s not ideal for a workshop on its own.usegalaxy.org does have a free “Training as infrastructure service” where they can provide extra dedicated compute and a special queue for trainings, but it requires coordinating with the Galaxy team. I joined the Bioconductor Team from the Galaxy team a year ago, so happy to make the connection if that seems to be the best way to go, depending on timing. > In terms of a Bioconductor hosted Galaxy, we currently havehttps://workshop.bioconductor.org/ which we are talking about using at the Biocondcutor conference, and will also remain as a year-round resource. It is still in its infancy and is meant to include RStudio/Jupyter instances for Bioc workshops, but could be expanded. There is the possibility, fairly easily, to spin up an adjacent server at a new URL specific to the workshop/type of analysis and populate the tools with whatever might be relevant for that specific usecase, and we can potentially combine that with RStudio and/or other Biocodnuctor workshops in the same realm as well. > For these deployments I use containerized tools, and >90% of Galaxy tools are containerized but some have errors hence why some time might be needed to tweak details, but most of it should work with some configuration and not much tweaking.
Alex Mahmoud (15:49:22) (in thread): > In terms of finding training material, you can browse throughhttps://training.galaxyproject.org/ . I foundhttps://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html for an NGS analysis, but my understanding here is very limited so I am not sure what type of tutorial is best suited for what audience - Attachment (Galaxy Training Network): Galaxy Training > Collection of tutorials developed and maintained by the w… - Attachment (Galaxy Training Network): Galaxy Training: NGS data logistics > Galaxy is a scientific workflow, data integration, and da…
Krithika Bhuvanesh (17:05:15) (in thread): > Thank you@Alex MahmoudThis is excellent information ! Let me talk to the program director and see how he wants to proceed. Is there a contact that we can reach out to about the “Training as infrastructure service” . That looks very interesting. This would for a course in the Fall semester. I am on the group for the “Bioconductor hosted Galaxy for Bioc2023” meetings, so I look forward to learning more about that
Alex Mahmoud (17:07:59) (in thread): > https://training.galaxyproject.org/archive/2022-08-01/topics/instructors/tutorials/setup-tiaas-for-training/tutorial.html this would probably be a good place to start - Attachment (Galaxy Training Network): Galaxy Training: Training Infrastructure as a Service > Galaxy is a great solution to train the bioinformatics co…
Krithika Bhuvanesh (17:35:47): > Thoughts on Nextflow vs Snakemake for setting up pipelines in bioinformatics ? I would like to try one of these, but wanted to get more feedback first. thanks
2023-01-28
Moritz E. Beber (04:00:58) (in thread): > Do you have a specific pipeline in mind? Maybe start from one that is already implemented, for example,https://nf-co.re/ has a wide range of existing pipelines. - Attachment (nf-co.re): nf-core > A collection of high quality Nextflow pipelines
Vince Carey (06:59:00) (in thread): > Also see dockstorehttps://dockstore.org/ - Attachment (dockstore.org): Dockstore > Dockstore, developed by the Cancer Genome Collaboratory, is an open platform used > by the GA4GH for sharing Docker-based tools described with the Common Workflow Language (CWL), the Workflow > Description Language (WDL), or Nextflow (NFL)
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2023-01-29
Krithika Bhuvanesh (13:00:30) (in thread): > Thank you ! I will look up these links shared.@Moritz E. BeberI’m looking to run some basic pipelines for NGS analysis - RNA-seq quantification from fastq to gene counts; and DNA-seq variant calling.
2023-01-30
Hans-Rudolf Hotz (02:20:51) (in thread): > to get in contact with the Freiburg (aka European) Galaxy team wrt TIaaS, just click on “Request Training Infrastructure” here:https://usegalaxy-eu.github.io/tiaas.html or get directly in contact with Björn:https://usegalaxy-eu.github.io/freiburg/people - Attachment (usegalaxy-eu.github.io): Training Infrastructure as a Service > The European Galaxy Instance - Attachment (usegalaxy-eu.github.io): Galaxy Europe > The European Galaxy Instance
Aedin Culhane (05:02:33): > Federated analysis for polygenic risk score calculations > Description > Polygenic risk scores (PRS) provide an estimate of an individual’s disposition to a trait or complex disease which are calculated as the sum of the risk alleles weighted by the effect size estimate of the genome-wide association study data on the phenotype. PRS scores help in understanding the shared aetiology of certain traits and also in risk prediction and prevention of certain diseases. > > As a part of the CINECA project we have been working on the development of a demonstrator of federated genetic analyses utilising a computational pipeline for PRS analysis. We have implemented this workflow using Nextflow, a modular and reproducible workflow manager that can be deployed and autoscaled to many different working environments including Slurm-based clusters and Kubernetes deployed using AWS amongst other computing environments. In this webinar, we will provide an overview of this PRS pipeline utilising the CINECA UK1 synthetic dataset, derived from the 1000 genomes project, as a demonstrator. As part of the work package we will further extend the demonstrator to other datasets and GWAS workflows, and integrate it to be run in a federated setting utilising the GA4GH guidelines on using Beacons for data discovery along with AAI passports for data access authorisation and deployments. > > Speakers: > Will Rayner, head of the Data and Analytics group at the Institute of Translational Genomics in the Computational Health Department at Helmholtz Munich. > Anshika Chowdhary, Data informatician at the Institute of translational genomics in Helmholtz Zentrum Munich.https://embl-org.zoom.us/webinar/register/WN_1q1dogLvSMOdh6nrqI-vEQ
Frederick Tan (08:19:59) (in thread): > > Anyone providing training on using Galaxy is eligible to request the use of this service. > Just to clarify, anyone means anyone (i.e. not restricted to EU?)
Frederick Tan (08:22:35) (in thread): > nf-co.re/rnaseq has been pretty helpful to us as a generic workflow (note that v2.0 is the last to use featureCounts) with pretty good community support viahttps://nfcore.slack.com/archives/CE8SSJV3N
Hans-Rudolf Hotz (08:24:40) (in thread): > yes, it is open to the world-wide Galaxy communityhttps://usegalaxy.eu/tiaas/stats/
Frederick Tan (08:25:39) (in thread): > :clap:
Krithika Bhuvanesh (08:37:37) (in thread): > Thank you ! This is helpful. I will try it out
Krithika Bhuvanesh (08:42:14) (in thread): > This is awesome information. Thank you !
mahamtariq58 (09:34:04): > @mahamtariq58 has joined the channel
Juan Monroy-Nieto (13:36:15) (in thread): > Nextflow community has a very active community and user needs are considered and resolved actively during development. > > Nextflow had a revamp of concepts with the release of the ‘DSL2’ syntax that has simplified a lot of the things that used to make it daunting. migration into DSL2 is robust enough now to generate production workflows. > > Concepts are easier and more flexible than snake make since you work in the natural direction of thought inputs process -> outputs as opposed to snakemake’s outputs first paradigm. By all this I mean you get to program workflows faster because you develop them in the same way you write other code. > > Haven’t used snakemake outside of NextStrain so I cannot trully make a comparison. Please also consider that I am not a regular python user so the syntax is not something that I am sufficiently familiar with to develop. This should also be one of your considerations. Nextflow is Groovy based, which is itself an extension of Java. The C-like syntax is intuitive for me so I like that too (Hot take: Strongly typed languages are better).
Moritz E. Beber (14:21:33) (in thread): > I’m a long time Python user so it was definitely a challenge for me to pick up the nextflow DSL, as well as Groovy where needed. I stayed for the fantastic community, though! The only thing that’s still horrible is error reporting. It’s generally hard to pinpoint the source of an error. I’ve started collecting common pitfalls herehttps://midnighter.github.io/nextflow-gotchas/ maybe it will be of help. - Attachment (midnighter.github.io): Nextflow Gotchas > A collection of unexpected challenges and learnings with nextflow and nf-core.
Krithika Bhuvanesh (16:04:43) (in thread): > Thank you ! My python is super basic, since I work with R all the time. Let me see..
2023-01-31
Ahmad Al Ajami (08:14:37): > @Ahmad Al Ajami has joined the channel
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2023-02-01
Laurent Gatto (01:56:20): > The EuroBioc 2023 conference will be in Ghent, Belgium on the 20, 21, 22 September 2023. More details, including keynote speakers and calendar athttps://eurobioc2023.bioconductor.org/ . > > Oh, and abstract submissions are already open!
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2023-02-02
Yogesh Lakhotia (01:56:04): > @Yogesh Lakhotia has joined the channel
Alex Pan (11:03:39): > Hey all! I apologize if this question should be posted in another channel, but do y’all have any recommendations for software that simulates bulk RNA-seq coverage? I know that packages likepolyester andrsem exist, but I want to simulate non-uniform fragmentation events (ie certain locations on the transcriptome are more likely to fragment than others). Thank you in advance!
Wancen Mu (21:08:11) (in thread): > Hi Alex, I have simulated some non-uniform fragmentation(the original row in figure) using script herehttps://github.com/Wancen/bootRangespaper/blob/master/script/simulation.R . Not sure if this is what’s you ask for. Hoping it would be helpful! - File (PNG): image.png
2023-02-03
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Alex Pan (11:08:45) (in thread): > Thank you! I’ll definitely take a look at this. To be more specific, I want to simulate RNA-seq reads that come from a library where an enzyme preferentially fragments cDNA at particular motifs and loci. I would like the simulation to produce more reads that originate near those loci
Wancen Mu (11:57:27) (in thread): > I see. I am randomly selecting the start sites here. But maybe you can give those loci by change this line code.https://github.com/Wancen/bootRangespaper/blob/2f28c8a6cf19ae6e00e81a1344cb428cffbabd41/script/boot_and_match_script.R#L15
2023-02-05
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2023-02-06
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Maria Doyle (10:28:12): > :mega:Bioconductor has joined Mastodon. Follow us athttps://genomic.social/@bioconductor We’ll post on both Twitter and Mastodon to communicate with our global community. - Attachment (genomic.social): Bioconductor (@bioconductor @genomic.social ) > 2 Posts, 0 Following, 5 Followers · The mission of the Bioconductor project is to develop, support, and disseminate free open source software that facilitates rigorous and reproducible analysis of data from current and emerging biological assays. We are dedicated to building a diverse, collaborative, and welcoming community of developers and data scientists.
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2023-02-07
Samuel Gamboa (11:55:24) (in thread): > I just registered as a volunteer organizer (hope is not too late). Just wanted to mention that I may have accidentally changed the titles of the questions. I corrected them to what I remembered, but maybe someone else would like to take a look.
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Maria Doyle (15:38:24): > :mega:Abstract submission is now open for the BioC2023 conference in Boston August 2-4bioc2023.bioconductor.org Submit an abstractby March 19 https://openreview.net/group?id=bioconductor.org/BioC/2023/Conference
2023-02-08
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2023-02-09
Umar Ahmad (03:12:01) (in thread): > Impressive!
Riccardo L. Rossi (10:26:25): > Hello everyone, I’m writing to those of you dealing (or willing to deal) with ANY kind of integration between gene expression data AND quantitative phenotypes … > > In this recently open Topic in frontiers in Bioinformatics I’m interested in gathering experiences and work on methods/ideas/ways to use NUMBERS of quantitative (=measurable) phenotypes as BAITS to select or rank genes & features from gene expression datasets. > If you’re working on such things, please give the Topic a look. Thanks!Multi-Domain Quantitative Phenotypes to Extract Meaning and Context From Gene Expression Data > One recurrent question today is how to improve gene expression analyses and provide a wider framework of biological interpretation using measurable phenotypic data from different domains or experimental setups. Multiomics methods are successfully leveraging numerous approaches in genomics research. This is particularly evident in the context of NGS readouts, especially single-cell where CITE-seq or spatial protocols are relevant examples. It would be useful to investigate how quantitative data from very diverse domains such as clinical chemistry, topological imaging, genetic traits, even behavioral data - anything that is measurable, associated to and extracted from the samples under analysis - can be integrated with gene expression data and how such methods improve understanding of the latter. Our particular interest focus is two complementary perspectives. The first is the
2023-02-10
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2023-02-13
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Michael Lynch (09:38:33): > FYI for anyone using Seurat HTODemux after converting Seurat object to SingleCellExperiment object then back again, or otherwise with a metadata called ‘ident’:https://github.com/satijalab/seurat/issues/6945 - Attachment: #6945 HTODemux/as.SingleCellExperiment ‘ident’ conflict > HTODemux gives different results after being converted to SingleCellExperiment (as.SingleCellExperiment) then back to Seurat (as.Seurat). This appears to be due to the ‘ident’ metadata column added during as.SingleCellExperiment. I believe the ident metadata column is being used in AverageExpression within HTODemux instead of the object idents. Removing ‘ident’ column manually fixes the issue but no warnings are given to alert the user that AverageExpression has not been correctly calculated. > > Data is imported and preprocessed as per https://satijalab.org/seurat/articles/hashing_vignette.html > > > #convert to sce then back to seurat > sce<-as.SingleCellExperiment(pbmc.hashtag) > pbmc.converted<-as.Seurat(sce) > > #htodemux on original seurat object > pbmc.hashtag <- HTODemux(pbmc.hashtag, assay = "HTO", positive.quantile = 0.99) > table(pbmc.hashtag$hash.ID) > > #htodemux on converted seurat object > pbmc.converted<-HTODemux(pbmc.converted) > table(pbmc.converted$hash.ID) > > #comparison > table(pbmc.converted$hash.ID,pbmc.hashtag$hash.ID) > > sum(pbmc.converted$hash.ID==pbmc.hashtag$hash.ID)/length(pbmc.converted$hash.ID) > > > > gives:> Doublet HTO-H HTO-D HTO-E HTO-G HTO-F HTO-B HTO-C HTO-A Negative > > > Doublet 1789 0 0 0 0 0 0 0 0 0> #convert to sce then back to seurat > sce<-as.SingleCellExperiment(pbmc.hashtag) > pbmc.converted<-as.Seurat(sce) > > #htodemux on original seurat object > pbmc.hashtag <- HTODemux(pbmc.hashtag, assay = "HTO", positive.quantile = 0.99) > table(pbmc.hashtag$hash.ID) > > #htodemux on converted seurat object with removed idents > pbmc.converted$ident<-NULL > pbmc.converted<-HTODemux(pbmc.converted) > table(pbmc.converted$hash.ID) > > #comparison > table(pbmc.converted$hash.ID,pbmc.hashtag$hash.ID) > > sum(pbmc.converted$hash.ID==pbmc.hashtag$hash.ID)/length(pbmc.converted$hash.ID) > > > > Cutoff for HTO-A : 52 reads> Doublet HTO-H HTO-D HTO-E HTO-G HTO-F HTO-B HTO-C HTO-A Negative > > > Doublet 2598 0 0 0 0 0 0 0 0 0
2023-02-14
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2023-02-15
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2023-02-16
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2023-02-17
rohitsatyam102 (01:22:35): > hi everyone. I have multiple VCFs from different Variant callers for the same sample. Is there a package/tool to quantify what proportion of variant callers support that variation? I tried using bcftools isec but it gives me common variants rather than fraction against each variant.
Spencer Nystrom (09:04:47) (in thread): > slivarmight be useful to you:https://github.com/brentp/slivar
Spencer Nystrom (09:05:45) (in thread): > Vcf is kind of a nutty format, so it can be tricky to compare directly between two files. So you may want to export them to a common format (like tsv from slivar) to be able to compare against your metric of interest if that makes sense.
Spencer Nystrom (09:06:02) (in thread): > I should say, between two files from different tools.
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2023-02-18
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KritikaVerma (05:56:32): > Hello. I am Kritika Verma. > I just started learning about Bioconductor and would like to contribute in the open source community. I was also interested in a project which used probability and statistics for gene expression. Can you recommend some packages as well as documentation for that?
Laurent Gatto (08:57:05) (in thread): > Hi, welcome. A good place to start to find relevant packages is the software page:https://bioconductor.org/packages/release/BiocViews.html#___Software
Laurent Gatto (08:58:03) (in thread): > you can search the table and filter packages that match broad or specific domains/tags (called biocViews) using the left panel.
KritikaVerma (09:35:24) (in thread): > I’ll definitely check them out. Thank you
Vince Carey (12:06:34): > Research Software Alliance is looking for steering committee members, deadline for nominations 10 March.https://www.researchsoft.org/people/ , scroll down for the form - Attachment (researchsoft.org): People > CHAIR: Daniel S. Katz, Chief Scientist, National Center for Supercomputing Applications (NCSA), University of Illinois, USA > Juan Bicarregui, Head of the Data Division, Scientific Computing Department, Science and Technology Facilities Council, UK > Neil Chue Hong, Director, Software Sustainability Institute, University of Edinburgh, UK > Mark Leggott, Director of International Relations, Digital Research Alliance of Canada > Eva Mendez, Associate Professor, Universidad Carlos III de Madrid, Spain > Chris Mentzel, Executive Director, Data Sciences, Stanford Data Science Initiative, Stanford University, USA
2023-02-20
Maria Doyle (06:29:28): > :mega:Do you want to find & connect with Bioconductor users and developers who share similar interests to you? > > If so, you could suggest an idea and host a community event:busts_in_silhouette:, see the form below for information:point_right:https://forms.gle/VaqWrzqK24GLbkh28 - Attachment (Google Docs): Call for Community-Led Events > Do you want to find and connect with Bioconductor users and developers who share similar interests to you? > The Bioconductor Community Advisory Board are calling on new and experienced Bioconductor users and developers to suggest ideas and host (or co-host) community events with our support. > > We would like to enable Bioconductor community-led events that are engaging and open to all. Have you creative ideas you think will engage Bioconductor users or developers? Would you like to host (or co-host) a Bioconductor webinar series, vignette presentation by new package developers, journal club, Discord, Twitch, TikToks, Reddit Ask Me Anything sessions, viewing parties for Bioconductor workshops or social Bioconductor discussions? If so, we would love you to get involved! > > Why get involved? > As a host you’ll be empowered to create amazing opportunities for members to connect. You’ll also raise your profile and obtain valuable leadership experience to add to your CV. > > How do you apply? > Complete this form if you are interested to contribute events for the Bioconductor community! > > Events must abide by the Bioconductor Code of Conduct
2023-02-21
Alex Mahmoud (13:10:28): > Hey all! For anyone who might be interested, there is a new channel#cloud-working-groupand a first meeting today at 3 PM ET, to discuss the formation of a new working group spanning the topics of Using Bioconductor in the Cloud, Containerization, and Github Actions
Fatima Zohra (15:30:28): > @Fatima Zohra has joined the channel
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2023-02-22
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Jennifer Foltz (10:49:38) (in thread): > thank you for sharing!
2023-02-23
Filip Stachura (02:38:19): > Hi all! I want to share that ourshiny.gosling package is right now publicly available :slightly_smiling_face:Hopefully some of you will find it useful! (all feedback welcomed of course) - Attachment (appsilon.com): Shiny.gosling Examples and How to Run Them: Genomics Visualizations in R Shiny - R programming > Shiny.gosling makes genomics visualizations easier to access the grammar of Gosling.js in R Shiny. See examples and how to set them up.
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Martin Morgan (05:33:14): > CuratedAtlasQueryR allow the programmatic exploration and retrieval of harmonized, curated and re-annotated CELLxGENE single-cell human cell atlas.Retweat the announcement! - Attachment (stemangiola.github.io): Queries the Human Cell Atlas > Provides access to a copy of the Human Cell Atlas, but with > harmonised metadata. This allows for uniform querying across numerous > datasets within the Atlas using common fields such as cell type, tissue > type, and patient ethnicity. Usage involves first querying the metadata > table for cells of interest, and then downloading the corresponding cells > into a SingleCellExperiment object. - Attachment (twitter): Attachment > :dna::computer::fire: We are excited to launch #CuratedAtlasQueryR! millions of cells at your fingertips. A thread :thread:. > > The harmonized and reannotated #CELLxGENE #singlecell human #atlas can be > explored and retrieved as #SingleCellExperiment. Please RT! > > -> http://stemangiola.github.io/CuratedAtlasQueryR/
Maria Doyle (05:49:14) (in thread): > :writing_hand:and see this new Bioconductor blog posthttps://bioconductor.github.io/biocblog/posts/2023-02-23-CuratedAtlasQueryR/ if you want to read more about the CuratedAtlasQueryR package above. > > Congrats@stefano mangiolaand team!:clap::tada::partying_face:
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2023-02-26
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2023-02-28
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Vince Carey (09:39:14): > just putting it out there … any interest in a bioconductor app for ios? tired of looking for the next event, conference dates, call info? get the app!
Ramin (15:26:57): > @Ramin has joined the channel
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Peter Hickey (17:32:05): > BioC Asia 2022 presentations are now available for viewing on YouTube:https://www.youtube.com/playlist?list=PLdl4u5ZRDMQRjQRyAlm4KpRbs1AD1ZODk - Attachment (YouTube): BiocAsia2022 > Share your videos with friends, family, and the world
Stephanie Hicks (17:43:22): > Thank you@Peter Hickey! Just tweeted it out to amplify the amazing resource!
Peter Hickey (17:45:08) (in thread): > Big thanks to@Amelia Dunstoneand@Kayla Interdonatofor editing the videos and putting the playlist together!
2023-03-02
Maria Doyle (04:59:58): > :rotating_light::loudspeaker:OnMarch 8th [git.bioconductor.org](http://git.bioconductor.org) to devel. > > For more details, see the > 1. Blog post > 2. Branch Rename FAQ
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2023-03-03
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Michael Love (10:52:45): > Is there a long-read RNA channel already?@Stephanie Hicksare interested in trying out tools, etc. CC@Charlotte Soneson@Matt Ritchie@Shian Su@Peter Hickey@Ying Chen@Jonathan Goekeor any others. If not let’s start one. (Also is there a BiocViews? maybe we can get one going before release)
Michael Love (11:25:15) (in thread): > Ok, i’ve made#longread, let’s think about a BiocViews in that channel
Natalie Kucher (11:26:42): > Hi All, > In case you haven’t heard,GCC2023 will be held in Brisbane, Australia :flag-au:, 10-16 July ****. ****Early registration andabstract submission are now open. This will be the first time that GCC is held outside of North America and Europe, and it is a great opportunity to visit Australia, and enjoy Brisbane’s subtropical climate (and:koala::koala::koala:!) - Attachment (galaxyproject.org): 2023 Galaxy Community Conference (GCC2023) > The annual gathering of the Galaxy Community with opportunities to hear latest developments, get training, and meet everyone involved. - Attachment (galaxyproject.org): Galaxy Community Hub - Galaxy Community Hub > All about Galaxy and its community. - Attachment (galaxyproject.org): Galaxy Community Hub - Galaxy Community Hub > All about Galaxy and its community. - File (JPEG): gcc2023.jpg
2023-03-05
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2023-03-06
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2023-03-07
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Maryam Gbemisola (01:01:32): > Hi, may I know what the general group is for?
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Ameerah Kabir (02:36:28): > Everyone! I am Ameerah Kabir, from Nigeria, a contributing intern from Outreachy internship. I can’t wait to make an impact. Thank youu.
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Patricia Brianna (02:58:20): > hello good people, i am Brianna(Brian in short), an outreachy applicant who needs guidance to make contribution to the world,
Maria Doyle (03:21:50): > Welcome Outreachy applicants:wave:To answer Maryam’s question above and give info on some channels here:#generalchannel is for Bioconductor community-wide announcements and questions#introductionschannel is for introducing yourself to the community (see intros from Outreachy applicants there)#outreachyis for communications with the Outreachy participants (this is the main channel I think you’ll want to use)
Ameerah Kabir (03:32:07): > Thank you so much@Maria Doyle
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Ameerah Kabir (10:31:02): > Hi@Maria DoyleI am interested in the Microbiome Study Curation contribution project, I am yet to see information about it, I would love to know if it is still available?
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Maria Doyle (12:36:52) (in thread): > I see you posted this in#outreachychannel which is good as that is the best place for this question, we will update you there.
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2023-03-08
Kelvin Joseph (00:28:11): > :wave:Hello, team! I am Kelvin Joseph an Outreachy intern applicant and was hoping I could contribute to your microbiome study curation
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MaryJones (01:29:21): > Hello Everyone, My name is Mary Jones, an Outreachy intern applicant, a novice in working with Bioconductor project , please may you guide me to the repository we are expected to fork ? Thank you in advance
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Busayo Ojo (01:51:02) (in thread): > Hi Mary welcome, plz all outreachy related questions should be asked here#outreachyYou’ll also find all the other information you need there.
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Palak Tahlyani (03:30:52): > Hello Mentors and Fellow participants, My name is Palak Tahlyani. I am an Outreachy intern. I am interested in contributing to the project titled “Convert Sweave Vignettes to R Markdown”.would love to connect with people who are already working on it and also for the guidelines.
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kashish ramani (03:41:18): > Hello Mentors and Fellow participants, My name is Kashish Ramani. I am an Outreachy intern. I am interested in contributing to the project titled”Microbiome Study Curation”.would love to connect with people who are already working on it and also for the guidelines.
Aliyu Atiku Mustapha (04:03:49) (in thread): > Hi Palak. I am Aliyu, from Nigeria. I am working on the same project, I chose the graph vignette. How about you, which are you looking at?
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Palak Tahlyani (06:48:47) (in thread): > I’m working on the first contribution task.
Levi Waldron (08:33:24) (in thread): > Welcome, interns! In addition to these channels, there is discussion about the Microbiome Study Curation project specifically in#bugsigdb, and about the Sweave2Rmd project in#sweave2rmd.
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Namusisi Sharon (09:19:16): > Hello mentors and fellow participants, Am sharon Namusisi,an Outreachy intern and new when it comes to the tech world but am interested in contributing to the project called microbiome study Curation , I would like to connect with people who are already working with it for guidance and help , for easy contributions.
Jared Andrews (10:20:15): > Sign-ups for the St. Jude KIDS23 BioHackathon (May 3-5th) are open through March 15th! Projects can be seenhere , and the sign-up form ishere . A small number of travel awards (travels, lodging, meals) will be available for select US-based applicants to come participate in person, though virtual participation is welcome as well. DM me with any questionsAttachment > Projects for the @StJudeResearch https://www.stjude.org/research/why-st-jude/biohackathon/projects-2023.html
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Desire Oluwarotimi (10:33:34): > Hello everyone, I’m Desire, an Outreachy applicant and I’m looking forward to contributing positively to the community.
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Lori Shepherd (14:29:46): > The Bioconductor Core Team has moved forward with the branch renaming from master to devel ongit.bioconductor.org . > > Please see > 1. BiocBlog:https://bioconductor.github.io/biocblog/posts/2023-03-01-transition-to-devel/ > 2. Branch Renaming FAQ:https://contributions.bioconductor.org/branch-rename-faqs.html > Anyone having trouble can post to the community-bioc slack#bioc_git - Attachment (bioconductor.github.io): Bioconductor community blog - Renaming the Default Branch to Devel > During the 3.17 devel cycle, Bioconductor will rename the default branch devel. - Attachment (contributions.bioconductor.org): Chapter 27 Branch Rename FAQs | Bioconductor Packages: Development, Maintenance, and Peer Review > The Bioconductor project has chosen ‘devel’ to be the default branch for GitHub and git repositories. To prepare for this transition, we have compiled a list of Frequently Asked Questions (FAQs)…
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2023-03-09
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Chioma Grace (04:01:09): > Hello,
Chioma Grace (04:01:43): > Greetings everyone.
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Advit Mittal (23:49:32): > Hello mentors and fellow applicants, Advit Mittal this side, an Outreachy intern. I am interested in contributing to the project “microbiome study curation”, thus I would like to connect with people who are already working on it for further guidance and help. Looking forward to building connections!
2023-03-10
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Busayo Ojo (01:59:15) (in thread): > Hi, welcome, I’m also working on the microbiome project > To start off join the#bugsigdbchannel. That’s our main communication channel.
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Dennis Ndubi (04:23:31): > Greetings mentors and fellow applicants, Dennis Ndubi here, an Outreachy intern. I am interested in contributing to the project “Optimize microbiome data science framework”, thus I would like to connect with people who are already working on it for further guidance and help. Looking forward to building a great network.
Maria Doyle (06:08:54): > This is a beautiful new book:closed_book:highlighting Women in Statistics, DataScience, RStats:female-technologist::woman::woman::woman::woman::woman:In celebration of this week’s #IWD2023 we encourage you to check it outhttps://twitter.com/stephaniehicks/status/1633261075859644416 - Attachment (twitter): Attachment > Dear world, Happy #InternationalWomensDay! > > In honor of #IWD2023, I am extremely excited to share with you a new #childrensbook featuring some brilliant #Women in #Statistics and #DataScience! > > :book: book: https://www.stephaniehicks.com/superwomen > :computer: blog: https://www.stephaniehicks.com/blog/super-women-statisticians-and-data-scientists
Maria Doyle (06:13:59) (in thread): > Great, you can join the#outreachyand#miaversechannels to connect with those people:simple_smile:
Stephanie Hicks (06:51:48) (in thread): > Aww thank you@Maria Doyle!
Dennis Ndubi (07:46:50) (in thread): > thank you
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Aguobi Amara (10:48:24) (in thread): > Hello welcome, join#bugsigdbChanel and introduce yourself to start off
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2023-03-11
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Hannah Honda (02:24:49): > Hello everyone! My name is Hannah, an outreachy applicant looking to get participate in the Microbiome study curation. I look forward to contributing here
Kozo Nishida (03:33:51) (in thread): > Hi@Hannah HondaThere are several ways to contribute here, as follows. > 1. Joining the Bioconductor Working Group[s][https://workinggroups.bioconductor.org/](https://workinggroups.bioconductor.org/) > 2. Package development, as inhttps://bioconductor.github.io/biocblog/posts/2023-01-22-OutreachyInternship/ > 3. Holding community events likehttps://bioconductor.github.io/biocblog/posts/2022-01-18-metaRbolomics-2021/ andhttps://bioconductor.github.io/biocblog/posts/2023-01-20-hacktoberfest/ . > 4. Becoming a Community Advisory Board member (but I think the application period for this year has already passed.)https://bioconductor.github.io/biocblog/posts/2022-01-31-join-the-bioconductor-community-advisory-board/ - Attachment (workinggroups.bioconductor.org): Welcome | Bioconductor Working Groups: Guidelines and activities > This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. - Attachment (bioconductor.github.io): Bioconductor community blog - Our experience as Outreachy interns with Bioconductor > Bioconductor participated in the Outreachy Internship program for the December 2022 cohort. Our interns share their experience working on their various projects and bioconductor in general. - Attachment (bioconductor.github.io): Bioconductor community blog - metaRbolomics hackathon to improve interoperability of metabolomics-related R packages > The 3rd metaRbolomics hackathon took place as a in-person workshop in > Wittenberg (Germany) in November 2021. - Attachment (bioconductor.github.io): Bioconductor community blog - Bioconductor Hacktoberfest 2022 review and looking ahead to 2023 > Last October, Bioconductor joined Hacktoberfest and got great community contributions there. > Here, we describe its success and notify the community we plan to participate in 2023. - Attachment (bioconductor.github.io): Bioconductor community blog - Join the Bioconductor Community Advisory Board > Each year the Bioconductor Community Advisory Board (CAB) puts out a public call for new board members. This post tells you more about what the CAB does and how you can apply to become a member.
Harrydas Ombati (04:51:39): > @Harrydas Ombati has joined the channel
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Hannah Honda (06:54:52) (in thread): > Thank you!
Jeffery Orazulike (07:16:07): > @Jeffery Orazulike has joined the channel
Prudence Levison (08:34:56): > @Prudence Levison has joined the channel
MaryJones (09:25:59) (in thread): > Ok thank you
Steffen Neumann (10:30:35): > Hi, I want to run (and debug) mylongtests/locally, I am pulling my hair because I always end up testing the normaltests/instead.
Steffen Neumann (10:34:07) (in thread): > Let’s say, I am insidexcms/longtests/testthatand executetestthat::test_local("."). > But what it executes instead is (among others)./tests/testthat/test_Chromatogram.R
Cindy Apiyo (10:53:14): > @Cindy Apiyo has joined the channel
Marcel Ramos Pérez (11:01:15) (in thread): > It looks like the test path is hard coded, you might have to run the internal commands manuallyhttps://github.com/r-lib/testthat/blob/main/R/test-package.R#L62
Steffen Neumann (12:12:49) (in thread): > Ah, the following seems to work: > > test_dir(path="/vol/R/BioC/devel/xcms/longtests/testthat", > package="xcms", > reporter=NULL, > load_package="installed") >
2023-03-12
Taofeekat Olorunkosebi (20:51:24): > @Taofeekat Olorunkosebi has joined the channel
2023-03-13
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Emile-Daisy (05:51:20): > Please are the task being distributed
Ibizugbe Merit (05:55:14) (in thread): > Hello fellow Outreachy applicants, there are a couple of channels reserved for Outreachy Contributions so you’ll need to join to get updates and more information on how to contribute: > 1. #outreachyis the general outreachy channel > 2. #sweave2rmdis for the “Convert Sweave Vignettes to R Markdown ” project. > 3. #bugsigdbis for the “Microbiome Study Curation ” project. > 4. #miaverseis for the “Optimize microbiome data science framework ” project > I hope this has been helpful. - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website! - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website! - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!
Lori Shepherd (08:23:56): > The release schedule for Bioconductor release 3.17 has been announced. Please be mindful of important dates and deadlines.Bioconductor 3.17 Release Schedule
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2023-03-14
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2023-03-15
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Erica Feick (09:21:21): > Registration for BioC2023 is now open! Early registration rates apply.:tada:https://hopin.com/events/bioc2023 - Attachment (hopin.com): BioC 2023 Annual Conference - Aug 02 | Hopin > Get tickets to BioC 2023 Annual Conference, taking place 08/02/2023 to 08/04/2023. Hopin is your source for engaging events and experiences.
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2023-03-16
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Alexander Bender (05:05:35): > I redirected this user frombiostars.org to the Bioc support site as it is very Bioc-specific. Can someone have a look please.https://support.bioconductor.org/p/9150144/ They’re looking for a programatic way of checking which packages support which genome builds.
Patricia Brianna (07:13:19): > hello friends
Patricia Brianna (07:13:44): > should we wait till the review is done to make more curations
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2023-03-17
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2023-03-18
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2023-03-19
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2023-03-20
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Sean Davis (22:06:46): > Don’t forget or be humble about posting your#papersandpreprints!
2023-03-21
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victory lelekumo (06:47:38): > Hello everyone, my name is Victory Lelekumo, a Data Scientist and an Outreachy applicant. I’m very excited for the opportunity to contribute to the Microbiome Study Curation project. I look forward to sharing and gaining knowledge from everyone.
Suwaibat Suleiman (07:52:30) (in thread): > Hi Victory. > You can join the#bugsigdband the#outreachychannels!
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2023-03-22
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Michael Lawrence (15:02:55): > Who is the organizer of the BiocAsia conference for next year? The R Consortium is interested in reaching out, in part to find contacts into different Asian communities.
Maria Doyle (15:07:41) (in thread): > It’s@Dario Strbenacand@Ellis Patrick
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Janani Ravi (23:27:22): > Hi all, wondering if those of you who give workshops regularly have a form to collect evaluations systematically—an equivalent of our university-provided teaching evaluation (sirs) but for informal or conferencetutorials/workshops?
2023-03-23
Frederick Tan (08:45:35) (in thread): > Discussed this a little at BiocTeaching Oct 10, 2022 (minutes linked to atbioconductor.org/help/education-training // ). Think it’d be great to start with what the Carpentries has developed and customize a bit more towards the Bioconductor audience > * workshop-reports.carpentries.org/?aggregate-workshops > * docs.carpentries.org/topic_folders/lesson_development/lesson_pilots.html#collecting-feedback-on-the-lesson
Maria Doyle (10:26:25) (in thread): > This is something I’m looking at. Aswell as Carpentries, I’m seeing if we can link in with what Elixir have done and this is one of the things we’re planning to discuss at our#elixirAll Hands workshop in June. Elixir have a training metrics database herehttps://training-metrics-dev.elixir-europe.org/ that they’ve said we could load data into if we wanted. It’s about to undergo a development hackathon and they are open to further developing their questions, it’s possible to have general/common and custom/workshop-specific questions. We could potentially build off both the Elixir and Carpentries survey questions, adapting for Bioc.
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Janani Ravi (14:04:07) (in thread): > Thanks,@Frederick Tan&@Maria Doyle! I’ll check out carpentries & elixir.
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Aedin Culhane (17:04:04): > @Vince Careywhat article should I use if I want to describe the quality checks in Bioconductor aka build system/dockerization/github actions /unit testing etc Should I cite the devel contributions guide?
Vince Carey (17:09:58): > IMHO there is no unified description. The BBS is in github and is well-documented (https://github.com/Bioconductor/BBS ). The docker work is managed now by@Alex Mahmoudand he can point you to relevant repos. GHA is being discussed by a working group. If you want to work on an overview document about what I call the “deep stack” of the project, I would be happy to help. Your question reminds me of a concept of three key personas: sci-devs (contributing developers), infra-devs (creators and maintainers of the deep stack, hubs, development tools, and core software and data components) and sci-users (analyst who uses the works of the other two personae).
2023-03-24
KritikaVerma (00:35:26): > Hi everyone! > I was working on a project and in which I used GEOquery and then I got assay matrix representing gene expression. Can anyone tell me more about assay data and what it represents specifically?
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Vince Carey (08:17:27) (in thread): > Hi@KritikaVerma.That would be a question to pose atsupport.bioconductor.org . You should provide more information about which experiment you retrieved so that responders can provide more details.
KritikaVerma (08:55:06) (in thread): > I’lldo that. Thank you!
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2023-03-25
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2023-03-28
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2023-03-29
Wes W (09:57:24): > To all the faculty academics here, i have been hearing conflicting information on committees for K99/R00 grants. Can you have a committee member from a different institution? some people are saying yes and others are saying no… thanks!
Stephanie Hicks (14:04:47) (in thread): > can you clarify by what “committee member” means? Is this a mentor or co-mentor? or is this like an scientific advisory board type thing?
2023-03-30
Eineje Ameh (01:50:07): > Hello I applied for Outreachy and I will like to contribute to this projectplease how can I go aboutit
Davide Risso (02:30:37) (in thread): > Hi!:wave:You may want to have a look at the#outreachychannel!
Eineje Ameh (02:32:30) (in thread): > Thank you soo much
Sean Davis (09:48:55) (in thread): > @Wes WThere should be an NIH contact email (who may/may not be the PO) attached to the opportunity. You may want to reach out to that person to ask your question. It is possible that the answer varies and that person should be able to answer with the specifics of the opportunity in mind.
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2023-03-31
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Aedin Culhane (08:35:22): > Do we need a guide to the channels??? There are 125 ish of them
Frederick Tan (08:49:55) (in thread): > That would be appreciated. As well as guidance on Slack vssupport.bioconductor.org vs bioc-devel mailing list
Frederick Tan (08:49:58) (in thread): > Perhaps an update tobioconductor.org/help/support/posting-guide ?
Wes W (10:36:58) (in thread): > I will endevouer to find that contact! thanks@Sean Davis@Stephanie HicksI am a first gen, i have no idea how this works. i think its like some sort of advisory board if I understand it correctly. not mentors or co-mentors, from what my PI mentioned some of them may only reach out to chat once or twice a year. but he doesnt know for sure, he has never done one or had any fellows apply for one before. all i was told in a K99/R00 institute seminar was that I should put together my committee 4 months before the application is due, but they sure as hell assumed I already knew I needed a committee and that I knew what the committee did… which I did not.
Stephanie Hicks (10:40:05) (in thread): > hey, i’m happy to chat more. will DM and let’s find a time to zoom?
Vince Carey (19:27:20) (in thread): > There is a slackr package that can use the API to interrogate the slack “data”. I have not figured out how to use a token to extract and annotate channels. Could be nice to have some help with this and provide functions to learn about activity and content in our slack community.
2023-04-01
Maria Doyle (13:06:10) (in thread): > Something likethis ? uses slackr. Should we archive old channels that haven’t been used for a long time?
2023-04-03
Laurent Gatto (06:59:16) (in thread): > Very nice, Maria. Something like that would be a good addition to a modernised posting-guide on the (new) website!
2023-04-04
vedha (07:53:46): > Hello everyone! > We’re working onshiny.gosling and would like to publish it to the bioconductor. But before that we would like to add more examples on how it can be used with some popular packages in the ecosystem. > I do not have experience working with any bioconductor packages yet so I am looking for ideas and suggestions of what you feel would be a natural fit for using shiny.gosling with. > Any ideas or comments is appreciated.
Ludwig Geistlinger (08:48:45) (in thread): > My suggestion would be to illustrate how to use shiny.gosling to visualize genomic region data stored in aGRangesobject (from theGenomicRanges packages). This is Bioconductor’s core class for storing genomic region data. > > It would also be interesting to demonstrate visualization of RNA-seq data in aRangedSummarizedExperiment(from theSummarizedExperiment package). This would provide for overlay of data on top of the genomic intervals. > > And finally: the go-to place for static genomic region plots in Bioconductor is theGviz package. If you can illustrate how shiny.gosling plays with Gviz you likely get folks on board quicker.
vedha (09:11:55) (in thread): > Thank you Ludwig, This is very helpful.
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2023-04-08
Wangchen Tsering (15:45:42): > @Wangchen Tsering has joined the channel
Y-h. Taguchi (18:26:20): > http://bioconductor.org/checkResults/devel/bioc-LATEST/TDbasedUFEadv/nebbiolo1-checksrc.html My package in development version has faced suddenly “TIME OUT” in R CMD check. But I did not commit anything since ACCEPTED. I am glad if someone can check what has happened. The above report said that it has tookEllapsedTime
Y-h. Taguchi (18:29:57) (in thread): > http://bioconductor.org/spb_reports/TDbasedUFEadv_buildreport_20230328095129.html#nebbiolo1_check_anchor Here is a link to the build report when it was accepted.
Y-h. Taguchi (18:34:38) (in thread): > There seems to be some problems on R CMD check in linux. For example , the following package which has been in BioC over four years also failed in R CMD check in linux.http://bioconductor.org/checkResults/devel/bioc-LATEST/AMARETTO/
Lori Shepherd (19:54:43) (in thread): > I’m not sure about your package in particular but the error in amaretto is expected based on the new environmentvariable set only on the Linux that will detect undeclared dependencies.Amaretto needs to add biocstyle to their list of suggest dependencies in the description
Lori Shepherd (19:56:42) (in thread): > https://community-bioc.slack.com/archives/CEQ04GKEC/p1679947886937889 - Attachment: Attachment > On March 29, we’ll add _R_CHECK_SUGGESTS_ONLY=true to our devel 3.17 Linux builder to detect missing package dependencies. You can read more about the motivation behind the issue at https://github.com/Bioconductor/BBS/issues/248 . > > If you notice after March 29 that one of your packages is failing R CMD check, consider adding this line to your Renviron.bioc. To reproduce the error, you will need to have a site-library directory in your R home directory, so you’ll have to reinstall R and make the site-library before you see the error. > > To resolve the error, you should identify the missing dependency and add it to Suggests in the DESCRIPTION file.
Y-h. Taguchi (19:57:57) (in thread): > @Lori ShepherdThank you very much for your quick reply. In that case, can anyone help me to solve my problem? I have no idea what to do since I did not commit anything since accepted. And if I cannot resolve this problem, is mine not included in BioC 3.17? If so, it is really terrible.
Y-h. Taguchi (20:21:31) (in thread): > I realize the reason of the problem. Previously, > –no-vignettes > is on, but presently it is off. Can anyone change the set up of R CMD check options to > –no-vignettes > on again?
Lori Shepherd (20:23:38) (in thread): > I believe this also has to do with the new settings but@Hervé Pagès/@Andres Wokatycan comment further?
Lori Shepherd (20:24:43) (in thread): > Also if we know a maintainer is actively trying to fix the issues we will generally still include unless it’s been failing for some unreasonable amount of time (months… Full release cycle…etc)
Y-h. Taguchi (20:27:06) (in thread): > @Lori ShepherdWhat do you mean? Must I rewrite Vignettes form the scratch so as to pass new setting? It is terrible and unfair. I have spent a lot of time so as to adapt to the previous setting. Sudden change prevents me from including mine to Bioc 3.17!
Y-h. Taguchi (20:28:10) (in thread): > @Lori ShepherdI am pleased to know that mine is in Bioc 3.17.
Lori Shepherd (21:38:37) (in thread): > @Y-h . Taguchiyes it will still be included. Please allow us some time to investigate if it is on our side or something you need to look into further.
2023-04-09
Hervé Pagès (04:50:11) (in thread): > I’ll take a look but I would be surprised that the new setting (_R_CHECK_SUGGESTS_ONLY=true) would cause a TIMEOUT.@Y-h. TaguchiIt looks like you submitted 2 packages (TDbasedUFE TDbasedUFEadv Description. > ForTDbasedUFE TDbasedUFEadv TDbasedUFE Descriptionfields reflect that difference. Otherwise, how is the user supposed to choose which package to use? > Also theTitleforTDbasedUFEadv https://cran.r-project.org/doc/manuals/r-release/R-exts.html ): > > The mandatory ‘Title’ field should give a short description of the package. Some package listings may truncate the title to 65 characters. It should use title case (that is, use capitals for the principal words: tools::toTitleCase can help you with this), not use any markup, not have any continuation lines, and not end in a period (unless part of …). Do not repeat the package name: it is often used prefixed by the name. Refer to other packages and external software in single quotes, and to book titles (and similar) in double quotes. > FinallyTDbasedUFEadv https://bioconductor.org/packages/TDbasedUFEadv ) which is not reasonable. Packages with so many dependencies tend to break often, even if no changes are made to them.
Y-h. Taguchi (05:03:30) (in thread): > @Hervé PagèsWhat do you mean？ Would you like to reject mine in this stage? It is unfair. For 228 dependencies, I do not know the reason why it has happened. > NAMESPACE does not include so many. See belowhttps://code.bioconductor.org/browse/TDbasedUFEadv/blob/devel/NAMESPACE Please tell me how to reduce 228 to the reasonable numbers. > I dislike mine to be excluded from BoiC 3.17 in this stage, since mine was once accepted. Please advise me how to avoid the exclusion of both package from BioC 3.17. I have spent a lot of time to make both accepted. - Attachment (code.bioconductor.org): Bioconductor Code: Browse > Browse the content of Bioconductor software packages.
Vince Carey (07:48:33) (in thread): > @Y-h . Taguchiyour package won’t be rejected. But every contributor has to make their package workable in the build system. Sometimes there are problems that the core developers can solve by expanding or improving the build system. Sometimes the package is unbuildable for reasons the core can’t solve given current arrangements. Herve mentioned a few peculiar aspects of the pair of packages you’ve submitted and I hope you will take his advice to clarify the differences. The dependency count is a problem that can be analyzed using a tool like pkgnet.
Vince Carey (07:49:14) (in thread): - File (JPEG): TD.jpg
Vince Carey (07:50:31) (in thread): > That’s produced using library(pkgnet); CreatePackageReport(“TDbasedUFEadv”)
Vince Carey (07:53:39) (in thread): > The timeout for your package is occurring in vignette rendering. Why would this happen? I will time the build of your vignette on my laptop to see if I can understand the cause.
Y-h. Taguchi (08:00:34) (in thread): > @Vince CareyPreviously, because of –no-vignettes, the time for vignettes is not counted. Now it counts. It is the reason. I know that building vignettes took long but it was not a problem when it was accepted. Please do not change the system. I have spent lot of time to compile this vignettes. If I am required to re-build vignettes to fulfill new requirement , it is terrible for me. It is not fair to change criterion after acceptance.
Vince Carey (08:12:23) (in thread): > Dear@Y-h. TaguchiI will get back to you. I don’t think there will be any onerous consequences of these events. The build system may be having a problem with one of the dependencies of your package, leading to a timeout that is not immediately diagnosable from the build report. We need to increase transparency of event reporting so that causes are more apparent. On my laptops I am not seeing timeouts for your packages – linux laptop completes build and check in under 8 minutes.
Y-h. Taguchi (08:15:39) (in thread): > @Vince CareyI am pleased to know that it took only eight minutes on your laptop. Other issues I will try to resolve, but the number of dependencies might not be reduced if all of 228 packages are really used. I will check it using pkgnet you suggested.
Vince Carey (08:25:55) (in thread): > Note that the dependent packages aren’t necessarily used for any given computation. But the various packages imported or depended upon have declared that they won’t work if their depends/imports declarations are not satisfied. Thus if you get to a situation where, e.g., a fifth level dependent can’t be INSTALLED because of some new problem, a chain of unusability may arise once the fifth-level dependencyhas been removed
Vince Carey (08:28:26) (in thread): > I noticed that a system for which TDbasedUFE installs must be upgraded substantially (dozens of packages added, presumably mostly transitive dependencies) for TDbasedUFEadv to be installed. So there must be considerable differences between the packages and these should be briefly explained in DESCRIPTION, and made very clear in vignettes.
Y-h. Taguchi (08:32:20) (in thread): > I will denote the deference between two in DESCRIPTION as much as possible. As for dependency problem, I have not yet grasped what you mean very well. Are there anyways to remove fifth level dependencies manually?
Vince Carey (08:34:11) (in thread): > I don’t think you should be concerned about the dependencies at this time. In the future you may find that some dependency causes a problem for the reason I mention. You then have to decide whether to change your code to avoid the dependency or to negotiate with the developer of the deep dependency to restore the functionality somehow.
Vince Carey (08:35:24) (in thread): > Knowing and understanding your dependency graph is important though.
Y-h. Taguchi (08:36:15) (in thread): > @Vince CareyI see. I did understand this point (i.e. many dependences). I was prepared to fix the future problem. I’m ready for this issue.
Y-h. Taguchi (08:37:07) (in thread): > @Vince CareyI will check dependence graph at the earliest opportunity. Thanks.
Lori Shepherd (09:18:12) (in thread): > Also worth noting, for others that find this thread, the vignette was always built just during the build stage only before and why we did –no-vignettes in check. I expect with the new setting to check dependencies requires the vignettes to be built in check now. If that’s true than the check is a time for examples, test, and vignette.
Hervé Pagès (13:34:14) (in thread): > @Y-h . TaguchiR CMD check TDbasedUFEadv_0.99.19.tar.gztakes less than 10 min on my laptop. I also ran the command on our Linux builder nebbiolo1 and it completed in about 6 min, so I’m not sure why the TIMEOUT on the daily report. Let’s see what the report says tomorrow (no reports on Sundays). > About the high number of deps (direct and indirect): all I’m saying is that packages with so many deps are known to be hard to maintain because they are inherently fragile. It’s in your best interest, and the interest of your users, to try to reduce the things you rely on as much as possible.
mgunady (17:01:11): > @mgunady has joined the channel
Y-h. Taguchi (17:34:53) (in thread): > @Hervé PagèsI will see why there are so many dependences using pkgnet that@Vince Careysuggested.
2023-04-10
Y-h. Taguchi (19:31:17) (in thread): > https://bioconductor.org/packages/devel/bioc/html/TDbasedUFEadv.html Build in Linux seems to be OK Now. Thanks a lot. - Attachment (Bioconductor): TDbasedUFEadv (development version) > This is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. It can perform unsupervised feature extraction. It uses tensor decomposition. It is applicable to gene expression, DNA methylation, and histone modification etc. It can perform multiomics analysis. It is also applicable to single cell omics data sets.
Jayaram Kancherla (19:38:04) (in thread): > i know you
2023-04-12
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2023-04-13
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Y-h. Taguchi (06:47:59) (in thread): > @Vince CareyI have checked my package using pkgnet. Most of “too many” dependences turned out to come from packages used only in vignettes. Thus, unavoidable to use them. Thanks for you notions.
Jiefei Wang (15:22:34): > @Jiefei Wang has joined the channel
Stephanie Hicks (16:46:06): > Congratulations@Shila Ghazanfar@Jean Yang@Josh Moore!:bioc::tada::cell:https://chanzuckerberg.com/science/programs-resources/single-cell-biology/data-insights/?cycle=2 - Attachment (Chan Zuckerberg Initiative): Single-Cell Biology Data Insights Cycle 2 > CZI supports computational experts to gain insights into health and disease from single-cell biology datasets
Martin Morgan (17:03:50) (in thread): > And@Stephanie Hicks!
Stephanie Hicks (17:21:28) (in thread): > Thank you!:relaxed:
Y-h. Taguchi (17:34:16) (in thread): > I have commited the change to DESCRIPTION, although it was too late to be included into the release of BioC 3.17 …..
Shila Ghazanfar (20:52:11) (in thread): > Congratulations to you too Stephanie and all!:tada:
Hervé Pagès (22:46:54) (in thread): > Thanks! Not too late, BioC 3.17 has not been released yet. Will be on April 26.
2023-04-17
Lori Shepherd (14:14:01): > Nominations for Bioconductor 2023 Awards are now open. Bioconductor is excited to announce an opportunity to recognize those making significant outstanding contributions to the Bioconductor community. The Bioconductor project is announcing the call for Bioconductor Awards, honoring various forms of contributions to the project. Four awardees will be selected, each having contributed to the project in an outstanding way based on one or more of selection criteria. More information and details foundhttps://bioconductor.org/about/awards/ and the nomination form can be found athttps://forms.gle/gPzmH8ewHNHWckdv6 . The deadline for nominations is May 31, 2023. The awardee’s will be recognized at the annual Bioc2023 conference August 2-4. - Attachment (Google Docs): Bioconductor Awards 2023 > Nomination form for the Bioconductor Awards (see https://bioconductor.org/about/awards/ for more details). > > Please fill out all the fields in the following sections. > > In the Nominator section, please provide your own contact information in case we need to contact you with any question. > > In the Nominee section, please indicate how the nominee provides outstanding contributions for each of the selected nomination criteria. Four awards will be given using the selected criteria as justification.
Lori Shepherd (14:18:04) (in thread): > The webpage for the awards will be updated within the hour to reflect 2023 information.
2023-04-18
Matthew Broerman (13:50:18): > @Matthew Broerman has joined the channel
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Y-h. Taguchi (16:50:47): > Sorry for troubling you many times. > I have had a trouble again, but this time for TDbasedUFE.http://bioconductor.org/checkResults/devel/bioc-LATEST/TDbasedUFE/palomino3-install.html It has produced build error > “there is no package called ‘promises’” > 1. I did not push anything since the last successful build > 2. Because of this error, my another package, TDbasedUFEadv has also has error, since it uses TDbasedUFE > http://bioconductor.org/checkResults/devel/bioc-LATEST/TDbasedUFEadv/palomino3-install.html I am glad if you can confirm that the error is not in myside, but your side and fix it asap, since the release of BioC 3.17 is soon. > Thanks for your every efforts to maintain Bioconductor:slightly_smiling_face:
Andres Wokaty (17:15:59) (in thread): > The error is not on your side. I updated R to the release candidate on the devel builders yesterday and it usually takes a couple of days for the problem to resolve. I’ve checked palomino3 and promises is installed, so the errors related to promises missing should resolve soon.
Y-h. Taguchi (17:33:03) (in thread): > @Andres WokatyThanks for your quick reply. I am pleased to know that the problem is not in my side.
2023-04-19
Maria Doyle (05:26:41): > :mega:Reminder for Bioconductor users and developers::alarm_clock:#EuroBioc2023 abstract submission deadline is just a few days away, Monday April 24, 5pm CEST. > > Don’t miss the chance to present your work in beautiful Ghent, Belgium!:flag-be::point_right:Submit your abstract now athttps://openreview.net/group?id=bioconductor.org/EuroBioC/2023/Conference - Attachment (OpenReview): EuroBioC 2023 Conference > Welcome to the OpenReview homepage for EuroBioC 2023 Conference
Y-h. Taguchi (17:23:29): > https://master.bioconductor.org/checkResults/3.17/bioc-LATEST/TDbasedUFEadv/nebbiolo1-checksrc.html Thanks for your every effort to maintain bioconductor. > I am so sorry, but TDbasedUEEadv had a problem again. Since I did not commit since the last successful build, the problem seems to be not in my side, but in the system. > I am glad if you can check the problem in the eraliest opportunity and fix it,
Hervé Pagès (18:36:54) (in thread): > Hi@Y-h. Taguchi, please post build related questions in the#bioc-buildschannel, thanks!
Y-h. Taguchi (20:07:32) (in thread): > thanks > I did
2023-04-21
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2023-04-22
Luca (08:32:28): > @Luca has joined the channel
2023-04-24
Josh Moore (02:23:21) (in thread): > :raised_hands:to all as well.
Maria Doyle (13:05:43): > :sun_with_face::mortar_board:Dive into the world of Bioinformatics this summer with rstats & Bioconductor at CSAMA 2023!:dna::microscope::spiral_calendar_pad:When? 11-16 June 2023:earth_africa:Where? Bressanone-Brixen, Italy:it::pizza::ice_cream:Come for the science, stay for the gelato & pizza!:wink::rocket::mag:More info:https://csama2023.bioconductor.eu/
Joshua Ho (13:16:15): > @Joshua Ho has joined the channel
2023-04-27
Maria Doyle (16:45:57) (in thread): > :loudspeaker:Calling all Bioconductor wizards! Have a tutorial you want to include in the biggest online, bioinformatics training week globally? Now’s your chance! We’re inviting you to include your Bioconductor tutorial in Smörgåsbord 2023, happening May 22-26.Why join? What you need to do? the Bioconductor workshop template even better!), > it’s just two simple steps::white_check_mark:Let us know you’re in!:white_check_mark:Ensure someone from your team can answer questions on Slack during the training week. > > Feel free to get in touch with me with any questions.
Y-h. Taguchi (19:10:52) (in thread): > I am interested to provide tutorial although I have no experience to do this.
2023-05-01
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2023-05-03
Ahmad Alkhan (07:46:16): > @Ahmad Alkhan has joined the channel
Aidan Lakshman (10:08:39): > Quick question for the Bioc team–is there a reasonbioconductor.org isn’t https secured? I’m happy to help out with securing it, just not sure who is in charge of the website
Martin Morgan (10:13:18) (in thread): > it is (https://bioconductor.org ). In the past it has been the case that http:// was actually required by some of the global user community (for instance and as frightening as it seems some earlier R versions did not supporthttps:// for package installation) socould not simply be disabled. I often find myself with an http:// link even when I (think I have) started with https://, and I’m not sure how this default occurs; it might be that the redirects athttps://github.com/Bioconductor/bioconductor.org/blob/b175f6661daeda48946359a068bbd66583ffa009/assets/.htaccess#L51 are somehow less-than-optimal
Hervé Pagès (12:33:19) (in thread): > would be good to maybe open an issue for this, or to bring it to the attention of the folks on the#biocwebsitechannel
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2023-05-04
Franck RICHARD (07:52:36): > Hello to all, > > Some neuroscience researchers I know sometimes complain about the slowness of some indexing and alignment operations on basic machines. > I wonder if it wouldn’t be interesting to try to incorporate some Cuda features into packages like bowtie2 to speed up processing on simple PCs. > > There is this attempt by Nvidia, the famous graphics card manufacturer:https://nvlabs.github.io/nvbio/nvbowtie_page.html but the associated GitHub site doesn’t mention any update since 2015 and indicate that the issues sent by users are still not resolved. > > I would just like to try to understand the reason for these errors and propose a R Wrapper that would offer this hardware accelerated version of Bowtie2. A RBowtie2_cuda package or something like that… > > If I can’t do it, it won’t be a big thing. Do you have any objections or comments for me? > > I would also like to see if it would be possible to use RAPIDS (https://rapids.ai ) in Bioconductor to see if we can’t speed up some basic processing… > > Kind regards! > > Franck - Attachment (rapids.ai): RAPIDS | GPU Accelerated Data Science > Open source GPU accelerated data science libraries
Maria Doyle (10:26:47): > We would appreciate your support in spreading the word about the BioC2023 pre-conference Carpentries RNA-seq workshop. Please consider sharing the following text and posts with your networks to help us reach a wider audience. Thank you for your help in making this workshop a success! > ———- > Are you ready to dive into the world of RNA-seq data analysis and elevate your research to new heights? Join ourBioC2023 pre-conference workshop in Boston, Jul 31-Aug 1, on RNA-seq analysis with Bioconductor and master the essential tools and techniques to make sense of your gene expression data! > > In this hands-on workshop, you will: > * Learn from leading experts in the field of bioinformatics and genomics > * Acquire a solid understanding of the RNA-seq analysis pipeline using Bioconductor’s state-of-the-art tools > * Gain insights into best practices for processing and analyzing RNA-seq data > * Explore a variety of methods for identifying differentially expressed genes, pathway analysis, and functional enrichment > * Develop the skills to interpret and visualize your results effectively > * Engage in interactive sessions and group discussions to address your specific questions and challenges > * Network with fellow researchers, bioinformaticians, and industry professionals > Whether you’re a graduate student, a bioinformatics analyst, or a researcher looking to expand your expertise in RNA-seq data analysis, this workshop is designed for you. Prior experience with R programming is required, but all levels of RNA-seq expertise are welcome. > > Don’t miss this fantastic opportunity to enhance your skills and stay at the forefront of cutting-edge genomics research. Spaces are limited, soapply before May 31 to secure your spot and unlock the full potential of your RNA-seq data with Bioconductor! > ———- > Twitterhttps://twitter.com/Bioconductor/status/1654097829420302337 Mastodonhttps://genomic.social/@bioconductor/110310382788316790
Hassan Kehinde Ajulo (11:38:03): > @Hassan Kehinde Ajulo has joined the channel
Davide Risso (15:24:10) (in thread): > I’m not an expert, but it looks like parabricks is now the nvidia pipeline for sequence alignment (among other things):https://www.nvidia.com/en-us/clara/genomics/ - Attachment (NVIDIA): NVIDIA Genome Sequencing Analysis
Davide Risso (15:24:42) (in thread): > The license looks pretty restrictive at first glance though
Davide Risso (15:26:22) (in thread): > We’re currently trying out Rapids, for the moment in Python, to benchmark it against common single-cell analysis workflows
Franck RICHARD (15:55:36) (in thread): > Hello Davide and thank you for your reply. > Yes, Clara sounds very interesting but I have the impression that it is a commercial solution. > I will try to see what can be done with Bowtie Cuda. I am currently having compilation problems with Cuda 11.8 > I will insist a little more…
Sriya Malladi (17:34:48) (in thread): > Hi@Maria Doyle! How would someone go about signing up to do this? For example, where would things be sent after they were completed?
Theary Chhim (19:03:49): > @Theary Chhim has joined the channel
Martin Morgan (21:21:07) (in thread): > I opened an issue athttps://github.com/Bioconductor/bioconductor.org/issues/223 with what I think is a reproducible example (clicking on a badge when on a package ‘landing page’). But maybe there are other scenarios?
Aidan Lakshman (21:50:45) (in thread): > Thank you! Sorry for not following up on this sooner,I’vehad a lot going on:sweat_smile:much appreciated!
2023-05-05
Maria Doyle (04:58:15) (in thread): > Hi Sriya, you can message me directly in this Slack or email me atmaria.doyle@ul.ie
Franck RICHARD (09:27:08) (in thread): > nvBio finally compiles after some modifications. This is very encouraging. I can align two fastq files to a reference index 5x faster with a Geforce 3060 than with a ryzen 1700x running with 16 threads.
Franck RICHARD (09:27:50) (in thread): > It remains to be seen if this does not cause problems…
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Fabricio Almeida-Silva (10:17:26): > Hello, everyone! I don’t know who maintains the Bioconductor support site, but I’ve received many email notifications over the past few weeks of “users” commenting on old questions that tagged my packages, but the comments seem to have been created by bots. It’s starting to get a bit annoying, and I assume some of you have experienced the same. Is there any plan to create an anti-bot system on the support site? > > You can find examples of apparently bot-generated comments here:https://support.bioconductor.org/p/9147902/#9151197
Lori Shepherd (10:46:04) (in thread): > There is a#support-sitefor reporting issues@Natay Aberra
Lori Shepherd (10:51:44) (in thread): > We will look into it
Natay Aberra (10:57:02) (in thread): > We have a spam checker but from the looks of that comment, it looks like spammers are using chat gpt to come up with some text and have their link embedded at the end. All in all, we’ll need a better spam checker. In the mean time, think we can silence comment emails from new users thatdidn’tcreate the thread. As Lori pointed,it’sbetter to create aGitHubissue to track the issue.
Lori Shepherd (11:00:43) (in thread): > https://github.com/Bioconductor/support.bioconductor.org is the code repo to make future issues
Fabricio Almeida-Silva (11:36:04) (in thread): > Thanks a lot,@Lori Shepherdand@Natay Aberra. I’ll open an issue on the GitHub repo.
2023-05-06
Martin Morgan (13:42:18): > Not that I have any complaints, but if I did, how would I raise concerns about inappropriate slack communications? I kind of know that I could google for ‘code of conduct’ or something, but it seems like it should be easier to find in this forum? Minimally, rOpenSci includes a link to their code of conduct in the dialog box that shows up when I click on the ‘#general’ channel.
Maria Doyle (14:02:07) (in thread): > Great point! I’ve just added it as a bookmark to the top of#generalDo you think that’s enough or something else needed?
Charlotte Soneson (14:10:56): > Do you want to join the Bioconductor Technical Advisory Board, or do you know someone who would be a great fit? Then fillthis short form (if you’re nominating someone else, please first confirm that they are interested) before May 31 (at midnight in a time zone of your choice). If you are unable to access Google Forms, please seethis pdf of questions, and email your answers tocharlottesoneson (at)gmail.com . For more information about the current board and the election process, seehttps://bioconductor.org/about/technical-advisory-board/ , and if you have questions, feel free to post them in the#tech-advisory-boardchannel. Please help spread the word!
Martin Morgan (14:20:32) (in thread): > Wow thanks@Maria Doylein the slack app on macOS when I click on the#generalchannel I see the attached image. This is a really big improvement and makes the code of conduct much more accessible, thanks! Really this is great. Any chance that this could appear onall channels? - File (PNG): image.png
Maria Doyle (14:43:32) (in thread): > That would be great, I’ll need to figure out how to do it as we’d need to add it to the >100 channels already existing and ideally by default to every new channel created. If anyone knows how please chime in.
Spencer Nystrom (16:49:37) (in thread): > You can use the slack API to get the current description & append the CoC info. > > Here’s the endpoint you’d need, I think:https://api.slack.com/methods/admin.teams.settings.setDescription - Attachment (Slack API): admin.teams.settings.setDescription API method > Set the description of a given workspace.
2023-05-07
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2023-05-08
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2023-05-09
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2023-05-11
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2023-05-12
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Lori Shepherd (11:51:45): > Please remember to nominate members of the Bioconductor community for BiocAwards! Deadline for 2023 awards is May 31.https://forms.gle/gPzmH8ewHNHWckdv6 Additional information about the awards can be found at:https://bioconductor.org/about/awards/ - Attachment (Google Docs): Bioconductor Awards 2023 > Nomination form for the Bioconductor Awards (see https://bioconductor.org/about/awards/ for more details). > > Please fill out all the fields in the following sections. > > In the Nominator section, please provide your own contact information in case we need to contact you with any question. > > In the Nominee section, please indicate how the nominee provides outstanding contributions for each of the selected nomination criteria. Four awards will be given using the selected criteria as justification.
Sebastien Lelong (20:36:53): > @Sebastien Lelong has joined the channel
2023-05-15
Franck RICHARD (07:54:15): > Hello, > > I have just developed a new package. The .tar.gz file passes the R CMD check and BiocCheck validation tests… > What should I do next with this file? > There is another thing that worries me a bit. It is absolutely necessary that the Cuda environment has been installed on a machine to allow the compilation. > I suggest an installation script under Ubuntu… > > Good day to all !
Lori Shepherd (08:16:20): > You need to submit the package to the new submission tracker for reviewhttps://github.com/Bioconductor/Contributions/issues and if there are system requirements installation instructions should be included in a top level INSTALL filehttp://contributions.bioconductor.org/sysdep.html as well as in the Description as a SystemRequirments
Franck RICHARD (10:39:37): > Thanks Lori !
2023-05-17
Artur Sannikov (02:57:01): > @Artur Sannikov has joined the channel
2023-05-19
Franck RICHARD (05:19:13): > Hello, I have just finished writing a new package for bioconductor that should work with Cuda and c++ code. The problem is that the package requires the installation of many development suites (cuda devtools, Rtools, MSVC compilations tools) under Windows and that the compilation time under Windows is important (15 minutes or more). I am afraid that this discourages many people. Also, I would like to be able to provide the Windows executables directly in the package… Under linux, the compilation seems to me unavoidable because of the risk of incompatibility with the libc library… Is it possible to indicate a compilation under linux and no compilation under windows in the DESCRIPTION file or should I make two different packages? > Thanks for your help!
Lori Shepherd (06:29:47) (in thread): > We have a standard way of building, installing, and compiling packages on our builder and exceptions to that are generally not allowed.@Hervé Pagèscould maybe comment further. Also package development questions might also more traction from developers on the bioc-devel@r-project.org.
Vince Carey (10:09:34) (in thread): > plz provide url if repo for detailed advice
Maria Doyle (10:16:42): > :alarm_clock::mortar_board:3 days until the annual (and 1st Bioconductor) Smörgåsbord training course starts! There is still time to register if you want to participate. > > Join us for a week of free, online, self-paced #Bioconductor and #UseGalaxy #bioinformatics learning!:date:May 22-26:arrow_right:https://gallantries.github.io/video-library/modules/bioconductor
Lluís Revilla (10:42:49) (in thread): > There’s also#package_submissionsand#package-submission
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Hervé Pagès (12:15:25) (in thread): > > the compilation time under Windows is important (15 minutes or more). I am afraid that this discourages many people > Windows users won’t need to compile anything because they’ll install the Windows binary package that we provide. This is no different from what happens with CRAN packages. Jennifer (@Andres Wokaty) will know the details but I think that most of the things you listed above (Rtools, MSVC, etc…) are already on our Windows build machines. Anything but Rtools should be listed in yourSystemRequirementsfield. > > Under linux, the compilation seems to me unavoidable > Except for when people use our docker image, we don’t provide Linux binary packages (CRAN doesn’t either) so Linux usersalways install from source. > > Is it possible to indicate a compilation under linux and no compilation under windows in the DESCRIPTION file > Don’t try to indicate anything like that.
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Michael Kesling (14:28:04): > Hi everyone. I’m new here. I’m wondering if there’s a package or function in bioconductor for querying genes that have a tissue-specific pattern. For most of what I’ve found on the web, I need to start with a single gene and then browse its attributes. At NCBI Gene, I can see tissue-specific expression for that particular gene. I’d rather perform a query for tissue-specific expression and then get a list of genes back. Is there a way to do that? Thanks very much!
Steve Lianoglou (14:58:34) (in thread): > Tissues-specific, or celltype specific? Here are some ideas:Cell Type Specific Genes genesets available from the C8 collection of MSigDB (cell type signature gene sets [830 gene sets]) > 2. Theclustermole package has also collected cell type specific signatures > Tissue Specific aforementioned clustermole package provides an “organ” annotation/column for each of its cell-type specific gene lists. You can aggregate by organ directly, or exclude certain celltypes from the organ first, then aggregate. > 2. If you want to put in some more elbow grease, you can download the RNAseq data from GTEx (via recount3, for instance) then manually do a “your-tissue” vs “all the rest” DGE analysis and get as many of the the top N genes as you like.
Steve Lianoglou (14:59:51) (in thread): > If I wanted to tissue specific genes, I’d probably do both of the suggestions I enumerated above, and the compare the clustermole lists with their expression patterns in the GTEx atlas to see how well the match up (or not)
Michael Kesling (15:04:16) (in thread): > Thank you@Steve Lianoglou. I will start there and go from there.
Lluís Revilla (18:47:35) (in thread): > Linux users might use cran2u for ubuntu or other repositories to install binaries packages via the bspm package (or directly from their OS package manager)
2023-05-20
Hervé Pagès (05:12:19) (in thread): > Sure but from the perspective of a package developer that doesn’t really count. The default distribution method for R packages on Linux is the source tarball, so package developers should focus on that. They should not make assumptions about possible alternate distribution methods, or target a particular Linux distro.
Vince Carey (05:40:01) (in thread): > Another tissue-oriented resource is ExperimentHub EH1044 which has 741 “matched normal” samples related to TCGA tumor samples. > > > eh[["EH1044"]] -> tno > see ?GSE62944 and browseVignettes('GSE62944') for documentation > loading from cache > require("SummarizedExperiment") > > tno > class: SummarizedExperiment > dim: 23368 741 > metadata(0): > assays(1): NormalRaw > rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR > rowData names(0): > colnames(741): TCGA-K4-A3WV-11A-21R-A22U-07 > TCGA-49-6742-11A-01R-1858-07 ... TCGA-BH-A0H5-11A-62R-A115-07 > TCGA-22-5489-11A-01R-1635-07 > colData names(2): sample type > > table(tno$type) > > BLCA BRCA CESC CHOL COAD ESCA GBM HNSC KICH KIRC KIRP LIHC LUAD LUSC PAAD PCPG > 19 113 3 9 41 13 5 44 25 72 32 50 59 51 4 3 > PRAD READ SARC SKCM STAD THCA THYM UCEC > 52 10 2 1 37 59 2 35 >
Vince Carey (05:51:14) (in thread): > GenomicSuperSignatures and refine.bio also seem relevant to the general question. For examplehttps://www.refine.bio/search?q=bronchus produces a lot of references … and helps frame the question, which seems quite difficult. - Attachment (Bioconductor): GenomicSuperSignature > This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.
Franck RICHARD (05:52:34) (in thread): > Thank you for your answers to all of you and your clarifications!
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2023-05-21
Steve Lianoglou (12:09:33) (in thread): > I haven’t ran into these packages before – thanks for pointing these out,@Vince Carey!
2023-05-22
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2023-05-24
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2023-05-25
Steffen Neumann (03:56:14): > Hi, for a few days,remotes::system_requirements("ubuntu", "20.04")is giving meError: JSON: EXPECTED value GOT <both on a laptop and GitHub actions. Any ideas how to get the actual URL this tries to retrieve so I could debug what’s going on ?
Steffen Neumann (03:59:30) (in thread): > Locally, I useR version 4.2.3 (2023-03-15)onUbuntu 22.04.2 LTSusingremotes_2.4.2, and probably different versions on GitHub
Charlotte Soneson (04:00:59): > Only a few days left for nominations to the Bioconductor Technical Advisory Board:https://community-bioc.slack.com/archives/C35G93GJH/p1683396656889889 - Attachment: Attachment > Do you want to join the Bioconductor Technical Advisory Board, or do you know someone who would be a great fit? Then fill this short form (if you’re nominating someone else, please first confirm that they are interested) before May 31 (at midnight in a time zone of your choice). If you are unable to access Google Forms, please see this pdf of questions, and email your answers to charlottesoneson (at) [gmail.com](http://gmail.com). For more information about the current board and the election process, see https://bioconductor.org/about/technical-advisory-board/ , and if you have questions, feel free to post them in the #tech-advisory-board channel. Please help spread the word!
irem Kahveci (04:07:45) (in thread): > ∑To retrieve the actual URL thatremotes::system_requirements("ubuntu", "20.04")is trying to access, you can enable verbose output in thehttrpackage, which is used byremotesfor HTTP requests. for ex: > > #in R > library(httr) > > # Enable verbose output > options(httr_verbose = TRUE) > > # Run the system_requirements function > remotes::system_requirements(“ubuntu”, “20.04”) > > > #By settinghttr_verbosetoTRUE, you will see the complete HTTP request information in the console, including the requested URL. Look for the line that starts with-> GETin the output. This line will display the URL being accessed byremotes::system_requirements. > > This approach should help you obtain the actual URL and assist in debugging the issue. Remember to disable the verbose output by settinghttr_verboseback toFALSEwhen you are finished with the debugging process.
Steffen Neumann (05:36:34) (in thread): > Will try, but the help page forremotes::system_requirementssuggests that it is using command line curl . I’ll report back
Steffen Neumann (05:37:24) (in thread): > > > #in R > > library(httr) > > # Enable verbose output > > options(httr_verbose = TRUE) > > # Run the system_requirements function > > remotes::system_requirements("ubuntu", "20.04") > Error: JSON: EXPECTED value GOT < >
Steffen Neumann (05:46:09) (in thread): > So my system_requirements says > > system_requirements( > os, > os_release = NULL, > path = ".", > package = NULL, > curl = Sys.which("curl") > ) > > andcurl: The location of the curl binary on your system.-> Would that bypass the httr debugging settings ?
irem Kahveci (06:22:52) (in thread): > by enabling httr_verbose, you should still be able to see the HTTP request details and the requested URL, even if you have specifiedcurl = Sys.which("curl")in the system_requirements function call.
Steffen Neumann (06:33:58) (in thread): > Don’t think so, sincesystem_requirementsdoes its own > > system2(curl, args = c("--silent", shQuote(sprintf("%s/sysreqs?all=false&pkgname=%s&distribution=%s&release=%s", .... > > so no way for httr to get the URL. > BUT: I was able to run steps manually, and found > > curl --data-binary @/.../DESCRIPTION "[https://packagemanager.rstudio.com/__api__/repos/1/sysreqs?distribution=ubuntu&release=20.04&suggests=true](https://packagemanager.rstudio.com/__api__/repos/1/sysreqs?distribution=ubuntu&release=20.04&suggests=true)" > <html> > <head><title>301 Moved Permanently</title></head> > <body> > <center><h1>301 Moved Permanently</h1></center> > </body> > </html> > > So 1) make curl follow the 301 and 2) update remotes to the new location
Jacques SERIZAY (06:35:52) (in thread): > This is likely due to redirection ofrstudio.com toposit.co . This was fixed by Gábor in the development version ofremotes:https://github.com/r-lib/remotes/commit/e199c1bdda3858600bbef8e4bbc3f5868b899587 If you install the development version ofremotes(withremotes:smirk:), it should fix this issue
Jacques SERIZAY (06:42:41) (in thread): > btw, pinging@Brian Schilderbecause this problem makes all myrworkflowsto fail in ubuntu.
Steffen Neumann (07:20:57) (in thread): > indeed, I get a valid response withcurl --data-binary @/vol/R/BioC/devel/mzR/DESCRIPTION "https://packagemanager.posit.co/api /repos/1/sysreqs?distribution=ubuntu&release=20.04&suggests=true "In the meantime,@Jacques SERIZAYyou can set an environment variableRSPM_ROOT=https://packagemanager.posit.co Rscript -e 'remotes::system_requirements("ubuntu", "20.04")'
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2023-05-30
Lori Shepherd (08:40:22): > <!channel>Deadline to nominate Bioconductor community members for awards is tomorrow May 31st! Please consider nominating community members and members from your labs! From long time contributors, to enhancing diversity, to education, to a specialized junior developer / new package contributor award; we want our members to be recognized for their outstanding contributions to the project:https://support.bioconductor.org/p/9152415/
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Levi Waldron (10:37:05) (in thread): > Somehow I just stumbled across this, but it’s great Maria!
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2023-06-06
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2023-06-07
Martin Grigorov (09:45:49): > Hi! What is the correct syntax for passing several arguments to configure.args on the command line: > > $ R CMD INSTALL --configure-args='--with-openbabel-lib=/home/biocbuild/openbabel-3.1.1/lib --with-openbabel-include=/home/biocbuild/openbabel-3.1.1/include/openbabel3' ChemmineOB > Warning: unknown option '--with-openbabel-include=/home/biocbuild/openbabel-3.1.1/include/openbabel3' > ... > > Both –with-openbabel-lib=… and –with-openbabel-include=… are valid, but the way I pass them is not correct
Martin Grigorov (09:49:20) (in thread): > I think I found it: > > R CMD INSTALL --configure-args='--with-openbabel-lib=/home/biocbuild/openbabel-3.1.1/lib' --configure-args='--with-openbabel-include=/home/biocbuild/openbabel-3.1.1/include/openbabel3' ChemmineOB >
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Kasper D. Hansen (10:54:28) (in thread): > Im surprised that one string (your first attempt) didn’t work, but if you have something that works now … It is kind of finicky
Martin Grigorov (11:03:29) (in thread): > It seems one needs to pass a ’—configure-args’for each argument
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Maria Doyle (09:11:15): > Hello<!channel>:wave:We’re redesigning the Bioconductor website and we need YOUR input:index_pointing_at_the_viewer:We’ve created a survey to understand the needs of our diverse user base. Whether you’re a wet lab biologist, student, data analyst, developer, system administrator, educator, or any other role, we’d love to hear from you! > > This is your chance to shape the future ofBioconductor.org ! Your experiences, challenges, and ideas will help us to enhance the website’s design and structure. > > The survey takes about 5-10 minutes and closes on Friday, June 23rd. Link:https://t.maze.co/169169456 We value your time and insights. Let’s improveBioconductor.org together!
Maria Doyle (10:05:29) (in thread): > We would greatly appreciate if you could share our survey with your networks to help us gather diverse perspectives. The more feedback we get, the better we can makeBioconductor.org for everyone! > > You can share the news by retweeting, reposting, or sending the survey link directly. Every share helps!:gratitude-thank-you:Twitter:https://twitter.com/Bioconductor/status/1668610761323859969 Mastodon:https://genomic.social/@bioconductor/110537136393527330 LinkedIn:https://www.linkedin.com/feed/update/urn:li:activity:7074382496020189184
2023-06-15
Lori Shepherd (02:46:34): > Yes we can update wiki. > We (the core)doesn’tmaintain anything on data camp so it’s whoever wrotethat’sresponsibility to update it.
Aedin Culhane (07:26:02): > Please retweet our message asking for people to complete the survey on the Bioconductor website. We are trying to get a good community responsehttps://twitter.com/bioconductor/status/1668610761323859969?s=12 . Thanks. - Attachment (Twitter): Bioconductor on Twitter > :mega: We’re redesigning the #Bioconductor website and we need YOUR input! > > Whether you’re a wet lab biologist, expert developer or other, your perspectives will shape Bioconductor’s future. Takes 5-10 minutes. Closes June 23. > :arrow_right:https://t.co/0F3DWIivPX > > #Bioinformatics #rstats
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2023-06-19
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Maria Doyle (06:52:33) (in thread): > Hello @channel:wave:Quick update on our Bioconductor redesign survey. We’ve mapped responses by countryhere and noticed some regions are underrepresented. > If you or your network are from these areas, we encourage you to participate or share the survey. > Survey only takes a few minutes and closes this Friday June 23rd:https://t.maze.co/169169456 Thanks for helping makeBioconductor.org more inclusive and user-friendly for our global community!:earth_africa::earth_americas::earth_asia:
2023-06-20
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2023-06-23
Maria Doyle (09:51:00): > Last chance<!channel>!:alarm_clock:Give your input on thebioconductor.org website survey before it closes today. Also, please share survey if your country is underrepresented in the responses map::world_map::earth_africa:bit.ly/biocwebsite - File (PNG): newplot (2).png
2023-06-26
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2023-07-01
Pedro Sanchez (04:29:02) (in thread): > Oh, thank you!!
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2023-07-02
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Pageneck Chikondowa (07:06:43): > hello,
Pageneck Chikondowa (07:07:08): > can you kindly send me a link to join capentries slack channel.
Maria Doyle (15:06:56) (in thread): > Hi Pageneck, you’ve been approved to join so you should be able to access the link you were sent now. If not, let me know.
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2023-07-06
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Maria Doyle (14:06:59): > :mega:Late poster abstracts for EuroBioc2023 in Ghent:flag-be:, September 20-22 can now be submitted until Aug 21! Don’t miss out, submit now:point_right:https://forms.gle/eQKzppMTuCx9wvWe6 :admission_tickets:Registration is open until Aug 31! Secure your spot now:point_right:https://eurobioc2023.bioconductor.org/registration/ :school:Got what it takes to host EuroBioC2024? The call is open! Apply here:point_right:https://forms.gle/tv4dEBdn3sDK5ZwE6 - Attachment (eurobioc2023.bioconductor.org): Registration > Registration
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2023-07-11
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2023-07-12
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Maria Doyle (12:44:18): > :mega:Reminder. In-person registration for #BioC2023 closes in just one week! Be sure to register before Wednesday 19th July! > > Registration for BioC2023:https://buff.ly/3nKEq72
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Kishori (19:02:03): > I am doing some 10x single-cell RNA seq analysis for mouse tumor data. I noticed a huge amount of Neutrophils (after processing through SingleR), but I was hoping to see some MDSC (Myyeloid-derived suppressor cells) as well. I don’t even see MDSC labels in MDSC. Has anyone encountered this situation or has any idea how to detect MDSC? Any comments would be much appreciated.
Peter Hickey (19:05:01) (in thread): > It’s very unlikely there are MDSC in the reference you are using, so there’s no way any cells in your dataset will get that label. BTW, questions like this are better posted to#singlecell-queries
Kishori (19:13:43) (in thread): > Thank you!
2023-07-13
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Janani Ravi (18:14:51): > Computational Biology + Bioinformatics R-Ladies+ aboard https://bioc2023.bioconductor.org As you know, the R / BioconductorBioC 2023 conference image.png
2023-07-17
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Physalia-courses (06:20:03): > Hey<!channel>! Physalia-courses (www.physalia-courses.org ) is gearing up to offer a series of Bioconductor courses in the upcoming months.:rocket:Don’t miss the chance to explore captivating topics like Network Analysis in Systems Biology, RNAseq, and much more!
Lisanna Paladin (10:13:10): > Reminder about this course, approaching the registration deadline!:loudspeaker:REMINDER: Calling all learners!:star2:Join us for****#BioNT’s first workshop titled “A practical introduction to bioinformatics and RNA-seq using Galaxy”!:dna::rocket::spiral_calendar_pad:Date: September 4, 2023 - September 8, 2023 :hourglass_flowing_sand:Registration Deadline: July 23, 2023 **:globe_with_meridians:https://www.cecam.org/workshop-details/1260
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Leonardo Collado Torres (15:33:55): > https://twitter.com/LIBDrstats/status/1681023981959401472 - Attachment (Twitter): LIBD rstats club on Twitter > From 2023-03-31 we have @geo_pertea on “Power Ranges: Efficient genome annotation handling in R” > > #GenomicRanges, #GenomicFeatures, #rtracklayer, #Rsamtools, #SummarizedExperiment, #qs > > #rstats @Bioconductor > > :spiral_note_pad: https://t.co/DSpTWxVTMf > :film_projector: https://t.co/ulbvXZlBVo
2023-07-18
Ismael Rodriguez (09:03:03): > Hello everyone:clap:, I’d like to share with you a new open-source R package we have developed at Appsilon for large-scale molecular data visualization:shiny.molestar .:bulb:Our package combines > 1. Molstar (https://molstar.org/ ) > 2. Shiny.react (Developed by Appsilon) > :bulb:This package exports various components that can be used in a Shiny application such as::sparkles:Molstar: Visualize proteins effortlessly.:mag:AlphaFoldMolstar: Visualize proteins from the AlphaFold database.:books:AlphaFoldDetails: Retrieve intricate details of AlphaFold protein IDs.:bulb:Visualizing the molecular associations that hold together large biomolecules gives us insights into their function and interactions (i.e., with small molecules), which is crucial for discovering new drug candidates. To understand how to use this R package please visit thispost . > > Feel free to reach out! - Attachment (appsilon.com): Unveiling a New Era in Molecular Visualization: Introducing shiny.molstar for Large Molecular Structures Visualization in R - R programming > Discover the capabilities of shiny.molstar for interactive molecular visualization, protein fold analysis, and more, leveraging R and Molstar.
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2023-07-19
Pedro Sanchez (14:13:57): > Does someone know how to accesscbiodfci.org by{cBioPortalData}(v2.8.2)? I am using the following code with my token downloaded today from the web, but it prints and error > > cbio <- cBioPortal(hostname = "[cbiodfci.org](http://cbiodfci.org)", protocol = "https", > token = "../misc/cbioportal_data_access_token.txt", > api. = "/api/api-docs") >
Marcel Ramos Pérez (16:22:51) (in thread): > Hi Pedro, I can help you with that. Would you mind opening an issue athttps://github.com/waldronlab/cBioPortalData ? Thanks!
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2023-07-20
Pedro Sanchez (04:02:49) (in thread): > Thanks Marcel! I’ll write it there ASAP !
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Alexandru-Ioan Voda (08:28:55): > Is there a recommended differential expression software for finding cyclical RNAs (eg circadian rhythm) in Bioconductor (for RNA-seq)? > > If I just fit a linear or ordinal regression with DESeq2 or something else, on 4 time-points, then I won’t pick up the things that are expressed like a cosine/cyclical function, right?
Krithika Bhuvanesh (10:36:51) (in thread): > If your data is total RNA, then all the RNA’s would be included. Once you do the gene annotation, you could use pathway analysis to find which pathways/ cell processes your genes belong to. See if any biological processes related to interests show up or not. Would such a solution work for you ?
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Alexander Bender (12:53:03) (in thread): > Cosinor regression is one of the more established methods in the field. I like limma for that since it’s so generic. You can apply the same strategy to almost any type of data. limma-voom or trend for RNA-seq.
Alexander Bender (12:54:33) (in thread): > a specialized Bioc package is discorhythm which wraps JTKcycle, some sort of cosinor regression and MetaCycle plus offers some basic qc and plotting things. Though I find limma is the most flexible, hence most powerful one.
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jgearing (22:24:47) (in thread): > The Cyclical Models section of this limma guide to design matrices could be helpful.https://bioconductor.org/packages/release/workflows/vignettes/RNAseq123/inst/doc/designmatrices.html#cyclical-models
2023-08-02
Harkirat Sohi (00:58:31): > @Harkirat Sohi has joined the channel
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Estefania Mancini (07:00:19) (in thread): > Hi@Alexandru-Ioan Voda! We worked in circadian rhythm and we dd this type of anaysis for RNA-Seq+Splicing:https://pubmed.ncbi.nlm.nih.gov/32314836/ , tell me if we can help you - Attachment (PubMed): Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana - PubMed > The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in their environment. However, developing a detailed understanding of how oscillations in mRNA levels are connected to oscillations in co/post-transcriptional …
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Martin Grigorov (09:14:37): > Hi! Are there any known problems withhttps://support.bioconductor.org/new/post/ at the moment ? I am trying to post a question but the page just reloads without any feedback. The post preview looks good to me.
Martin Grigorov (09:16:14) (in thread): > Not sure whether it is related or not: after the reload I need to “touch” the body to trigger rendering of the preview
Martin Grigorov (09:18:38) (in thread): > finally -https://support.bioconductor.org/p/9153572/ ! > I had to replace all single quotes in the code snippet (triple quotes) with double quotes to overcome the problem
Trisha Timpug (09:24:32): > @Trisha Timpug has joined the channel
Lori Shepherd (09:44:30) (in thread): > @Natay Aberrawe should make note of this to explore further.
Brian Gural (10:23:32): > @Brian Gural has joined the channel
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Qian Liu (16:33:03): > https://docs.google.com/presentation/d/1Dvtk-AN_JTDn90la0lqSBeYXJGamHlQ3I3OAoDRvOAM/edit?usp=sharing
2023-08-03
Nithya Rangasamy (02:09:25): > @Nithya Rangasamy has joined the channel
Martin Grigorov (07:08:54) (in thread): > Actually the problem is only with‘(Unicode\u2018) characters.'(ASCII code 39) are fine: > > The following objects are masked from 'package:matrixStats': // OK > * checking package vignettes in 'inst/doc' ... OK // NOT OK >
Scott Norton (11:02:05): > @Scott Norton has joined the channel
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Maria Doyle (15:36:35): > Hello everyone<!channel>:wave:, > > Thank you all for expressing interest in participating in our website redesign initiative. As revealed this week at BioC2023, we’re excited to share that we now have a preview of the newBioconductor.org !:tada:We kindly ask for less than 5 minutes of your time to complete our feedback survey bythis Sunday, 6th August. Bioconductor.org . Here’s the link to the survey:https://bit.ly/bioc-website-feedback2 Thank you again for your time and assistance. We are looking forward to your valuable feedback!:pray:
Ryan C. Thompson (15:39:21): > Please send another reminder after the conference is over for all of us that are enjoying the conference right now!
Hervé Pagès (15:41:25) (in thread): > Thanks Maria. The links above take me to the old website. What is the URL to the preview of the new website? Thanks again!
Ritika Giri (15:55:20): > @Ritika Giri has joined the channel
Andres Wokaty (16:20:57) (in thread): > I couldn’t submit without entering my email on the feedback. I was using a browser on my phone.
Maria Doyle (16:23:26) (in thread): > The preview is linked in the feedback survey (e.g. see screenshot below) but here is the direct linkhttps://bit.ly/bioc-website-preview - File (PNG): Screenshot 2023-08-03 at 16.22.01.png
Maria Doyle (16:24:16) (in thread): > > Jennifer Wokaty
Izabela Mamede (19:32:35): > Hello all tomorrow on the last session of BioC2023 me and Lucio Queiroz will be presenting our package demo for isoform specific biological interpretation of transcriptomic datahttps://github.com/luciorq/isoformic I invite everyone to join. We hope to do some live coding and get the community suggestions to submit this as a formal BioConductor package in the end of this year. - File (PNG): image.png
Izabela Mamede (19:33:10) (in thread): > Also the logo is great, so come join us even if it is just to say the logo is great <3
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2023-08-04
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2023-08-05
Maria Doyle (10:03:30): > Hope all BioC2023 attendees had good journeys back home! Just a quick reminder that the website feedback survey will be closing end of day tomorrow, Sunday, August 6th. We appreciate your input and feedback. > > Here’s the link to the survey:https://bit.ly/bioc-website-feedback2 Thank you!
2023-08-07
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2023-08-08
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Erica Feick (10:18:14): > It’s not too late to let us know what you think! Help us plan 2024 with your thoughts on BioC2023
Andres Wokaty (10:18:58): > Seeking Outreachy internship project proposals https://www.outreachy.org/communities/cfp/bioconductor/ If you want help crafting your project proposal, you’re welcome to reach out to me. I also spoke about proposing a project at the conference and our interns from the first cohort presented their projects. > > Mentors should read the mentor FAQ:https://www.outreachy.org/mentor/mentor-faq Full details about the Outreachy program and the internship timeline can be found on the Call for Participation page on the Outreachy website:https://www.outreachy.org/communities/cfp/
Richard Dushime (10:53:16): > Don’t Miss Out - Register Now for the RSE Asia Australia Unconference 2023! > Hey everyone, > Are you ready to delve into the exhilarating world of Research Software Engineering (RSE)? Brace yourselves, because the RSE Asia Australia Unconference 2023 is right around the corner, and we don’t want you to miss out!REGISTER HERE: RSEAA Unconference 2023 Registration This is your chance to connect, collaborate, and converse with an enthusiastic and diverse community passionate about RSE. The Unconference is a platform for everyone - whether you’re a seasoned professional, an enthusiast, or just curious about RSE. > Want to learn more? Hop onto ourOfficial Website and delve into the details. > To stay updated with the latest news, interesting facts, and the countdown to the Unconference, make sure you’re following us on social media: > * LinkedIn > * Twitter - RSE Australia > * Twitter - RSE Asia > We’d like to express our immense gratitude to our key partners, Australian Research Data Commons (@* ARDC_AU ) and Australian BioCommons (@* AusBiocommons ), and our allied partners: AARNet (@* AARNet ) and QCIF (@* qcifltd ). Your support makes this all possible! > Register today, mark your calendars, and join us in shaping the future of RSE. We can’t wait to meet you at the Unconference!****#RSEAA2023 #RSE** - Attachment (events.humanitix.com): RSE Asia Australia Unconference 2023 | Humanitix > RSE Asia Australia Unconference 2023, Hosted online, Wed 13th Sep 2023, 1:00 pm - Fri 15th Sep 2023, 5:00 pm AEST. Tickets are between $10-$20. Only on Humanitix - Attachment (RSE Asia Australia Unconference): Welcome to the RSE Asia Australia 2023 unconference! > Website for the RSE Asia Australia Unconference 2023 - Attachment (Twitter): RSE Australia and New Zealand (@rse_aunz ) / Twitter > We aim to build awareness of the diverse Research Software Engineer (RSE) roles, to connect volunteers in the domain, and to help build practical solutions. - Attachment (Twitter): RSE Asia Association (@RSE_Asia ) / Twitter > The #RSEAsia Association account.
jamie_park (13:03:04): > @jamie_park has joined the channel
2023-08-09
Ismael Rodriguez (10:53:58): > :rocket:We have good news for R/Shiny users involved in clinical trials!:microscope::dna:We’ve successfully adapted the R Submissions Pilot 2 Shiny App submitted to the FDA to our latest framework -#Rhino :bar_chart:Using a function of the {pkglite} package, we’ve made the R/Shiny app suitable for submission through the eCTD gateway.:bar_chart:Our open-source app (FDA pilot app) provides a groundbreaking example of an R/Shiny app that can be submitted to the FDA. > > The full story is here:https://appsilon.com/fda-clinical-trial-submissions-with-r-shiny-rhino/ - Attachment (appsilon.com): Advancing FDA Clinical Trial Submissions with R: Reproducing the R Submissions Pilot 2 Shiny App Using Rhino - R programming > Discover how to submit a Shiny app through the FDA e-CTD with Rhino. Optimize efficiency and compliance in the drug development process with R programming.
Krithika Bhuvanesh (16:02:17): > I’m looking for some small sized whole genome sequencing data for teaching. From human genome. Could be part of one chromosome so that the size of the data is small . Any suggestions ?
Abdullah Al Nahid (16:04:37) (in thread): > Is it possible to find such data with this tool?https://github.com/vanheeringen-lab/genomepy
Krithika Bhuvanesh (16:11:01) (in thread): > Thanks. Let me see
2023-08-10
Hans-Rudolf Hotz (01:58:47) (in thread): > Have a look at the example data of the QuasR package (https://code.bioconductor.org/browse/QuasR/tree/RELEASE_3_17/inst/extdata/ ). hg19sub contains three small fragments of chromososme 1,2 and 3 . Different sets of reads mapping these fragments, as well as the corresponding annotation are available. - Attachment (code.bioconductor.org): Bioconductor Code: Browse > Browse the content of Bioconductor software packages.
Rajesh Shigdel (11:07:29): > Microbiome data science with R/Bioconductorhttps://norbis.w.uib.no/microbiome-data-science-with-r-bioconductor/
Marcel Ramos Pérez (12:30:06) (in thread): > @Rajesh ShigdelIs this held in person only?
Rajesh Shigdel (12:52:46) (in thread): > yes it is
Lambda Moses (21:12:56): > Quick question for the Acknowledgement section of my paper: what’s thecancerdatasci.org organization that hosted Orchestra for Bioc conference workshops in the past years? Also, for Bioc2023, who hosted the Galaxy workshops? Bottom line, I need to acknowledge the organizations that hosted the workshops in which I demonstrated the contents of the paper.
Sean Davis (21:33:40) (in thread): > Hi,@Lambda Moses. I built and then maintained Orchestra. I own the domaincancerdatasci.org . The development and maintenance of Orchestra was unfunded. The compute costs were generously covered by thehttps://isb-cgc.appspot.com/ . - Attachment (isb-cgc.appspot.com): ISB-CGC > ISB-CGC Cancer Gateway in the Cloud
Lambda Moses (21:34:45) (in thread): > So I thank you and ISB-CGC for Orchestra.
Sean Davis (21:35:39) (in thread): > @Alex Mahmoudcan answer on the Galaxy front.
Sean Davis (21:37:08) (in thread): > I’d also suggest trying to generally acknowledge the many contributors (over 100) of the high-quality workshops. And the Bioc organizing committee work to build on the platform each year.
Alex Mahmoud (22:34:08) (in thread): > The underlying NSF Jetstream2 cloud for the Galaxy workshop instance has thiscitation and you can acknowledge ACCESS allocation BIR190004 for the compute. For the development, it’s a blurry line since some of it was just me developing on my own time but also some work funded by NIH project 2U24HG004059-17 so could acknowledge that too. Thank you! - Attachment (Jetstream2): Research > Jetstream 2 brings a powerful cloud-based environment to researchers around the United States.
2023-08-11
Krithika Bhuvanesh (11:22:50) (in thread): > I think this might be just what I’m looking for ! Thanks for sharing !
2023-08-12
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2023-08-14
Guido Putignano (03:13:08): > @Guido Putignano has joined the channel
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2023-08-15
Erica Feick (13:12:10): > Last call for your comments on the BioC2023 conference! Your thoughts shape conferences in the future, so please complete the survey atforms.gle/wk9mxJasKPUcFLtM7
Tamnjong Larry Tabeh (16:09:28): > @Tamnjong Larry Tabeh has joined the channel
2023-08-17
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2023-08-18
Anna Šenovská (04:44:41) (in thread): > Hi Laurent, do you know if the second workshop Analysis and Interpretation of Bulk RNA-Seq Data has still some free spaces? Also, I have a different question and I suppose you can answer that as a member of the organizing committee of the conference in Ghent. I am considering to submit a poster. However, I am a biologist, studying ALS snRNA-seq data and not even using bioconductor packages for that (I use seurat instead). Do you think a poster like that would be interesting to show at the conference? I am worried that the majority of the posters will be about package development and shiny apps.
Laurent Gatto (05:28:54) (in thread): > Hi Anna. Yes, there’s space for the workshop.
Laurent Gatto (05:28:56) (in thread): > Re your poster, what I can say is that’s it’s a Bioc conference, so some Bioc would be expected. You could possible frame your poster in a way to address your needs for scRNA-Seq, and how Bioc could (or is) address them. Having said that, nothing stops you from submitting your poster, and see whether it will be accepted - I can’t confirm any option.
Victor Yuan (12:34:37): > @Victor Yuan has joined the channel
2023-08-21
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2023-08-22
Juan Ignacio Eizaguirre (07:40:44): > @Juan Ignacio Eizaguirre has joined the channel
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Aedin Culhane (21:08:57): > Program for the MAQC meeting in Helsinki 10-12 sept - File (PDF): MAQC 2023_Sept11-12_2023-08-21_prelim agenda
2023-08-24
Lachlan Baer (01:11:23): > @Lachlan Baer has joined the channel
Aedin Culhane (09:31:13): > ICYMI theAstera Institute https://astera.org/science-opportunities/
Aedin Culhane (12:08:37): > Interesting seminar starting now Greetings Aedin Culhane, > > Thank you for registering to attend the Cancer Moonshot Seminar Series on August 24, 2023 from 12:00 PM to 1:00 PM ET. > > Theme: Spatial Data Analyses and AI Models for Cancer Research > Speakers: Adam Spannaus, Ph.D., Oak Ridge National Laboratory; Chenchen Zhu, Ph.D., Stanford University > Recommendations: Build a National Cancer Data Ecosystem and Generate Human Tumor Atlase > > Please download the attached calendar invite with the virtual access details. > > CMSS Webinar, August 24, 2023 12:00 PM Eastern Time (US and Canada) > Zoom Link:https://us02web.zoom.us/j/88532372706?pwd=bjRsbU5kL05lV1NDV3JvN3VLUms4Zz09 Passcode: 346805 > Webinar ID: 885 3237 2706 > International numbers available:https://us02web.zoom.us/u/kczOUZPiE6
2023-08-25
chihurumnanya ikevude (01:05:31): > Are you ready to embark on a remarkable journey into the world of programming seamlessly? The key to unlocking your full potential lies within the pages of “What I Wish I Knew Before Kickstarting My Programming Career” by the insightful Chukwuka Ikevude. This isn’t just a book – it’s your personalized roadmap to conquering the challenges and seizing the opportunities that lie ahead.:rocket:Start Your Journey Today: > Whether you’re a budding programmer or a seasoned pro, “What I Wish I Knew Before Kickstarting My Programming Career” is the catalyst you need for transformative growth. Don’t miss out on the chance to navigate your path to success with unwavering confidence.:chart_with_upwards_trend:Elevate Your Programming Journey – Get Your Copy Now!:chart_with_upwards_trend:Buy on Selar -https://selar.co/98s9n6 Buy on Amazon -https://a.co/d/8EyRBHs - File (JPEG): IMG-20230825-WA0004.jpg
Jared Andrews (16:54:08): > Are there any guidelines/have there been any discussions regarding packages that use rust via rextendr or similar?
Vince Carey (17:18:21): > no guidelines the only example i am aware of was withdrawn when u have a draft package can we have an early look?
Jared Andrews (17:23:56): > I don’t really have any hard and fast plans, I was more just curious (as I’d rather learn rust than cpp if I wanted more performant code).
Sridhar N (22:15:18): > :crab:
2023-08-28
Sean Davis (15:04:06): > Hi, all. We have a#fundingchannel to share or discuss funding opportunities that is underutilized.
Thurman Lincoln (17:48:59): > @Thurman Lincoln has joined the channel
2023-08-29
Sean Davis (10:17:52): > First#fundingpost is a joint NSF/UKRI program. - Attachment: Attachment > https://www.nsf.gov/pubs/2023/nsf23143/nsf23143.jsp > Funding opportunity jointly offered by UKRI and US NSF. > Proposals should develop informatics approaches and cyberinfrastructure resources to enable novel and more effective use of data in biological research. Proposals should address important current or emerging challenges faced by researchers, supporting generation of new knowledge from biological data. > Proposals should clearly identify their relevance to one of two biological informatics focus areas, either: > 1. Research to design novel or greatly improved research tools and methods or > 2. The implementation of, scaling of, or major improvements to research tools, products, and services for biology applicable to a wide range of researchers. > Proposals can be in any bioinformatics research area within the scope of both the NSF Directorate for Biological Sciences and BBSRC. Proposals should clearly describe their potential to advance and enable data driven research undertaken by biological research communities primarily supported by both NSF/BIO and BBSRC. > Proposals must be aligned to NSF’s Division of Biological Infrastructure informatics (Innovation) OR cyberinfrastructure (Capacity) programs, but NOT both. Principal investigators are advised to consult the appropriate program officers of both agencies to ensure that their portion of the project is compliant with the targeted program.
2023-08-30
Julia Lohr (08:02:29): > @Julia Lohr has joined the channel
Oluwafemi Oyedele (12:54:05): > Good Evening All, a colleague of mine want to learn how to perform GWAS, please can you suggest a very good book in which I can recommend to him that has all the implementations in R. Thank you very much!!!
Sagun Maharjan (13:06:10): > @Sagun Maharjan has joined the channel
Ching-Ho Chang (15:32:47): > @Ching-Ho Chang has joined the channel
Aaron Olschefski (16:22:55): > @Aaron Olschefski has joined the channel
Krithika Bhuvanesh (21:58:17) (in thread): > Its not in R, but i have used PLINK suite of tools for GWAS analysis. Their newer version is very fast. Lot of documentationhttps://zzz.bwh.harvard.edu/plink/plink2.shtml
2023-08-31
Oluwafemi Oyedele (09:12:14) (in thread): > Thank you@Krithika Bhuvanesh
Ray Su (10:28:56) (in thread): > You might also be interested in reading this paper:https://www.nature.com/articles/s43586-021-00056-9#Sec34 The book chapter below also provides examples of how to call Plink functions in R.https://genomicsbootcamp.github.io/book/your-first-plink-tutorial.html - Attachment (Nature): Genome-wide association studies > Nature Reviews Methods Primers - Uffelmann et al. describe the key considerations and best practices for conducting genome-wide association studies (GWAS), techniques for deriving functional… - Attachment (genomicsbootcamp.github.io): Chapter 7 Your first PLINK tutorial | Genomics Boot Camp > This book shows in a beginner friendly way how to handle and analyse genomic data.
Maria Doyle (11:44:00): > :mega:BioCAsia2023 abstract submission now open ! - File (PNG): BioCAsia2023.png
Maria Doyle (11:45:29) (in thread): > Please see below for more details. > > Dear Colleagues, > > We are delighted to invite you to theJoint Bioconductor Asia – Hong Kong Bioinformatics Symposium 2023 ,October 16-17, 2023 https://biocasia2023.bioconductor.org This joint conference aims to foster collaboration, exchange knowledge, and explore cutting-edge developments in bioinformatics research in Hong Kong and beyond. The event will feature an engaging program that includes informative bioinformatics research sessions, a dedicated workshop on Bioconductor and R, and enlightening keynote presentations by renowned speakers. > > We are now acceptingabstract submissions September 15th open for registration October 1st - October 16, AM: Bioinformatics Research Session 1- October 16, PM: Bioconductor and R Workshop- October 17, AM: Bioinformatics Research Session 2- October 17, PM: Bioinformatics Research Session 3 For more information about the symposium, please visit our website. You can also find updates and news by following us on Twitter [@Bioconductor] . > Thank you for your attention, and we look forward to welcoming you to the symposium. > > Best regards, > > Organising Committee (Joshua, Yuanhua, Xueyi, Yingying, Jiguang, Can, Dario and Ellis)
Ebru Kocakaya (15:01:19): > @Ebru Kocakaya has joined the channel
2023-09-01
Y-h. Taguchi (01:16:00): > I am not sure if it is suitable to post this here, My paper that announce implementation to Bioconductor was accepted in academic journal. Thanks for your cooperations.https://www.frontiersin.org/articles/10.3389/frai.2023.1237542/full - Attachment (Frontiers): Application note: TDbasedUFE and TDbasedUFEadv: bioconductor packages to perform tensor decomposition based unsupervised feature extraction > MotivationTensor decomposition (TD)-based unsupervised feature extraction (FE) has proven effective for a wide range of bioinformatics applications ranging from biomarker identification to the identification of disease-causing genes and drug repositioning. However, TD-based unsupervised FE failed to gain widespread acceptance due to the lack of user-friendly tools for non-experts.ResultsWe developed two bioconductor packages—TDbasedUFE and TDbasedUFEadv—that enable researchers unfamiliar with TD to utilize TD-based unsupervised FE. The packages facilitate the identification of differentially expressed genes and multiomics analysis. TDbasedUFE was found to outperform two state-of-the-art methods, such as DESeq2 and DIABLO.Availability and implementationTDbasedUFE and TDbasedUFEadv are freely available as R/Bioconductor packages, which can be accessed at https://bioconductor.org/packages/TDbasedUFE and https://bioconductor.org/packages/TDbasedUFEadv , respectively.
Kasper D. Hansen (09:30:27): > Congratulations. There is also a#papersandpreprintschannel, which - perhaps - is more appropriate
Eddie Ruiz (09:31:34): > @Eddie Ruiz has joined the channel
2023-09-02
Y-h. Taguchi (03:26:14) (in thread): > Thanks, I will post it there and will do it next time.
2023-09-04
Oluwafemi Oyedele (05:36:41) (in thread): > Thanks@Ray Su
Anna Lewkowicz (16:49:50): > @Anna Lewkowicz has joined the channel
2023-09-05
Lori Shepherd (08:21:49): > The release schedule for Bioconductor release 3.18 can be found at:https://bioconductor.org/developers/release-schedule/ . Please be mindful of important deadlines.
Pooja Shah (11:09:45): > @Pooja Shah has joined the channel
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Serges Shilo (Earth Sentry) (17:40:12): > @Serges Shilo (Earth Sentry) has joined the channel
2023-09-06
Helene Hemmer (03:14:38): > @Helene Hemmer has joined the channel
Aedin Culhane (07:01:42) (in thread): > and there is a#humble-bragchannel too
Erica Feick (10:48:19): > :tada:The videos from BioC2023 are now live on theBioconductor YouTube channel . - Attachment (YouTube): BioC2023 > Bioconductor conference, August 2-4, 2023, Dana-Farber Cancer Institute, Boston, MA.
2023-09-07
Sonali Tamhankar (13:01:41): > @Sonali Tamhankar has joined the channel
2023-09-08
Ismael Rodriguez (06:32:16): > Hello there!:star2::tada:I’ll be attending the Posit Conf 2023 in Chicago next week:dart:Is anyone else in this community going to be at the event? It would be an absolute pleasure to connect over coffee and chat!:coffee:
Jaclyn Mallard (13:51:42): > @Jaclyn Mallard has joined the channel
2023-09-10
Jane Zhang (17:56:46): > @Jane Zhang has joined the channel
2023-09-11
Amarinder Singh Thind (20:15:35): > Heloo, I am in search of a comprehensive dataset that includes matched WGS/WES, RNA-seq, and EPIC array (optional) data across various cancer types for one of my research projects. Any suggestions?
Steve Lianoglou (23:26:20) (in thread): > Something likeThe Cancer Genome Atlas ? - Attachment (ccg - National Cancer Institute): The Cancer Genome Atlas Program (TCGA) > The Cancer Genome Atlas (TCGA) is a landmark cancer genomics program that sequenced and molecularly characterized over 11,000 cases of primary cancer samples. Learn more about how the program transformed the cancer research community and beyond.
2023-09-12
Vince Carey (06:43:01) (in thread): > andits curation andrelated utilities - Attachment (Bioconductor): curatedTCGAData > This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-’omics experiment. - Attachment (Bioconductor): TCGAutils > A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.
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Amarinder Singh Thind (19:41:11) (in thread): > Thank you very much. I am searching something, where I can get sufficient meta (clinical data), so prefer some big study with sufficient sample size along with metadata.
2023-09-13
Vince Carey (06:18:16) (in thread): > https://docs.cancergenomicscloud.org/docs/tcga-metadata - Attachment (The CGC Knowledge Center): TCGA metadata > ABOUT METADATA FOR DATASETS > TCGA metadata
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2023-09-14
Maria Doyle (04:23:39) (in thread): > :alarm_clock:Reminder that abstract submission for BioCAsia closes tomorrow! Don’t miss out!
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shaimaa Elsafoury (14:47:47): > Hi Do you have any recommendations for health data analytics diplomas (using r)? Thanks
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2023-09-15
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2023-09-17
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2023-09-18
Dario Strbenac (00:00:00): > Bioconductor Asia Symposium in Hong Kong in Octoberabstract closing extended to Wednesday. - Attachment (hku.au1.qualtrics.com): Qualtrics Survey | Qualtrics Experience Management > The most powerful, simple and trusted way to gather experience data. Start your journey to experience management and try a free account today.
Hervé Pagès (00:41:26): > Hi there, a colleague of mine needs help with a large single-cell sequencing data set generated with the Tapestri Platform (from Mission Bio), and analyzed in Python. If you know a bioinformatician who has worked with these tools and is willing to help, please DM me. Thanks!
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Sridhar N (11:06:36): > @Hervé PagèsI have worked with Tapestry, Mission bio has their own analysis software that spits out hierarchy and most of the things that are useful, what help do they need? Is it data munging or something more custom.
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2023-09-19
Maria Doyle (03:30:08): > :mega:Bioconductor Community Survey on Twitter/X Use social media working group have created a short (< 5 mins) survey to gather your thoughts and preferences. Your feedback is important to shaping the future of how we communicate as a community.:link:Survey link:https://t.maze.co/187240083 Please note that the survey will close onTuesday, 3rd October
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2023-09-20
Hervé Pagès (01:53:07) (in thread): > Thanks@Sridhar N. I don’t have much details and I don’t know how they want to proceed. Let me check with them.
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Maria Doyle (04:26:07): > :movie_camera:Watching the EuroBioC2023 live stream this week?:rocket:Engage with the community and join the Virtual Social Media Challenge! It’s the perfect way to connect, share, and have some fun while streaming.:link:Need more info? Check out the detailshere . - Attachment (genomic.social): Bioconductor (@bioconductor @genomic.social ) > Attached: 1 image > > Are you planning to live stream the awesome talks at EuroBioC2023!? https://eurobioc2023.bioconductor.org/schedule/
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Jaykishan (05:01:07): > @Maria Doylehello guys i am new to MEDIP package i have 6 bam file i wanted to analyse differential MEDIP analysis can anyone guide me through some tutorial > > Thank you
Maria Doyle (05:19:48) (in thread): > Hi@Jaykishan, > > A great place to start would be the official vignette:https://bioconductor.org/packages/release/bioc/vignettes/MEDIPS/inst/doc/MEDIPS.pdf If you have any questions or run into any issues while using MEDIPS, the Bioconductor support forum is a fantastic resource. You can specifically ask questions related to MEDIPS using this link:https://support.bioconductor.org/tag/medips/ Hope this helps, and best of luck with your analysis!
Maria Doyle (05:29:19) (in thread): > Prize for virtual winner is box of Belgian chocolates posted to you!:chocolate_bar:
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Maria Doyle (06:35:43): > Lunch break now:knife_fork_plate:is good time to enter the challenge:camera: - File (PNG): selfie-frame.png
Simon Pearce (06:38:02) (in thread): > I would highly recommend using the qsea package instead of MEDIPS.
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2023-09-21
Ahmad Al Ajami (05:30:39) (in thread): - File (PNG): image.png
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2023-09-22
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Dario Strbenac (07:00:12): > The DataFrame section of S4Vectors’ vignette is empty:astonished: - File (PNG): Missing
Hervé Pagès (13:34:03) (in thread): > Fixed:https://github.com/Bioconductor/S4Vectors/commit/208afb7565d8881216a1303e4577564e3848af44
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2023-09-24
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2023-09-26
Lisanna Paladin (11:29:57): > Calling all learners!:star2:Join us for #BioNT’s second workshop titled “From zero to hero with Python’’!:dna::rocket:Are you eager to acquire the foundational skills of coding using the Python programming language? Join us at BioNT, for a 4-day workshop (comprising half-day sessions) designed to introduce Python3 programming to individuals with limited or no prior coding experience. By the end of this workshop, you will also gain insight into Jupyter Book and learn how to host a website on GitLab. > > Don’t miss out on this incredible opportunity! Visit our event webpage now to discover the program details, meet the organising team, and submit your application. Remember, participation in the workshop is completely free, but seats are limited! > > #LearningOpportunity #BioinformaticsWorkshop #DigitalLifeSciences #NetworkForTraining #ComputationalLifeSciences:globe_with_meridians:https://www.cecam.org/workshop-details/1265
2023-09-30
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2023-10-02
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2023-10-03
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Aleksey Chepovoi (09:11:56): > Hi everyone! We’re working on a platform that aims to connect startup founders and top-level IT talents: developers, designers, product managers, etc. > > Today we’ve launched on Product Hunt and would appreciate your feedbackhttps://developers.expertremote.io :wink: - Attachment (Product Hunt): Expert Remote - Hire remote developers vetted for tech & soft skills | Product Hunt > Choose from 400+ developers, AI/ML engineers, data scientists, UI/UX designers, product managers, DevOps, QAs, etc. All our talents have been vetted for technical and communication skills. Sign up this week to get a 10% discount on all hiring for 1 year! - Attachment (Expert Remote): Careers - Expert Remote > Join Expert Remote and get matched with the best US/EU startups. Only long-term well-paid projects with payment guarantee.
kan (09:42:32): > @kan has joined the channel
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Ismael Rodriguez (10:58:26): > Hello folks, I am proud to announce that our Rhino framework has made it to the pharmaverse repository of open-source packages for clinical trials reporting (https://pharmaverse.org/ ). > > Are you already using Rhino in your Shiny apps? - Attachment (pharmaverse.org): pharmaverse > This is meta description - File (PNG): image.png
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2023-10-04
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Chiagoziem David (04:14:19): > :wave:Hi everyone!
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Ajoke Yusuf (07:30:14): > Hi@Chiagoziem David. Welcome to the community. Free free to ask questions when you’re stucked
Iram Jamshed (07:33:57): > Hello everyone. I am an Outreachy applicant, very excited and enthusiast to contribute in this project. I have done my Bachelors and Masters in Biotechnology. I have also worked as a Research Fellow in All India Institute for Medical Sciences(AIIMS), New Delhi, India. I believe my background and passion for research completely aligns with the project requirements. I’m thrilled to join this community and look forward to engaging in insightful discussions and potential contributions. May I humbly inquire how to begin?:blush:
Joan C. Chukwuemeka (07:51:32): > Welcome@Iram JamshedOn how to begin - Check my response here:point_right:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696320152137519?thread_ts=1696284904.239279&cid=C04RATV9VCY - Attachment: Attachment > @Onalo Deborah There is an information on the GitHub Issues page (https://github.com/waldronlab/BugSigDBcuration/issues/94 ) with a form link: > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task.
Chinwendu Enyinna (07:51:58) (in thread): > Hi Iram:wave:, welcome to the community You can check out the#bugsigdbchannel. Most of the conversations for Outreachy applicants go on there.
Iram Jamshed (07:59:03): > Thank you so much for your response!
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Peace Sandy (08:52:41): > Welcome Outreachy Applicant ! > Kindly join the#bugsigdbchannel to get started and get more information on how to go about your task.
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Hervé Pagès (12:10:32) (in thread): > @Iram JamshedAlso please note that Outreachy applicants are encouraged to join the#outreachychannel for all Outreachy related discussions. Best
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2023-10-05
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Nana Fidausi Mohammed (14:17:38): > Hi everyone, I am Nana Fidausi and I’m an outreachy applicant. I’m happy to meet you all and also contribute to this project:wave:
Chioma Onyido (14:22:43) (in thread): > Hi Nana.:wave:Welcome to the community!
Andres Wokaty (14:22:56) (in thread): > Welcome Nana! I encourage you to join the#bugsigdbchannel for discussions related to Microbiome Study Curation.
Nana Fidausi Mohammed (16:02:34) (in thread): > @Chioma OnyidoThank you so much
Nana Fidausi Mohammed (16:04:47) (in thread): > I have already. Thank you so much@Andres Wokaty
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2023-10-06
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Hodan Abdirisak (04:26:53): > A Warm Hello to the Bioconductor Community! > > My name is Hodan Abdirasak and I from Somalia. > I am honored to be part of this esteemed program as an Outreachy intern. I learned veterinary medicine in my first degree with years of experience, with a strong interest in research and passion with IT related programs. > The prospect of contributing to open source projects and collaborating with experts in the field is incredibly exciting to me. I am excited to connect with all of you, learn from your experiences, and engage in meaningful discussions > > Thank you all for your warm welcome, and I look forward to embarking on this enriching journey together
Chioma Obioha (06:20:13): > @Chioma Obioha has joined the channel
Chioma Obioha (06:31:42): > Hello everyone, my name is Chioma Obioha. I’m a data analyst from Nigeria. I am delighted about this learning phase and can’t wait to contribute to this exciting project. Please how do I start. Thank you
Chinwendu Enyinna (06:35:11) (in thread): > Hi@Chioma Obioha,welcome to the community. Kindly join the#bugsigdbchannel to get started. You’d also get every information you need there.
Chinwendu Enyinna (06:36:34) (in thread): > Hi@Hodan Abdirisak,welcome to the community. Kindly join the#bugsigdbchannel to get started. You’d also get every information you need there.
Hodan Abdirisak (06:39:21) (in thread): > Thanks@Chinwendu EnyinnaI joined the channel
Hodan Abdirisak (06:40:14): > Thanks@Chinwendu Enyinnafor your response
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Chisom Obidike (06:43:55): > Hello everyone, my name is Chisom Obidike, from Nigeria. I am excited about this opportunity and hope to make the best of it.
Nwajei Edgar (07:43:01) (in thread): > Welcome Chisom:hugging_face::hugging_face:
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Hodan Abdirisak (08:02:23) (in thread): > @Chisom Obidikewelcome to this valuable community hope you enjoy to join here
Sara Mohammed (08:17:56): > Hi, I’m Sara. Nice to meet all. I’m excited to be here.
Hodan Abdirisak (08:46:29) (in thread): > Welcome@Sara Mohammed
Hodan Abdirisak (08:47:52) (in thread): > Also join#bugsigdbchannel where to get start
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2023-10-07
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Sara Mohammed (10:46:57) (in thread): > I have done that. Thank you.
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Chiagoziem David (21:48:20): > How’s it going guys
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Hodan Abdirisak (23:07:49): > Nice and well
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2023-10-08
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2023-10-09
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nyong godwill (05:47:47): > Hi, Everyone am Godwill from cameroon my initial application was accepted, will love to contribute to this project how do i get start
Nana (05:53:57): > @nyong godwillyou are welcome. On the slack check pinned messages all you seek is there to get you started
Hodan Abdirisak (05:59:12): > @nyong godwillwelcome to Community check to join#bugsigdb
Israel Anguiano (06:00:06): > @Israel Anguiano has joined the channel
nyong godwill (06:01:53): > ok thank you@Hodan Abdirisak
Mildred Anashie (06:20:49) (in thread): > Welcome@nyong godwillJust like@Hodan Abdirisaksaid join the#bugsigdbchannel > If you need any clarification along the linedon’thesitate to ask
nyong godwill (06:21:28) (in thread): > ok thank you
winnie (06:25:57): > @winnie has joined the channel
Sumbal (07:48:22): > @Sumbal has joined the channel
Sumbal (08:25:05): > Hello everyone! I am Sumbal from Pakistan, an Outreachy applicant and eager to contribute to the project.
Onyewuchi Esther Chikamso (08:25:37) (in thread): > Welcome sumbal!
Onyewuchi Esther Chikamso (08:26:27) (in thread): > Start by visiting the GitHub link.https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page . As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:link )link )link )link )link ) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount ) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499 . Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation .
Hodan Abdirisak (08:30:56) (in thread): > Welcome@SumbalJoin#bugsigdbchannel
Peace Sandy (09:32:20) (in thread): > Welcome
Mildred Anashie (09:57:18) (in thread): > Welcome
Odigiri Great Alume (10:07:20) (in thread): > You are welcome:hugging_face:
Aedin Culhane (12:44:41): > For anyone not in the eurobioc channel, the chapGPT description of Bioconductor (in the style of …) are so much fun…https://community-bioc.slack.com/archives/C05S0BZ3PM0/p1695375150073709 - Attachment: Attachment > Last night we interviewed some historical figures about Bioconductor. Here’s what they had to say: > https://chat.openai.com/share/3911ad51-7e3d-4ed7-a299-38caa1a64500 > > Inspiration for pitching Bioconductor to newcomers!:bulb:
Nana (13:20:06) (in thread): > Welcome
Steve Lianoglou (15:17:51) (in thread): > These are great, thanks for sharing!
Adeniji Agbolade (17:05:36): > @Adeniji Agbolade has joined the channel
Monika (23:42:16): > @Monika has joined the channel
2023-10-10
claudia isabel reyes moreno (00:16:48): > @claudia isabel reyes moreno has joined the channel
Oluchi Nwankwo (07:54:14): > @Oluchi Nwankwo has joined the channel
Bianca (09:03:47): > @Bianca has joined the channel
JulietMadu (09:17:58): > @JulietMadu has joined the channel
AKSHAYA (10:08:34): > @AKSHAYA has joined the channel
Björn Grüning (13:40:28): > @Björn Grüning has joined the channel
Krithika Bhuvanesh (15:57:40) (in thread): > The “Shakespearian sonnet” one can be sung in the same tune of the “in dublin’s fair city…”
Chima Gerald Ukwuoma (17:30:02): > @Chima Gerald Ukwuoma has joined the channel
2023-10-11
Leong Benny (06:42:17): > @Leong Benny has joined the channel
JulietMadu (07:40:59): > Hi > Please how do I begin the contribution
Nokuthula (07:52:44): > @Nokuthula has joined the channel
Hodan Abdirisak (08:05:01) (in thread): > Welcome find there how to contribute firsthttps://github.com/waldronlab/BugSigDBcuration/issues
Hodan Abdirisak (08:05:28) (in thread): > Also join#bugsigdbchannel
Julian (08:36:49): > @Julian has joined the channel
Francisca_Eze (13:34:10): > @Francisca_Eze has joined the channel
Fortune Nnamdi (18:51:21) (in thread): > And when you join the channel, try to read all pinned messages.It’llmake things a little bit easier for you.
Fortune Nnamdi (18:52:50) (in thread): > @JulietMaduYou ’ll find it at the top of the page - File (JPEG): IMG_5427
2023-10-12
Shruti Pal (04:22:09): > @Shruti Pal has joined the channel
Odigiri Great Alume (06:51:46) (in thread): > After reading the articles. Watch the videos on PREP WORK. then download the annotated pdf and study it. Thereafter start filling the surveys. You are sure to find all answers to the survey in the pdf. > > Reach out when you need help okay.
JulietMadu (06:54:10): > Please can someone explain this part , I don’t understand it - File (JPEG): Screenshot_20231012-115208_Chrome.jpg
Odigiri Great Alume (09:11:43) (in thread): > While reading the annotated pdf, You are going to see a mention of some organisms that are abundant or that increased after treatment was introduced to the samples. Copy one of them and go to NCBI taxonomy browser (by following the link provided). Next paste it in the search bar and search. A list of bacterial will pop out, you will then click on the one that best matches the bacteria you searched for. Just right after you click you will find the NCBI ID, usually a 3-6 digit. The taxa name and the rank will also be there. So fill your form with the info. > > I hope this helps. > Reach out if you have questions:clinking_glasses:
Andres Wokaty (10:01:28) (in thread): > @JulietMaduThis is a gentle reminder to ask questions like these on the#bugsigdb.
Uchechukwu Favour Ojunta (11:20:09): > @Uchechukwu Favour Ojunta has joined the channel
Erica Feick (12:18:42) (in thread): > Love the Star Wars one!
Ulenyo Attah (18:54:28): > @Ulenyo Attah has joined the channel
2023-10-13
Frank-Opigo Emmanuel (04:07:41): > @Frank-Opigo Emmanuel has joined the channel
Francisca_Eze (09:36:34): > Hello everyone, My name is Francisca Eze, and I am from Nigeria. I am a budding data analyst with a curious mind and a willingness to learn. I am happy to contribute to this project.
Nancy Wairimu Nyambura (09:45:05): > @Nancy Wairimu Nyambura has joined the channel
Mildred Anashie (10:01:52) (in thread): > welcome@Francisca_Ezeplease do join the#bugsigdbchannel if you haven’t
Hodan Abdirisak (10:19:35): > @Francisca_Ezewelcome to the community kindly Join#bugsigdb
Hodan Abdirisak (10:20:17): > Read the pinne masseges
Francisca_Eze (11:42:35): > thanks@Hodan Abdirisak
Francisca_Eze (11:43:09) (in thread): > thanks@Mildred Anashie
Odigiri Great Alume (18:13:44) (in thread): > You are welcome dear
2023-10-14
Manka Velda Manjong (05:15:19): > @Manka Velda Manjong has joined the channel
Manka Velda Manjong (05:21:31): > Hi everyone, I am Manka Velda, outreachy applicant eager to contribute to this project
Hodan Abdirisak (05:49:46): > @Manka Velda Manjongwelcome to the community kindly Join#bugsigdbchannel
Hodan Abdirisak (05:49:54): > Read the pinned massage
Mildred Anashie (05:53:20) (in thread): > Welcome@Manka Velda Manjong
Mariam Taleeb (13:41:53): > @Mariam Taleeb has joined the channel
2023-10-15
Rosita Uqueio (03:33:33): > @Rosita Uqueio has joined the channel
Boyd Tarlinton (05:17:33): > @Boyd Tarlinton has joined the channel
Yuanhua Huang (20:46:11): > Joint Bioc Asia - HK Bioinfo Symposium 2023 https://hku.zoom.us/j/91657475464?pwd=cEZ1YVY4VjIvRUFvNE14WTVmdnVYQT09 Meeting ID: 916 5747 5464 > Password: 135854
Karthik Desingu (23:47:07): > @Karthik Desingu has joined the channel
2023-10-16
Maria Doyle (06:16:19) (in thread): > Thanks for sharing the Zoom link! For those looking for the schedule for the symposium, you can find it here:https://biocasia2023.bioconductor.org/
Omoyemi (06:16:46): > @Omoyemi has joined the channel
Adanwam (07:14:49): > @Adanwam has joined the channel
Akorita Nehemiah (08:01:02): > @Akorita Nehemiah has joined the channel
saskia (18:27:18): > Reminder elections for the Code of Conduct Committee close on the 31st of October, please consider applying! This is a great opportunity to give back to the Bioconductor community and also gain some experience with leadership.https://docs.google.com/forms/d/e/1FAIpQLSeTRs3m3-XNM7iGs0kyHfoaXNiwRVsgebmce10t0ieKfamaPg/viewform?usp=sf_link
raphael miyoyo (20:11:29): > @raphael miyoyo has joined the channel
2023-10-17
Himmi Lindgren (02:32:07): > @Himmi Lindgren has joined the channel
Nana (03:41:30): > @saskiawould love to participate…will fill the form. please grant me access have requested for one .chinelsy@gmail.com
Kunal Bagga (04:09:58): > @Kunal Bagga has joined the channel
Chahat Bhatia (05:08:17): > @Chahat Bhatia has joined the channel
Hodan Abdirisak (05:33:04): > @saskiais it open to outreachy participants? Or only for particular applicants required
saskia (17:44:46): > This is open to anyone who considers themselves part of the Bioconductor community
Dario Strbenac (20:10:06): > Is there any downtime for the experiment hub? > > > pancreasMuraro <- MuraroPancreasData(ensembl = FALSE) > C:\Users\dstr7320\AppData\Local/R/cache/R/ExperimentHub > does not exist, create directory? (yes/no): yes > Error: failed to load resource > name: EH2692 > title: Muraro pancreas counts > reason: 1 resources failed to download > In addition: Warning messages: > 1: download failed > web resource path: '[https://experimenthub.bioconductor.org/fetch/2708](https://experimenthub.bioconductor.org/fetch/2708)' > local file path: 'C:\Users\dstr7320\AppData\Local/R/cache/R/ExperimentHub/2fa433272d57_2708' > reason: Conflict (HTTP 409). > 2: bfcadd() failed; resource removed > rid: BFC3 > fpath: '[https://experimenthub.bioconductor.org/fetch/2708](https://experimenthub.bioconductor.org/fetch/2708)' > reason: download failed > 3: download failed > hub path: '[https://experimenthub.bioconductor.org/fetch/2708](https://experimenthub.bioconductor.org/fetch/2708)' > cache resource: 'EH2692 : 2708' > reason: bfcadd() failed; see warnings() >
Kristyna Kupkova (23:25:12) (in thread): > I am having the exact same issue for some of the datasets from GenomicDistributionsData package.
2023-10-18
Lori Shepherd (08:17:16) (in thread): > There shouldn’t be. I’ll investigate this morning.
Lori Shepherd (09:07:12): > @Erdal Cosgunhas something changed on the Azure storage space ? > > > curlGetHeaders("[https://experimenthub.bioconductor.org/fetch/2708](https://experimenthub.bioconductor.org/fetch/2708)") > [1] "HTTP/1.1 302 Found\r\n" > [2] "Date: Wed, 18 Oct 2023 13:06:04 GMT\r\n" > [3] "Server: Apache/2.4.18 (Ubuntu)\r\n" > [4] "X-XSS-Protection: 1; mode=block\r\n" > [5] "X-Content-Type-Options: nosniff\r\n" > [6] "X-Frame-Options: SAMEORIGIN\r\n" > [7] "X-Powered-By: Phusion Passenger 4.0.46\r\n" > [8] "Location:[https://bioconductorhubs.blob.core.windows.net/experimenthub/scRNAseq/muraro-pancreas/2.0.0/counts.rds](https://bioconductorhubs.blob.core.windows.net/experimenthub/scRNAseq/muraro-pancreas/2.0.0/counts.rds)\r\n" > [9] "Status: 302 Found\r\n" > [10] "Content-Type: text/html;charset=utf-8\r\n" > [11] "\r\n" > [12] "HTTP/1.1 409 Public access is not permitted on this storage account.\r\n" > [13] "Transfer-Encoding: chunked\r\n" > [14] "Server: Windows-Azure-Blob/1.0 Microsoft-HTTPAPI/2.0\r\n" > [15] "x-ms-request-id: 31fa6d5a-401e-0030-4ac3-0141f3000000\r\n" > [16] "x-ms-version: 2009-09-19\r\n" > [17] "Date: Wed, 18 Oct 2023 13:06:04 GMT\r\n" > [18] "\r\n" > attr(,"status") > [1] 409 > > As indeed there is a 409 public access is not permitted on this storage account?
Lori Shepherd (09:31:33) (in thread): > True for both ExperimentHub and AnnotationHub. see also open issues :https://github.com/Bioconductor/ExperimentHub/issues/33 andhttps://github.com/Bioconductor/AnnotationHub/issues/44
PATIENCE ONAH (11:54:07): > @PATIENCE ONAH has joined the channel
saskia (17:05:18) (in thread): > Totally open to outreachy participants
2023-10-19
Timur (02:27:58): > @Timur has joined the channel
dorothyk (03:56:32): > @dorothyk has joined the channel
Karthik Nair (05:29:37): > @Karthik Nair has joined the channel
Lori Shepherd (07:05:09): > The hubs issue should be resolved now. thank you for your patience and understanding
Aedin Culhane (13:17:18): > R in Pharma is a free conference. Registration is still open. Its online, Oct 24-26? Register for a workshop or to hear talkshttps://rinpharma.com - Attachment (rinpharma.com): R/Pharma > R/Pharma. The conference for all things R related in the Pharma industry
2023-10-21
Ukwueze Pascaline Nnenna (00:14:25): > @Ukwueze Pascaline Nnenna has joined the channel
Michael (05:59:45): > @Michael has joined the channel
Michael (06:02:00): > Hello guys… Excited to work with the team
António Pedro (09:02:16): > @António Pedro has joined the channel
Doreen Wanyama (14:09:02): > @Doreen Wanyama has joined the channel
2023-10-23
Daniel Niiaziiev (07:07:42): > @Daniel Niiaziiev has joined the channel
Chiagoziem David (12:30:28): > hello
Dan Schnell (14:40:42): > @Dan Schnell has joined the channel
2023-10-24
Monica L. Rojas-Peña (22:03:11): > @Monica L. Rojas-Peña has joined the channel
2023-10-25
Changqing (00:12:49): > @Changqing has joined the channel
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Lori Shepherd (16:13:23): > Bioconductor Core Team is pleased to release Bioc 3.18! Thank you to all developers and community members for contributing to the project. The full release announcement can be found at:https://bioconductor.org/news/bioc_3_18_release/
2023-10-26
Janetta Top (10:26:38): > @Janetta Top has joined the channel
Brian Schilder (13:50:44): > Hi everyone! I’ve been trying to brainstorm ways to best sustain open-source projects in the long-run.specifically rworkflows. I think there may be some unique opportunities with foundational projects likerworkflowswith a potentially wide appeal to the R community. I’ve kicked things off with several linked issues in the 2nd comment, but any and all ideas/experiences/examples would be most welcome!:sparkles::pray::sparkles:https://github.com/neurogenomics/rworkflows/discussions/93 - Attachment: #93 :mantelpiece_clock: Longevity :mantelpiece_clock:
2023-10-27
Jagadeesh Puvvula (10:42:02): > @Jagadeesh Puvvula has joined the channel
Michael Steinbaugh (10:55:50): > is anybody else seeing thatr-project.org is down currently?
Marcel Ramos Pérez (11:04:36) (in thread): > it looks like it’s down for everyone
Brian Schilder (11:12:24) (in thread): > yes! sames here, just noticed it via GitHub Actions
Kasper D. Hansen (12:42:31) (in thread): > email list is down too I thjink. I got an email rejected to bioc devel
Christopher Carpenter (14:47:41): > @Christopher Carpenter has joined the channel
Hervé Pagès (15:03:01) (in thread): > me too:pensive:
Hervé Pagès (19:39:45) (in thread): > seems to be back!!:rocket:
2023-10-28
Thanh Nguyen (04:16:39): > @Thanh Nguyen has joined the channel
sahitya (05:49:12): > @sahitya has joined the channel
2023-10-29
JigyasaG (01:18:00): > @JigyasaG has joined the channel
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2023-10-31
Pedro Sanchez (15:45:00): > Hi:smile:does anyone know about any implementation in R/Bioconductor for theMaximum Diversity Problem
2023-11-01
rohitsatyam102 (13:58:42): > @Michael LoveHi everyone who performs Bulk RNAseq. I have raised a query onbioconductor related to batch effect correction and its weird consequences on DEGs. Can you guys offer your inputs on whether I should go with it or not?
Steve Lianoglou (15:35:34) (in thread): > A direct link to the question would probably also be nice:wink:https://support.bioconductor.org/p/9154903/
Michael Love (15:58:21) (in thread): > On the support site I focus on software-related questions and can’t handle all the experimental design ones obviously. If you have a batch that is influential you should always control for it.
2023-11-03
Lluís Revilla (09:19:14) (in thread): > I have coded something similar to distribute samples in batches, perhaps you find something useful (in the readme I link to other packages) see the experDesign package in CRAN
Pedro Sanchez (09:41:24) (in thread): > Many thanks Lluís! I think the problem is similar but the details differ. I did a sub-optimal implementation, but was thinking to talk with some experts from the field and create a Bioc package. It may be useful for genomics technologies development
Lluís Revilla (09:44:32) (in thread): > Great, I didn’t even know the right name for the problem:grin:I hope you find a good solution with an expert and maybe I can use it for the samples case. Good luck!
Pedro Sanchez (09:48:12) (in thread): > Let’s see if I manage to keep the motivation with this to find the required time:sweat_smile:
Blessy Boby (15:51:54): > Hello guys! I am performing ATAC seq analysis in R v4.2 and am trying to create a set of TSS positions from the gene models in theTxDb.Hsapiens.UCSC.hg19.knownGene
Hervé Pagès (16:53:56) (in thread): > Please use our support site for this kind of issues:https://support.bioconductor.org This Slack is not the right place to report packages installation problems. Thanks!
2023-11-05
rohitsatyam102 (10:14:21) (in thread): > Thanks for your input.
2023-11-06
Andrew (18:59:00): > @Andrew has joined the channel
2023-11-07
LAR (13:28:09): > @LAR has joined the channel
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2023-11-09
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2023-11-13
Manvi Yaduvanshi (03:26:33): > @Manvi Yaduvanshi has joined the channel
Lori Shepherd (13:21:30): > There is an announcement athttps://cran.r-project.org/ > > Dear users, > > The CRAN Admin Team will perform system upgrades during the period Wednesday November 15 until Thursday November 16, 2023. > There will be intermittent outages in service during this time. > We thank you for your understanding and apologise for any inconvenience this may cause. > > CRAN Admin Team > > This may effect BiocManager and the ability to download/install packages. > We appreciate your patience and understanding during the CRAN update period.
Zac Zhang (18:12:41): > @Zac Zhang has joined the channel
Brendan (19:46:38): > @Brendan has joined the channel
2023-11-14
Alexander Ehrenberg (12:11:59): > @Alexander Ehrenberg has joined the channel
Alexander Ehrenberg (12:17:55): > Is anyone else having issues accessingbioconductor.org webpages likehttps://bioconductor.org/packages/release/bioc/html/DESeq2.html ? I keep getting a dead page but then something when I add “new.” to the start (e.g.https://new.bioconductor.org/packages/release/bioc/html/DESeq2.html Issue is that I’m trying to install basic things in R and am getting error messages seemingly related to the installation links referencing a dead page. I put some more details on GitHub (https://github.com/Bioconductor/BiocManager/issues/183 ) but would love a sanity check from the community. - Attachment: #183 Version map cannot be validated - not mapping to new bioconductor website > Submitting the basic installation command for Bioconductor:if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.18") > > in R (version 4.3.0) returns the following error:Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignette > > None of the suggested solutions I’ve found online (adjusting the proxy/firewall settings, ensuring internet connection, etc) have helped. > > The documentation suggests that the version map can be found at https://bioconductor.org/config.yaml which, as of today (11/13/2023), cannot be reached. There is a version map I can reach through the new bioconductor website at this link, though, https://new.bioconductor.org/config.yaml . > > It seems like the version map cannot be validated because the bioconductor.org/config.yaml is a broken link, whereas the new.bioconductor.org/config.yaml would work. Can this be fixed?
Steve Lianoglou (13:19:30) (in thread): > As a data point: I’m not having any issues on my end navigating to the “normal” bioconductor web pages …
Alexander Ehrenberg (13:20:09) (in thread): > That’s helpful. I’m trying to see if there’s a weird firewall situation causing this. Thanks!
Alan O’C (13:25:25) (in thread): > Nope, definitely a connection issue/rule configuration on your end
Alan O’C (13:26:15) (in thread): > As Martin said on GitHub, if this was a general issue then bioc support would be on fire:slightly_smiling_face:
Alexander Ehrenberg (13:37:51) (in thread): > Good to know - I’ll figure out the troubleshooting on my end thanks
2023-11-15
Xiaosai Yao (22:40:38): > @Xiaosai Yao has joined the channel
2023-11-16
Marie Vendettuoli (12:57:40): > @Marie Vendettuoli has joined the channel
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2023-11-17
Maria Doyle (04:37:30): > :loudspeaker:Bioconductor is leaving Twitter/X. For more details, please read our blog posthttps://blog.bioconductor.org/posts/2023-11-17-twitter-exit/ - Attachment (blog.bioconductor.org): Bioconductor community blog - Bioconductor is leaving Twitter/X > We’re transitioning away from Twitter/X in favor of platforms more aligned with our Code of Conduct.
Mauricio Roza (05:16:40): > @Mauricio Roza has joined the channel
Svetlana Ugarcina Perovic (07:03:08) (in thread): > Have you consider maybe joining the BlueSky?
Maria Doyle (07:35:57) (in thread): > Hi, yes we have. There are Bioconductor community members on Bluesky and we have had ongoing discussions about it at our social media working group meetings. For now, we’re not creating a Bioconductor Bluesky account for a few reasons, such as it’s not open, people need an invite to join and it’s not yet integrated with Buffer, which we use to schedule posts. But we’re keeping an eye on it.
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Anna Konstorum (08:50:51) (in thread): > Thank you for the update! I’ve started following BioC on the Mastodon platform.
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Chiagoziem David (10:45:19) (in thread): > Wow
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2023-11-18
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2023-11-19
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2023-11-20
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2023-11-22
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2023-11-29
Alex Mahmoud (14:53:07): > Hey all, I’m taking suggestions for useful services to include in astatus.bioconductor.org page. Tentative plan is to currently include: > > Main site:bioconductor.org Workshop site:workshop.bioconductor.org Container availability: checking containers can be pulled and have correct versions for devel/release > Container binary repository: checking whether container binaries properly work in the docker images > > Are there any relevant Bioconductor services/commands for which people would like to be able to have a status?
Sean Davis (14:57:33) (in thread): > * Single package builder > * Data storage/downloads (ie., Azure) > * Support site (support.bioconductor.org ) > * git server > * all build machines > * The CRAN mirror that bioconductor uses for builds, etc.
Alex Mahmoud (14:59:21) (in thread): > TYSM! Very helpful suggestions! > * Data storage/downloads (ie., Azure) > * Support site (support.bioconductor.org ) > * git server > These I can do these fairly easily and will include. Will keep list of the others that require work from other core members to tackle afterwards
Sean Davis (15:08:49) (in thread): > You could even start with a “ping” of the build machines. Obviously, not a very rich test, but establishes a precedent.
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2023-11-30
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Mike Smith (03:27:05) (in thread): > If you want to interface withcode.bioconductor.org just let me know. There’s a few stats that are potentially useful e.g. when it last synced with the central git server, or the contents of last log file it created. I’ve thought about providing a status page for the various components to that site, but would be very happy to try and make an interface available to you and centralise the information.
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Vivek Nair (18:01:50): > Hi everyone! I am new to bioinformatics! I needed help using VEP in R > > I am trying to find the variant consequence cdot and pdot HGVS > > > library(httr) > > library(jsonlite) > > library(xml2) > > server <- "[https://rest.ensembl.org](https://rest.ensembl.org)" > > ext <- "/vep/human/region/11:66530950-66530952:1/A?" > > r <- GET(paste(server, ext, sep = "", hgvs ="1"), content_type("text/xml")) > > stop_for_status(r) > > print(content(r)) > {xml_document} > <opt> > [1] <data id="11_66530951_AC/-" allele_string="AC/-" assembly_name="GRCh38" end="66530952" input="11 66530950 66530952 ... > > I am not sure how to obtain the complete output as its not showing the cdot and pdot for the variant! Any help would be great. Thanks!!
Martin Morgan (18:38:21) (in thread): > Biostar (if your question is about using R per se) or the Bioconductorsupport site (if you think there is a Bioconductor package, e.g.,ensemblVEP that might do what you are after) might be a better place for seeking help. > > I asked forcontent_type("text/json")instead oftext/xml, and thencontent(r)returns an R data structure (list) that you can navigate with base R commands > > > r[[1]]$transcript_consequences[[2]]$hgvsc > [1] "ENST00000318312.12:c.1531_1532del" > > or maybe following the advice in R for Data Science for dealing withhierarchical data . I findlistviewer listviewer::jsonedit(r)very useful for understanding these nested structures. It might be useful to explore therjsoncons package and one of the query languages like JMESPath or JSONPath; the github version allows direct coercion to R > > > json = content(response, as = "text") > No encoding supplied: defaulting to UTF-8. > > rjsoncons::jmespath(json, "[].transcript_consequences[].hgvsc", as = "R") > [1] "ENST00000318312.12:c.1531_1532del" > [2] "ENST00000393994.4:c.1144_1145del" > [3] "ENST00000455748.6:c.1240_1241del" > [4] "ENST00000526760.5:c.*1238_*1239del" > [5] "ENST00000526986.5:c.560-1464_560-1463del" > [6] "ENST00000529955.5:n.1502_1503del" > [7] "ENST00000534073.5:c.560-3946_560-3945del" > [8] "ENST00000630659.2:c.*1238_*1239del" >
Vivek Nair (18:48:38) (in thread): > Hi Sir! Thanks for your quick reply. I will test this out
Vivek Nair (19:01:30) (in thread): > > > library(httr) > > library(jsonlite) > > library(xml2) > > library(rjsoncons) > > server <- "[https://rest.ensembl.org](https://rest.ensembl.org)" > > ext <- "/vep/human/region/11:66530950-66530952:1/A?" > > r <- GET(paste(server, ext, sep = "", hgvs ="1"), content_type("text/json")) > > stop_for_status(r) > > json = content(r, as = "text") > No encoding supplied: defaulting to UTF-8. > > rjsoncons::jmespath(json, "[].transcript_consequences[].hgvsc", as = "R") > [1] "[]" > > Unfortunately I am not getting a similar output! I am doing something wrong
Martin Morgan (22:23:33) (in thread): > Construct the URL as > > server <- "[https://rest.ensembl.org](https://rest.ensembl.org)" > ext <- "/vep/human/region/11:66530950-66530952:1/A?" > url <- paste0(server, ext, "hgvs=1") > response <- GET(url, content_type("text/json")) > > Also, theas = "R"argument requires the version of rjsoncons that is available on GitHub; follow the instructions in the ‘Installation and loading ’ section. > > (I do not think that there is an easy ‘cut and paste’ solution; you will need to understand the commands I am suggesting and adapt them to your specific situation….)
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2023-12-01
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2023-12-02
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2023-12-04
Matteo Tiberti (09:38:57): > hi everyone, I have a quick question about the availability of old BioC packages. Some time ago, I have usedrenvto make arenv.lock(here ) to have a more reproducible environment to rerun some test cases. This was back with BioC 3.16. We are now trying to restore it, however it looks like theliftOverpackage cannot be downloaded from BioC 3.16 Archive: > > Retrieving '[https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/liftOver/liftOver_1.23.0.tar.gz](https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/liftOver/liftOver_1.23.0.tar.gz)' ... > Warning: failed to find source for 'liftOver 1.23.0' in package repositories > Warning: failed to retrieve '[https://cloud.r-project.org/src/contrib/Archive/liftOver/liftOver_1.23.0.tar.gz](https://cloud.r-project.org/src/contrib/Archive/liftOver/liftOver_1.23.0.tar.gz)' [error code 22] > Warning: failed to retrieve '[https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/liftOver/liftOver_1.23.0.tar.gz](https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/liftOver/liftOver_1.23.0.tar.gz)' [error code 22] > Error: failed to retrieve package 'liftOver@1.23.0' > > When I attempt visitinghttps://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/liftOver/ , it indeed looks like the directory is empty. Many other packages however have tarballs in their directories. Is this expected or can you suggest what could be the reason or if I can find a workaround? For now I’ve copied the package from an old renv cache but that is of course not ideal. Thanks a lot!
Lori Shepherd (09:49:27): > Archive folders for packages only exist if there was an updates for the package per the release (ie if there was a change updated in the release branch) else the package tar is athttps://bioconductor.org/packages/3.16/bioc/src/contrib/ … releases will generally always have an even y of version x.y.z as odd indicates devel packages, we don’t keep archives of devel bioc packages as the development branch is intended for updates and instability. Per the landing pagehttps://bioconductor.org/packages/3.16/workflows/html/liftOver.html you would want versionliftOver_1.22.0.tar.gz for Bioc 3.16 and since there were no updates per release it would be at the top levelhttps://bioconductor.org/packages/3.16/bioc/src/contrib/ becasue there were no version bumps in release to activate an archive athttps://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/liftOver/
Matteo Tiberti (09:58:28): > I see - makes sense, thank you. I’m not sure why I had liftOver 0.23.z in my environment when I saved it in the first place (kind of weird I had a dev version installed), but I see the problem now
Marcel Ramos Pérez (10:13:20) (in thread): > FWIW I was able to useBiocArchivein the 3.16 docker container to get the correct version ofliftOver(1.22.0). Spin up the container: > > docker run -e PASSWORD=bioc -p 8787:8787 bioconductor/bioconductor_docker:RELEASE_3_16 > > Run in R: > > install.packages(c("devtools", "lubridate")) > devtools::install_github("Bioconductor/BiocArchive") > BiocArchive::install("liftOver") > packageVersion("liftOver") > #' [1] '1.22.0' >
Matteo Tiberti (10:15:00) (in thread): > thanks! The problem is that myrenv.lockis trying to install v. 1.23 rather than v. 1.22 which is why it breaks. I’ll have to change it so that it refers to 1.22 and that should be enough
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2023-12-06
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Devon Kohler (08:56:42): > Hi everyone, I was wondering if anyone had any idea how to fix a build error that is specific to the installed dependencies on the server? TheMSstatspackage has been reporting an error as of recently, and we were able to track the problem down to thelme4dependency (see error below). > > lme4::lmer(ABUNDANCE ~ GROUP + (1|SUBJECT), data = input) > Error in initializePtr() : > function 'cholmod_factor_ldetA' not provided by package 'Matrix' >
Devon Kohler (08:57:48): > I was able to fix this by installinglme4from source on my local machine. It seems to be an issue with how older versions of theMatrixpackage work withlme4(https://stackoverflow.com/questions/77481539/error-in-initializeptr-function-cholmod-factor-ldeta-not-provided-by-pack ) - Attachment (Stack Overflow): “Error in initializePtr() : function ‘cholmod_factor_ldetA’ not provided by package ‘Matrix’” when using lmer function in R > I am attempting to build a mixed effects linear regression model using the lmer function in R. I am building a fixed effects and mixed effects model using the following code to justify the use of a…
Devon Kohler (08:58:15): > I am curious if there is anyway to fix this on the Bioc build servers or what we might be able to do to clear up this error
Devon Kohler (08:58:19): > https://bioconductor.org/checkResults/release/bioc-LATEST/MSstats/
Andres Wokaty (09:48:14) (in thread): > I can try reinstallinglme4on the Win and Mac builders. It would be helpful to understand how you got the error as I don’t see that in the build report.
Devon Kohler (09:54:40) (in thread): > Yeah that part of the code is in a try loop, so the actual error is from trying to access the failed model.
Devon Kohler (09:55:07) (in thread): > I had to dig through with a debugger to figure out where it was actually coming from
Devon Kohler (09:55:37) (in thread): > generally this isnt a problem if one model fails (we run 1000s of models) but all failing causes issues downstream.
Andres Wokaty (10:26:46) (in thread): > I reinstalledlme4on the release intel mac andR CMD checkdoesn’t produce an error forMSstats. I’ll try to update the other builders today that I have access to.@Martin GrigorovCould you try to reinstalllme4on kunpeng2 when you have time?
Devon Kohler (10:27:54) (in thread): > awesome thanks@Andres Wokaty!
Martin Grigorov (16:17:15) (in thread): > @Andres WokatySure! I’ll do it tomorrow !
2023-12-07
Martin Grigorov (04:03:34) (in thread): > lme4has been updated to 1.1-35.1 andMSstatschecks now pass: > > ... > * checking tests ... > Running 'tinytest.R' > OK > * checking for unstated dependencies in vignettes ... OK > * checking package vignettes in 'inst/doc' ... OK > * checking running R code from vignettes ... > 'MSstats.Rmd' using 'UTF-8'... OK > NONE > * checking re-building of vignette outputs ... OK > * checking PDF version of manual ... OK > * DONE > > Status: 1 WARNING, 5 NOTEs > See > '/home/biocbuild/git/MSstats.Rcheck/00check.log' > for details. >
2023-12-08
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2023-12-11
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2023-12-12
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2023-12-13
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2023-12-16
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2023-12-17
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2023-12-18
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2023-12-19
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Maria Doyle (12:21:22): > :mega:Save the date for EuroBioC 2024 in Oxford, September 4-6 - File (PNG): EuroBioC2023 Save the Date - light blue.png
2023-12-21
Maria Doyle (12:21:34) (in thread): > :artist:Attention artists! EuroBioC2024 is hosting a fantastic sticker contest! > > Do you have a knack for creativity? Then why not participate and design the official conference sticker? The deadline for this exciting contest isJanuary 31, 2024 https://forms.gle/ALx3UUAuqzcazGbeA - File (PNG): eurobioc2024-sticker-contest.jpeg
Levi Waldron (16:13:26): > Postdoc and Bioinformatician positions in metagenomic data analysis available @cibiocm in Italy. In-person or remote work possible. To be filled ASAP. Further information and to apply: > 1. Postdoc:https://www.rfcuny.org/careers/postings?pvnID=PH-2312-006037 > 2. Bioinformatician / Curator:https://www.rfcuny.org/careers/postings?pvnID=PH-2312-006038 > Contact me (levi.waldron@sph.cuny.edu ) or Nicola Segata (nicola.segata@unitn.it ) for additional information.
Y-h. Taguchi (20:01:57): > There seems to be no updates on download stats since 6th Dec.https://bioconductor.org/packages/stats/ What has happened?
Lori Shepherd (20:55:37): > @Robert Shearthis will be remedied shortly. We are replacing the system that generates the stats as the old system needed updates. The old stats werent running correctly hence the Dec 6. Once the new system is up it will show updated stats
2023-12-22
Maria Doyle (09:47:23): > :mortar_board:**** Seeking New Members for Bioconductor Carpentries Team**We’re inviting Bioconductor/R users interested in teaching and earning Carpentries certification to join our team. Check out the details and apply here:https://forms.gle/X12vSZoNc6Z4DHNL8
Maria Doyle (10:54:37): > :loudspeaker:**** New Bioconductor Website Launching January 3rd ****:star2:**** ****Our new website design is focused on being more welcoming and accessible. Preview it athttp://new.bioconductor.org and share your feedback in Slack#biocwebsiteImportant: UseHTTP Website launch date notice.png
2023-12-24
Maria Doyle (06:41:44) (in thread): > I think that conference website hasn’t been set up yet
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2023-12-25
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2023-12-27
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2023-12-29
Manvi Yaduvanshi (08:58:00) (in thread): > Finally! I always wondered about the previous UI. This is so cool and well designed
Manvi Yaduvanshi (09:01:24): > Hey everyone! This is Manvi Yaduvanshi from India. I’m new to open source and really want to contribute to Bioconductor, but it seems bit confusing in the beginning. Can anyone help me, letting me know where to start and what documentations should I read?
Kozo Nishida (11:41:32) (in thread): > Hi Manvi, > How about starting with the documentation athttps://contributions.bioconductor.org/ ? - Attachment (contributions.bioconductor.org): Welcome | Bioconductor Packages: Development, Maintenance, and Peer Review > This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook.
Krithika Bhuvanesh (22:59:06) (in thread): > Thank you@Sean Davisand@Mikhail Dozmorov!! Happy new year !
2024-01-02
Vince Carey (05:37:29): > The counting/reporting infrastructure has changed.https://bioconductor.org/packages/stats/bioc/DelayedArray/ will appear after clicking on the “rank” badge on the landing page. The response is a bit slow. I believe the data depicted there are accurate. However, the alternate view athttps://bioconductor.org/packages/stats/bioc/DelayedArray/DelayedArray_2023_stats.tab is not consistent with the associated HTML report. And it does appear that the textual .tab files for DelayedArray and BiocVersion are identical with one another, though the HTML reports are not. I don’t think the use ofmaster.bioconductor.org to retrieve this information is endorsed. More later today.
Lori Shepherd (08:10:55): > @Michael Miltonplease don’t be usingmaster.bioconductor.org hittingbioconductor.org should be sufficient and is what is recommended – we will be looking into the discrepancy on the stats table immediately; thank you for bringing it to our attention.
Manvi Yaduvanshi (10:25:03) (in thread): > Thankyou@Kozo Nishida!! Yes , I’ve started reading it. Will ask my doubts on the channels if get any.:blush:
Krithika Bhuvanesh (14:30:16): > Happy new year to all ! I come asking for some sage advice. I have to analyse an RNA-seq dataset from patient derived cell lines . The goal is to compare two groups - lets call it case and control. Issue is that there is only one sample per group. I’m hesitant to proceed as i know there will be backlash from manuscript reviewers for sample size issue. But wanted to get feedback from this group. In the event that i need to proceed with this data analysis, would voom-limma be the most optimal choice
Sean Davis (14:38:09) (in thread): > Hi,@Krithika Bhuvanesh. I’d suggest asking these questions onhttps://support.bioconductor.org , but to deliver early bad news, with n=1 per group, there isn’t really a statistically justifiable approach.
Krithika Bhuvanesh (14:43:01) (in thread): > Thank you Sean ! will do. Yes i’ ve been pondering this since last week , and my gut reaction is to not proceed with analysis
Michael Milton (18:37:32) (in thread): > I’m using the regular stats URL in my actual code, not master. The actual statistics seem to be fixed now, thanks.
2024-01-03
Y-h. Taguchi (01:50:23) (in thread): > I recommend you to use my packagehttps://bioconductor.org/packages/release/bioc/html/TDbasedUFE.html that allows you to attribute P-values to genes even with one sample per group. - Attachment (Bioconductor): TDbasedUFE > This is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. It can perform unsupervised feature extraction. It uses tensor decomposition. It is applicable to gene expression, DNA methylation, and histone modification etc. It can perform multiomics analysis. It is also potentially applicable to single cell omics data sets.
Dario Strbenac (03:00:04) (in thread): > In that case, it will be necessary to provide orthogonal experimental validation, such as quantitative Polymerase Chain Reaction of a small number of the top-ranked features.
2024-01-04
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Brian Schilder (13:02:47): > Here’s my package for getting (reverse) dependency from GitHub@Vince Carey. Could still use some work, but in theory I could use it to get some metrics about how many R packages out there use Bioc:https://github.com/RajLabMSSM/echodeps
2024-01-05
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2024-01-06
Krithika Bhuvanesh (22:08:34) (in thread): > Thanks for the great feedback. I decided not to try group comparison and decided to do GSEA instead. Steps in detail - I first pre-filtered the RNA-seq data to remove lowly expressed genes. I cacculated the case/control gene exp to get an equivalent of fold change . Convert to log scale fold change. After removing dups, and sorting it, i used that as input to GSEA analysis.
Krithika Bhuvanesh (22:09:48) (in thread): > @Y-h . TaguchiThanks for sharing your package. It looks very interesting !
stefano mangiola (23:16:18): > Any interest in working on a squidR, to import some of the functionalities such as cell segmentation of squidpy? Does anyone know about similar efforts?
Juan Henao (23:38:33) (in thread): > I certainly don’t know. However, you can do contact the scverse initiative, they are up to date in all of that matter, including one the involved person is the creator of squidpy
2024-01-07
stefano mangiola (17:06:05) (in thread): > @Kevin Rue-Albrechtin case there is not eixting efforts (waiting for replies), I was thinking of adapting your Velociraptor package to interact with squidpy. > > Would you be interested in case to participate?
Ludwig Geistlinger (19:25:54) (in thread): > FWIW there is some overlap withimcRtools (spatial graph analysis, neighborhood testing, …) and withVoyager (spatial stats, Moran’s I, …).
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2024-01-08
stefano mangiola (01:57:44) (in thread): > I cannot find an image cell segmentation tool for example, in R. Am I missing something?
Juan Henao (02:50:39) (in thread): > As far as I know imcRtools has an image segmentation function and can use Mesmer as well
Mike Smith (04:40:03) (in thread): > Is it something you could do in EBImage? More a general purpose image processing toolkit, but it certainly has some capacity forsegmentation
Kevin Rue-Albrecht (04:43:10) (in thread): > @stefano mangiolasomehow I didn’t see the notification of your message yesterday. Do you mean making a copy of it and replacing the content with squipy related functionality? Or making a PR to velociraptor directly ? First option is highly preferable for various reasons
Dario Strbenac (07:00:04): > Does thegetLDSexample work for you? > > library(biomaRt) > human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") > mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl") > getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), > filters = "hgnc_symbol", values = "TP53", mart = human, > attributesL = c("chromosome_name","start_position"), martL = mouse) # Error: biomaRt has encountered an unexpected server error. >
Martin Grigorov (07:02:07) (in thread): > for me it fails with: > > > getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), > + filters = "hgnc_symbol", values = "TP53", mart = human, > + attributesL = c("chromosome_name","start_position"), martL = mouse) # Error: biomaRt has encountered an unexpected server error. > Error: biomaRt has encountered an unexpected server error. > Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl) >
Martin Grigorov (07:02:38) (in thread): > tested it onkunpeng2(the Linux ARM64 builder)
Dan Bunis (14:01:45): > Hi everyone! Sorry to spam, but I’m not sure if there’s a better channel for this Q… I’m wondering if anyone could provide some insight into how easy or frustrating it might be to maintain a package in bioconductor that will become heavily dependent on a new package which I am thinking of submitting to CRAN? (I’ll add further context in thread.)
Dan Bunis (14:05:00) (in thread): > Further Context: > The new / future dependency package has broad utility outside of biology, thus my lean towards CRAN even though I do generally vibe better with the Bioc ethos! > > I’ve pulled out most of the visualization machinery ofdittoSeq intodittoViz , which starts from a data.frame(-like object) rather than from a SummarizedExperiment/SingleCellExperiment/Seurat object. This generalized starting point makes dittoViz quite a bit more widely applicable outside of biology. I eventually plan to update dittoSeq to strip away its now-repeated code and to rely on dittoViz’s machinery as much as possible.It’s the maintenance strain after that point which I am concerned about. I’m imagining that making certain updates to dittoViz in CRAN would lead to needing to push any associated fixes to both the release and devel versions of dittoSeq && that the updated dittoViz version might not be inherited from CRAN by the BBS right away. I’m just not sure how annoying and burdensome dealing with that will ultimately feel?
Lluís Revilla (14:37:02) (in thread): > Lots of packages depend in packages in CRAN. In my experience the check system picks the dependencies from CRAN quite fast. The only problem would be if those changes are close to the Bioconductor release, in that case it could be more troublesome (problems in CRAN acceptance, machines picking the new version late…) . Ideally you could submit the dittoViz to CRAN and start working on the devel branch to use dittoViz. Then at the release of the new version of dittoSeq changes on dittoViz could be invisible if you only change the internals of dittoViz (the methods/function names stay the same). If they do change you could test in dittoSeq for the version of dittoViz and branch your code accordingly:if (packageVersion("dittoViz") < "0.9") {....}(I’ve done this to depend on a package as it was on CRAN and a version of it that was in development).
Henrik Bengtsson (14:52:45) (in thread): > I’d expect a smooth ride, especially so if you’re in control of both the package on CRAN and the package on Bioconductor.
Maia (16:21:17): > @Maia has joined the channel
Maia (16:24:31): > Hi everyone, I have a package (CellScape %20a%20single%20cell%20phylogeny.)) that I developed almost a decade ago. It’s publishedhere in Nature Methods, and is downloaded approximately 500 times per year. Its purpose is to enable the interactive visualization of single cell clonal evolution datasets (e.g. single cell cancer data). > > Unfortunately, this is failing checks. I am no longer a developer, and wonder if anyone here would feel so inclined to rescue this package? > > Details of the errorhere . - Attachment (Nature): E-scape: interactive visualization of single-cell phylogenetics and cancer evolution > Nature Methods - E-scape: interactive visualization of single-cell phylogenetics and cancer evolution
Lori Shepherd (17:50:59) (in thread): > For What Its Worth the fix for this error is relatively simple. You need to add devtools to the Suggests of your DESCRIPTION. But if you are no longer interested in maintaining the package finding a replacement maintainer would be good. You might also consider making an announcement on bioc-devel mailing list / support site as well.
Shixiang Wang (20:55:33) (in thread): > @MaiaI am interested, can fix the error and be a maintainer, but I cannot promise much time on this package.
Kasper D. Hansen (21:35:46) (in thread): > Itcould
Kasper D. Hansen (21:36:00) (in thread): > If you plan to do it piecewise, it will be much more painful
2024-01-09
Alik Huseynov (06:12:49) (in thread): > as for image processing/segmentation is RANTsR @stefano mangiolasquidR - how you that be then, > calling python in the background (reticulate-like style) or complete/new implementation in R (ie no python at all)?
stefano mangiola (17:33:45) (in thread): > @Kevin Rue-Albrechtfirst option@Alik Huseynovit would be a replica of what Velociraptor does (calling python in the background), just with other python functions
stefano mangiola (18:52:52) (in thread): > @Alik Huseynov, do you know of any tutorial for ANTsR on cell segmentation for H&E (and fluorescence, if possible)?
Alik Huseynov (19:13:57) (in thread): > > @Alik Huseynovit would be a replica of what Velociraptor does (calling python in the background), just with other python functions > I see, and do you think it will be stable of having python in the background? So far I was only usingreticulatewhich can be a pain > > @Alik Huseynov, do you know of any tutorial for ANTsR on cell segmentation for H&E (and fluorescence, if possible)? > Ok, that package is mostly for volumetric data, like CT or MRI, but it should work with 2D images as well, not sure how well it will work to segment the cells. I was mostly using that package for intensity-based image registration (long time ago) > You can try to check these > * https://stnava.github.io/ANTsR/ > * https://gist.github.com/ntustison/12a656a5fc2f6f9c4494c88dc09c5621 > btw, segmentation function is calledatropos
stefano mangiola (19:29:39) (in thread): > > I see, and do you think it will be stable of having python in the background? So far I was only usingreticulatewhich can be a pain > Veliciraptor uses basilisk, and handles it quite well. That’s why I was thinking of forking that (I have already forked on my githb user). > * https://gist.github.com/ntustison/12a656a5fc2f6f9c4494c88dc09c5621 > > > > I will give it a go
Maia (21:07:11) (in thread): > Thanks,@Lori Shepherdand@Shixiang Wang! > > Great to know the fix simple, and I would love it if you’re willing to maintain the package,@Shixiang Wang! This is the first error that’s arisen since its publication, so I suspect it will be a very easy package to maintain. > > I will DM you now with further details.
2024-01-10
Nils Eling (06:33:12) (in thread): > imcRtoolsdoesn’t offer cell segmentation. We usesteinbock(https://github.com/BodenmillerGroup/steinbock ) and then import the single-cell data into R. However, check outsimpleSeg(https://bioconductor.org/packages/release/bioc/html/simpleSeg.html ) for cell segmentation in R. - Attachment (Bioconductor): simpleSeg > Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.
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2024-01-11
Vince Carey (10:08:25) (in thread): > it would be nice to get some consensus on how to proceed in this area. EBImage and imager are both relevant … this uses imager to get some of the basic concepts into view for newcomers … very primitive and underdeveloped:https://vjcitn.shinyapps.io/mastApp/
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Juan Henao (14:37:50) (in thread): > There is always the possibility to do a benchmark and at least make available the results in “Open problems in single-cell analysis”. So far, they only have one benchmark regarding spatial data:https://openproblems-v2-results–openproblems.netlify.app/results/spatial_decomposition/ But I am deviating a bit the topic, sorry:pray:
Dan Bunis (15:26:37) (in thread): > Thanks for these notes all! > I decided on CRAN,and it’s in :tada:. > I will definitely be aiming to synchronize dittoViz into dittoSeq’s innards in a single go, probably first thing after the April Bioconductor release.:crossed_fingers:that it goes as smoothly as I’m hoping!
2024-01-12
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2024-01-15
Leo Lahti (14:24:08): > European Conference on Computational Biology ECCB https://eccb2024.fi/ Submission deadlines Conference themes
Leo Lahti (14:24:50): > ^ also Bioconductor events would be relevant, workshops & tutorials DL is approaching (Feb 15)!
2024-01-16
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stefano mangiola (18:55:30) (in thread): > I am wondering how can I segment an H&E image of a SpatialExperiment usingsimpleSeg taggind @Nils Eling**** ****@Ellis Patrick**** ****
Ellis Patrick (19:42:07) (in thread): > I’ve never tried…. I wouldn’t be surprised if simpleSeg doesn’t scale up to use on H&E, we’ve had issues with it on large images. Although I’m not sure what you mean by H&E image of a SpatialExperiment. Do you want to segment an H&E image into cells and then store these in a SpatialExperiment?
stefano mangiola (20:21:33) (in thread): > for example for SpatialExperiment from a Visium experiment, I would like to segment, and summarise the number of cells per spot - File (PNG): image.png
2024-01-17
Alik Huseynov (04:11:58) (in thread): > you mean segmenting the nuclei from H&E? > this one can help you I think, but it’s not Bioc and a bit old.https://htmlpreview.github.io/?https://github.com/ludvigla/cell_segmentation/blob/master/doc/cell_segmentation.html https://github.com/ludvigla/cell_segmentation That should be similar to whatSTUtility is doing, but not sure ifsemla::MaskImages()
Dario Righelli (04:12:13) (in thread): > Hi@stefano mangiolaI’m not sure how to do that. > AFAIK, H&E images are typically pretty big and I wouldn’t store them as they are in aspeobject. > At the same time, if you want to use alowresimage, as the ones coming from visium, also in that case I wouldn’t try to segment such a small resolution image. > In any case,SpatialExperimentstores images asrasterobjects, so it all depends on the type taken as input bysimpleSeg
Dario Righelli (04:15:27) (in thread): > But@stefano mangiolahow do you count the cells in a spot with visium experiment image?
Alik Huseynov (04:17:10) (in thread): > > But@stefano mangiolahow do you count the cells in a spot with visium experiment image? > I think given the coordinates of the segmented nuclei from H&E that fall within the spot box
Dario Righelli (04:19:01) (in thread): > Thanks! So you need the very high resolution image…
Federica Gazzelloni (06:05:23): > Hi Everyone! > my name is Federica and I am the organizer ofR-Ladies Rome . We are looking for people to join our team, no matter where you are. Please get in touch if you’d like to get involved. Thanks! - Attachment (Meetup): R-Ladies Rome | Meetup > ****R-Ladies Rome (rladiesrome.quarto.pub/website/ ) is a local chapter of R-Ladies Global ([rladies.org](http://rladies.org) ), a global organization dedicated to promoting gender diver
Alik Huseynov (14:40:57) (in thread): > @stefano mangiolaone moreTREXSeg similar to the previous post, these tools are from SciLifeLab
Dario Strbenac (19:15:08): > Is Ask A Question on support forum working? I see my question preview below the input field and I pass Captcha file. But, when clicking on Submit, it just refreshes and everything in the input field appears red, which it did not have while I was typing into it before.
Lori Shepherd (19:33:43): > Might not be captcha, if it’s the captcha we see a “this field is required”. there has been an issue with language validation we have been looking into and have you specified a valid tag with package name?
Dario Strbenac (19:40:09): > Yes, the tagSingleCellExperimentwas chosen from a drop-down list once the first few characters were typed. I attach a text file of the body of the question in case you can test it. Title is “Merging of Human and Mouse SingleCellExperiment Objects Error”. - File (Plain Text): question.txt
Lori Shepherd (19:53:46) (in thread): > Likely with all the copied code I’d guess the language or ascii validator is acting up and not recognizing a special character. Is a known issue we are actively working on.
2024-01-18
Martin Grigorov (01:49:04) (in thread): > I remember I had an issue with the quote symbols. I’m 99% sure here the problem is'mcols'. Replace these quotes with the ones from your keyboard and it should pass
2024-01-19
stefano mangiola (04:50:24) (in thread): > Thanks. > > Just as comparison with squidpy you segment the whole H&E (5 minutes or so) - File (PNG): image.png
stefano mangiola (04:51:16) (in thread): > And it outputs how many cells per Visium spot > > It behaves very well. using the Velociraptor framework to import also this python functionality would be awesome - File (PNG): image.png
stefano mangiola (04:52:16) (in thread): > I imagine in the future R and python will be so connected that we would not have to make compromises on languages
2024-01-25
Pavan Videm (06:14:32): > @Pavan Videm has joined the channel
Victor Eduardo (09:53:40): > @Victor Eduardo has joined the channel
Maria Doyle (11:06:51) (in thread): > :star2:EuroBioC2024 Sticker Contest Reminder :star2:Hello everyone! Just a reminder about our sticker design contest for EuroBioC2024. It’s a great opportunity to showcase your creativity and potentially win a fantastic prize.:gift:Prize: Free registration for this year’s EuroBioC conference in Oxford, September 4-6th!:rocket:Deadline:January 31st, 2024 https://forms.gle/ALx3UUAuqzcazGbeA Looking forward to seeing your amazing designs!
2024-02-01
Andres Wokaty (10:37:53): > Bioconductor is participating in theOutreachy May 2024 to August 2024 internship round. Outreachy’s goal is to support people from groups underrepresented in the technology industry. Interns will work remotely with mentors from our community. Since we started partnering with Outreachy, we’ve had 4 participating projects and 8 Outreachy interns. This will be our fourth round of participation. > > We are seeking mentors to propose open source projects within Bioconductor that Outreachy interns can work on during their internship. Feb. 23, 2024 at 4 pm UTC is the deadline to submit projects athttps://www.outreachy.org/communities/cfp/bioconductor/ . > > If you have questions or want help crafting your project proposal, you’re welcome to reach out to me on Slack or via email atjennifer.wokaty@sph.cuny.edu . > > Mentors FAQ:https://www.outreachy.org/mentor/mentor-faq More details:https://www.outreachy.org/communities/cfp/
2024-02-05
Courtney Zirkle (08:34:07): > @Courtney Zirkle has joined the channel
Dario Strbenac (21:00:00): > Is it intended that setting row ranges erases existing row data? I am manually setting the ranges becauseread10xCountsdoes not do it. > > > rowData(allHuman) > DataFrame with 36601 rows and 3 columns > ID Symbol Type > <character> <character> <character> > MIR1302-2HG ENSG00000243485 MIR1302-2HG Gene Expression > FAM138A ENSG00000237613 FAM138A Gene Expression > OR4F5 ENSG00000186092 OR4F5 Gene Expression > AL627309.1 ENSG00000238009 AL627309.1 Gene Expression > AL627309.3 ENSG00000239945 AL627309.3 Gene Expression > ... ... ... ... > > rowRanges(allHuman) <- genesDB > > rowData(allHuman) > DataFrame with 36601 rows and 0 columns > > A workaround is to stash row data before it is erased. > > allHumanRowData <- rowData(allHuman) > rowRanges(allHuman) <- genesDB > rowData(allHuman) <- allHumanRowData > > Putting it back duplicates it, however. > > > rowRanges(allHuman) > GRanges object with 36601 ranges and 3 metadata columns: > seqnames ranges strand | ID Symbol Type > <Rle> <IRanges> <Rle> | <character> <character> <character> > ENSG00000243485 chr1 29554-31109 + | ENSG00000243485 MIR1302-2HG Gene Expression > ENSG00000237613 chr1 34554-36081 - | ENSG00000237613 FAM138A Gene Expression > ENSG00000186092 chr1 65419-71585 + | ENSG00000186092 OR4F5 Gene Expression > ENSG00000238009 chr1 89295-133723 - | ENSG00000238009 AL627309.1 Gene Expression > ENSG00000239945 chr1 89551-91105 - | ENSG00000239945 AL627309.3 Gene Expression > ... ... ... ... . ... ... ... > > rowData(allHuman) > DataFrame with 36601 rows and 3 columns > ID Symbol Type > <character> <character> <character> > ENSG00000243485 ENSG00000243485 MIR1302-2HG Gene Expression > ENSG00000237613 ENSG00000237613 FAM138A Gene Expression > ENSG00000186092 ENSG00000186092 OR4F5 Gene Expression > ENSG00000238009 ENSG00000238009 AL627309.1 Gene Expression > ENSG00000239945 ENSG00000239945 AL627309.3 Gene Expression > ... ... ... ... >
Hervé Pagès (23:23:07) (in thread): > It’s not duplicated, it’s just thatrowData(<RangedSummarizedExperiment>)actually returnsmcols(rowRanges(<RangedSummarizedExperiment>)). > Can’t remember exactly the story behind this but I believe that this behavior was intended to preserve compatibility with the behavior that preceded the big refactoring of the SummarizedExperiment class and its split into 2 separate classes (SummarizedExperiment/RangedSummarizedExperiment) that happened about 9 years ago. Before this refactoring I believe that the row data was already bundled with the row ranges and stored as the metadata columns of the GRanges object. This means that when you dorowRanges(allHuman) <- genesDBthen the row data onallHumanare replaced by the metadata cols carried by the right object. > This is admitedly a little counter-intuitive but it’s hard to change something like this after it’s been around for so long. Maybe therowRanges()setter could get an extra argument to let the user specify that they wish to keep the existing row data? Please open an issue inSummarizedExperiment
2024-02-06
Vince Carey (06:31:07): > A reprex would be helpful. Continued in thread.
Vince Carey (06:31:25) (in thread): > > > library(DropletUtils) > > example(read10xCounts) > ... > > rowData(sce10x2) > DataFrame with 100 rows and 2 columns > ID Symbol > <character> <character> > ENSG00001 ENSG00001 GENE1 > ENSG00002 ENSG00002 GENE2 > ENSG00003 ENSG00003 GENE3 > ENSG00004 ENSG00004 GENE4 > ENSG00005 ENSG00005 GENE5 > ... ... ... > ENSG000096 ENSG000096 GENE96 > ENSG000097 ENSG000097 GENE97 > ENSG000098 ENSG000098 GENE98 > ENSG000099 ENSG000099 GENE99 > ENSG0000100 ENSG0000100 GENE100 > > myr = GRanges(seqnames=1, IRanges(start=1:100, width=1)) > > rowRanges(sce10x2) = myr > > rowData(sce10x2) > DataFrame with 100 rows and 0 columns >
Vince Carey (06:32:49) (in thread): > > Under development (unstable) (2024-01-10 r85797) > Platform: x86_64-pc-linux-gnu > Running under: Ubuntu 22.04.3 LTS > > Matrix products: default > BLAS: /home/vincent/R-4-4-dist/lib/R/lib/libRblas.so > LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > time zone: America/New_York > tzcode source: system (glibc) > > attached base packages: > [1] stats4 stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Matrix_1.6-4 DropletUtils_1.23.0 > [3] TENxIO_1.5.3 scran_1.31.0 > [5] scater_1.31.2 ggplot2_3.4.4 > [7] scuttle_1.13.0 SingleCellExperiment_1.25.0 > [9] SummarizedExperiment_1.33.3 Biobase_2.63.0 > [11] GenomicRanges_1.55.2 GenomeInfoDb_1.39.5 > [13] IRanges_2.37.1 S4Vectors_0.41.3 > [15] BiocGenerics_0.49.1 MatrixGenerics_1.15.0 > [17] matrixStats_1.2.0 rmarkdown_2.25 >
Vince Carey (06:33:14) (in thread): > Looks like a bug to me.
Vince Carey (06:36:22) (in thread): > It also appears that rowRanges<- may misbehave with a SummarizedExperiment.
Vince Carey (06:38:25) (in thread): > Now
2024-02-09
Maria Doyle (07:22:34): > :mega:Save the date for BioC2024 in Grand Rapids Michigan, USA, July 24-26 - File (PNG): BioC2024 Save the Date.png
2024-02-11
Siraj Farhan (07:54:50): > @Siraj Farhan has joined the channel
2024-02-12
Aedin Culhane (03:34:48): > Only a few days are left to apply for the May Institute on Computation and Statistics for Mass Spectrometry and Proteomics, taking place on April 29 – May 10, 2024 on the campus of Northeastern University in Boston MA. Please apply by February 15, 2024 for full consideration. > > Instructors are leading experts, who contributed numerous experimental and computational methods and software. The target audiences are both beginners and experienced scientists, with both experimental and computational expertise. > > Participants can select a subset of the following programs: > * April 29 - May 1, Quantitative proteomics with Skyline. Lead instructors: Tina Ludwig, Brendan MacLean and Lindsay Pino > * May 1 – May 3, Beginners R and beginners statistics. Lead instructor: Ryan Benz > * May 1 – May 3, Intermediate R, data visualization and statistics. Lead instructor: Kylie Bemis > * May 6 – May 8, Statistics for quantitative mass spectrometry: methods and case studies with MSstats. Lead instructors: Olga Vitek and Devon Kohler > * May 6, Analysis of mass spectrometry images with Cardinal. Lead instructor: Kylie Bemis > * May 7, Modern software development practice with Python. Lead instructor: Charles Tapley Hoyt > * May 8, Scientific writing. Lead instructor: Alicia Williams > * May 8 – May 10, Interpretation of proteomic experiments in the context of biomolecular networks with INDRA. Lead instructor: Ben Gyori > * May 10, Barnett Institute 50th Anniversary and Karger Medal Celebration. Featured speakers: Jenny Van Eyk and Nikolai Slavov > A limited number of registration fee wavers will be available for students and postdocs affiliated with academic or nonprofit institutions in the US. > > Please share this widely. More information is athttps://computationalproteomics.khoury.northeastern.edu/
brian capaldo (08:30:39) (in thread): > I participated in the first year of the course, and have to say it was one of the best training experiences I had.
2024-02-13
Jianhai Zhang (18:48:14): > My package has an error due to the missing Seurat package (https://bioconductor.org/checkResults/devel/bioc-LATEST/spatialHeatmap/kunpeng2-buildsrc.html ). Could anyone install it on the devel platform “kunpeng2 Linux (openEuler 22.03 LTS-SP1) / aarch64”.
Hervé Pagès (20:12:53) (in thread): > Not sure why you decided to post this in#general, asking to almost 3000 people to help you with a build issue? Please ask on the#bioc-buildschannel like you did in the past for other build-related questions. Note that if you search the channel you’ll see that this question has been asked on Feb 5.
Jianhai Zhang (20:29:34) (in thread): > I logged on with a new email address and I cannot see the bioc-builds channel. Anyway I will keep it in mind the future.
2024-02-14
Jamie Whitehouse (04:59:52): > @Jamie Whitehouse has joined the channel
Ludwig Geistlinger (09:34:56): > cross-posting for folks broadly interested in proteomics, protein structures, PPIs, PTMs, and protein design. - Attachment: Attachment > We are excited to announce our upcoming town hall on AI applications for protein structure prediction . Join us March 05, 10 AM - 1 PM ET, for talks and discussions with leading experts from academia and industry!
Andres Wokaty (11:10:51): > The Bioconductor community will participate in the Outreachy May-August 2024 internship round. Outreachy partners with open source communities to provide opportunities to individuals impacted by systemic bias in tech with open source internships. Anyone within our community can propose an open source project to mentor an Outreachy intern. > > The deadline to submit a project is Feb. 23, 2024 at 4 pm UTC athttps://www.outreachy.org/communities/cfp/bioconductor/ . > > If you have questions or want help writing a project proposal, you’re welcome to reach out to me on Slack or via email atjennifer.wokaty@sph.cuny.edu . > > Mentors FAQ:https://www.outreachy.org/mentor/mentor-faq More details:https://www.outreachy.org/communities/cfp/
Patrizia Piotti (12:26:00): > @Patrizia Piotti has joined the channel
2024-02-15
Maria Doyle (07:05:13) (in thread): > :tada:Announcing the EuroBioC2024 Sticker Design Contest Winner: Thomas Klammsteiner@Thomas Klammsteiner! > > His design elegantly captures the essence of Oxford’s charm with genomic science. > > Learn more about Thomas:https://www.linkedin.com/in/tklammsteiner and the molecular ecology working group he’s part of:https://ecoevo.social/@Mol_Ecol . > > Looking forward to seeing everyone at the conference Sep 4-6! - File (PNG): v3_standard_no_crest.png
rohitsatyam102 (12:43:42): > Hi everyone. I have a naive question and I know someone might have already asked it. Why don’t people use LOPIT annotated datasets (such as one provided bypRolocdata) as training and test-set to make sub cellular localization tools like DeepLoc2
Olly Crook (13:17:04) (in thread): > DeepLoc2 takes in sequence data rather than context specific experimental mass-spectrometry data
rohitsatyam102 (13:28:14) (in thread): > What if the dataset is not context specific. For instance what if the dataset tries to explore the spatial proteomics for an organism where we are studying the protein localisation for the first time. We know protein sequences and we will have labels from hyperLOPIT. Can we use these labelled proteins now to build a sequence based classifier?
rohitsatyam102 (13:29:43) (in thread): > Likehttps://www.sciencedirect.com/science/article/pii/S193131282030514X
Olly Crook (13:31:29) (in thread): > yes! People do this all the time with these data
Olly Crook (13:32:33) (in thread): > but I would still say this is context specific experiment - a particular strain with particular lab condition etc
rohitsatyam102 (13:33:53) (in thread): > I recently took this Toxo HyperLOPIT dataset of 3800K genes, retrieved their sequences and ran deeploc2 on them and tried to compare the deeploc2 assignment with the HyperLOPIT assignment to see if deeploc2 was able to predict accurately the localisation based on sequence only. Deeploc2 could only classify 55% of protein correctly
rohitsatyam102 (13:36:06) (in thread): > It’s correct that it is from a particular strain but we can use orthology then to infer what will be the localisation of similar proteins in other strains isn’t it?
Olly Crook (13:40:39) (in thread): > yes, and in general these sequence only methods are quite weak
Vince Carey (14:17:33): > We want to hear from YOU!:loudspeaker:Many of you know Bioconductor is featured on NHGRI’s AnVIL Platform. Take a moment to share your experience using AnVIL and help shape its future development. Complete the State of the AnVIL Community Poll here and enter to win trainings and more:https://bit.ly/sota2024 Your feedback will help us understand how Bioconductor is being used on AnVIL and identify priorities for new features or training! - Attachment (Google Docs): The State of the AnVIL 2024: Community Poll > Thank you for participating in the State of the AnVIL 2024 Community Poll! We estimate this will take between 10 and 15 minutes to complete. Your feedback will help us as we continue developing this platform to support your research and data storage needs. At the end of the poll, you will be asked if we may contact you in the future to give further input. If you respond yes, we will request your contact information. > The AnVIL is the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space which provides a unified environment for secure data management and computation. This allows for cloud-based analysis of large datasets without having to move those datasets. > Finally, you will be asked if you want to be entered in the prize raffle. This could include training or resource opportunities. Any contact information you provide for this will only be used for the prize raffle.
2024-02-18
Anna Quaglieri (she/her) (17:34:05): > Hello Bioconductor Community:wave:It is important to reflect on the importance of upholding Bioconductorvalues often: our commitment to an open approach to science, collaboration, diversity, inclusivity, and a welcoming environment is at the core of our community. > > The Bioconductor Code of Conduct serves as a guiding light, ensuring that we maintain a supportive space for all. Let’s continue working together to nurture an environment that encourages the exchange of ideas and fosters collective growth. > > Everybody can reach theCode of Conduct committee if you consider that some situation doesn’t reflect these values. > > Thank you for your dedication to the Bioconductor community.
2024-02-19
Christine Hou (09:51:28): > @Christine Hou has joined the channel
Maria Doyle (11:31:43): > :mega:Abstract submission is open for #BioC2024 conference in Michigan:us:July 24-26http://www.bioc2024.bioconductor.org/ ! > > Submit your abstractby March 25 https://cfp.bioconductor.org/2024/cfp - File (PNG): BioC2024 Call For Abstracts.png
rohitsatyam102 (15:32:53): > Hi everyone. Is there a a way to scrap google scholar for a list of 30 genes. I tried using Rvest but my IP got blocked so I was wondering if there is any other automated method to do that. Manual querying of 30 genes is too much. The reason I want google scholar and not pubmed is because I have seen GSc also look for query keyword, supplementary and most of the preprints are also indexed therein.
2024-02-20
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Jenny Drnevich (12:04:53): > I didn’t see any channels about bulk RNA-Seq (too mainstream by the time this Slack started?), so I’m dropping this in the general. We recently got a NovaSeq X Plus where a single lane gives 1 billion reads and is cheaper than the old NovaSeq 6000 SP. So smaller projects of 6 or even 2 samples are getting their own lane and ending up with 250 - 800 M reads per sample, well more than the recommended 30-40 M. Someone assumed I would down-sample them, but I don’t think I need to - alignments are so fast these days that it would take more time to randomly sample than to just run everything. I assume we’d get more random alignments but that could be taken care through gene filtering. Any other downsides I am not seeing? I just hate throwing away data!
Sridhar N (12:10:58): > that sounds about right
Sridhar N (12:11:25): > i’d look at duplication/saturation rates
Sridhar N (12:12:19): > not sure about your samples but also look in to reads being sucked up by ribosomal genes..
Sridhar N (12:12:52): > we used to bake this pacakge in the final reporthttps://bioconductor.org/packages/release/bioc/html/dupRadar.html - Attachment (Bioconductor): dupRadar > Duplication rate quality control for RNA-Seq datasets.
Jenny Drnevich (12:13:30) (in thread): > Thanks for the suggestion!
Sridhar N (12:13:58): > may be not the most latest and greatest but you could downsample and see if you loose gain somthing new, in general what we obsrved was you would loose low expressed genes when you downsamples thigns..
Sridhar N (12:14:17): > sample logic with reads spanning splice junctions
Frederick Tan (15:19:20) (in thread): > For what it’s worth, we runhttps://nf-co.re/rnaseq which includes dupRadar among other QC tools
Sridhar N (15:23:15) (in thread): > Good to know its still used!
2024-02-21
Maria Doyle (07:38:59): > :trophy:Nominate for the Bioconductor Awards 2024!:trophy:We invite you to nominate individuals making outstanding contributions to our community. > This is your chance to honour their hard work and achievements!:star2:Criteria: Significant contributions in one or more ways to the project:busts_in_silhouette:Selection: 4 awardees based on impact:date:Deadline: May 15, 2024 > > Nominate Now:Nomination Form Learn More:Awards Details Recognise their impact: Nominate someone who’s making our community better. - File (PNG): BiocAwards (1).png
Maria Doyle (11:30:26) (in thread): > :writing_hand:New Bioconductor blog post by our current Outreachy interns! Check out their journey and the great work they’ve been doing:https://blog.bioconductor.org/posts/2024-01-31-OutreachyInternshipJourney/ Thanks@Chioma Onyido,@Esther Afuape, and@Peace Sandy:star2:If you’re inspired by their work and would like to mentor for the May-August intake, remember the deadline to submit a project is**** this Friday, Feb. 23 2024, at 4 pm UTC**. Learn more and submit your proposal here:https://www.outreachy.org/communities/cfp/bioconductor/ .
2024-02-23
Ludwig Geistlinger (12:21:29): > A colleague of mine reports issues with signing up for the Bioc slack. How should he proceed? - File (PNG): image (1).png
Marcel Ramos Pérez (12:23:22) (in thread): > @Alex MahmoudDoes the token need renewing?
Alex Mahmoud (12:26:53) (in thread): > It shouldn’t, but I see the error message. Might be that this type of legacy token is deprecated so have to generate the new type of app token, looking into it
Alex Mahmoud (12:40:44) (in thread): > They have new scopes now, and the default ones did not include theadmin:inviteto be able to invite people to workspace. I updated the bot scope with the permissions, and reinstalled it to update, however, now the issue is that the new required scopes seem to require extra permissions? - File (PNG): image.png
Chris Magnano (14:23:45): > @Chris Magnano has joined the channel
Alex Mahmoud (14:51:07) (in thread): > we’ve decided to shut off the app for now, and redirect to an invite link directly as we look at possible replacements, and the redirect is now live. Thanks for reporting!!
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2024-02-25
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2024-02-26
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2024-02-27
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2024-02-28
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Erica Feick (13:30:20): > :tada:BioC2024 is coming up and we want your thoughts! Help us craft our schedule byanswering this poll . And don’t forget tosubmit your abstracts for short talks and package demos! - Attachment (Google Docs): BioC2024 Workshop Poll > BIoC2024 will take place from July 24-26, 2024 in Grand Rapids, Michigan USA - Attachment (pretalx): BioC2024 > Schedule, talks and talk submissions for BioC2024
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2024-03-01
Ye Meng (04:03:48): > @Ye Meng has joined the channel
Maria Doyle (07:18:39): > :writing_hand:New Bioconductor blog post about the recent launch of the redesigned Bioconductor website. Check it out here:Bioconductor Website Update Blog Post
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Maria Doyle (14:25:22): > :mega:BioC2024: Registration Open Now!:sparkles:BioC2024 registration is live. Don’t miss your chance to join the conversation and expand your expertise.:link:Sign up here:https://buff.ly/3OQmuTs Got a knack for design? Enter the BioC2024 Sticker Design Contest to win your spot at the conference.:art:Enter here:https://buff.ly/3PrejNR Join us to network, learn, and contribute to the Bioconductor community. - File (PNG): BioC2024 Registration Open.png
2024-03-04
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2024-03-05
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Rodney Ighalo (02:13:20): > Hello, I joined through Outreachy. Those this project require designers?
Peace Daniel (02:19:49) (in thread): > Hi, welcome. The requirements for this project is listed on outreachy, please read it again to be sure. Also, ask questions regarding this project on#bugsigdb
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Precious Orakwe (13:48:50): > Hello team, good evening to everyone and to the mentors. my name is precious an outreachy applicant. i am excited to contribute to this project because i know i have a lot to learn and a lot to give back to this community, i plead for the teams assistance and the the mentors support and guidline
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Rodney Ighalo (14:33:08) (in thread): > Thank you.
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Andres Wokaty (15:00:27): > Welcome Outreachy applicants! Please join#bugsigdbfor project-specific discussions. You’re also welcome to join#outreachyfor outreachy-related discussions. Good luck:slightly_smiling_face:
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Ayomide Solarin (17:04:17): > Good evening everyone. I am an Outreachy applicant and i am super excited to learn and contribute
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2024-03-06
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Ufomba Justina (03:08:49): > Hi good morning everyone and to our mentor@Svetlana Ugarcina Perovicmy name is ufomba Justina an outreachy applicant and I’m super excited to be here. i am open to learn and make my contributions thank you all .
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Bolarinwa Abosede Julianah (03:47:07): > Welcome@Ibukun Hassan@Ufomba Justina@Manideep
Bolarinwa Abosede Julianah (03:48:12): > Do well to join#bugsigdbchanel
Abiola Salako (03:53:08) (in thread): > You’re welcome precious. > > Good to have you here
Abiola Salako (03:54:24): > Welcome@Ufomba Justinayou’re welcome do well to join the#bugsigdbchannel
Ibukun Hassan (03:55:16): > Goodmorning Everyone > My name is Ibukun HassanI’mso excited to here:tada:I hope to learn and contribute!
Ufomba Justina (04:00:50): > welcome@Ibukun Hassanhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94 . > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
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Neelam Mahraj (04:50:04): > Hey Everyone, > Neelam Mahraj here,
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Aleru Divine (04:53:44) (in thread): > Hi@Neelam Mahraj, welcome:hugging_face:Please join the#bugsigdbchannel. > > Also, you can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699
Neelam Mahraj (04:54:41) (in thread): > ok thanks for guidance
Aleru Divine (04:54:48) (in thread): > You’rewelcome
Deborah Oyawale (05:01:58): > Hi everyone! My name is Deborah Oyawale and I’m so excited to be here. I’m looking forward to learning and being able contribute to the success of this project under the tutelage of our mentor on this project@Svetlana Ugarcina Perovic
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Tanya Dwivedi (06:54:34): > Hello Everyone, My name is Tanya ,I’m thrilled to be a part of the Outreachy program as a Contributer .Looking forward to learning and contributing to the success of the Microbiome Study Curation Project under the guidance of our mentor@Svetlana Ugarcina Perovicma’am.
Aleru Divine (07:08:32) (in thread): > Hi@Tanya Dwivedi, welcome:hugging_face:Please join the#bugsigdbchannel.Also, you can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94 . > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Aleru Divine (07:08:56) (in thread): > @Tanya DwivediI’dbe more than happy to help if you need any assistance.
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Tanya Dwivedi (07:36:08) (in thread): > Thank you so much@Aleru Divine
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Esther Nelson (09:21:11): > Hi everyone, I am sure we are all amazing. I am Nelson Esther, a prospective Outreachy intern. I am a passionate Data Analyst and Writer and I am super excited to contribute to this project. Glad to connect with every one of you. Feel free to ask anything, let’s connect.
Prakriti Maurya (09:30:51): > @Prakriti Maurya has joined the channel
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Oluwatoyosi Victoria Olanrewaju (11:37:12): > @Oluwatoyosi Victoria Olanrewaju has joined the channel
Oluwatoyosi Victoria Olanrewaju (11:45:29): > Hello everyone, I’m Oluwatoyosi and I am more than pleased to be here as part of the Outreachy program as a contributor. Looking forward to connecting and making meaningful contributions.
Okhuomon Ajayi (12:06:30): > @Okhuomon Ajayi has joined the channel
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Andres Wokaty (12:29:43): > Welcome Outreachy applicants! Please join#bugsigdbfor Microbiome Study Curation (BugSigDB) discussions. We also have an Outreachy-specific channel#outreachy. Project mentors are on those channels and we can better support you there. This channel#generalalerts the entire community so it’s better to do introductions on#outreachy. Thank you and good luck!
eneje promise (13:09:11): > @eneje promise has joined the channel
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Hamidat Mohammed (14:24:16): > Good Evening everyone. My name is Mohammed Hamidat. I am an outreachy intern Applicant. This is my first open source project and I am very excited to be here and ready to make meaningful contributions
Abbah Divine (14:32:51): > @Abbah Divine has joined the channel
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Idiat Alli (14:42:04) (in thread): > Welcome.
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Anju Maurya (23:07:50) (in thread): > Welcome@Hamidat Mohammed!
2024-03-07
Precious Chilaka (00:51:37): > @Precious Chilaka has joined the channel
Faith Ifeoluwa Alexander (00:57:42) (in thread): > Have you been able to make your first contribution?@Hamidat Mohammed
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USLACKBOT (10:31:13): > This message was deleted.
Sean Davis (10:32:09) (in thread): > Wrong channel?
Preethi grace Manthena (11:09:12): > Hii everyone.I’m Preethi Grace from India, currently pursuing my bachelor’s in Electronics and Communication Engineering. I’m thrilled to be here and eager to contribute my best to this project to the success of Microbiome Study Curation. under guidance of@Svetlana Ugarcina Perovicmam.I’m excited to get started and would appreciate any help or guidance.
Binita Dhakal (11:25:06): > @Binita Dhakal has joined the channel
wizdom Chris (11:44:28): > @wizdom Chris has joined the channel
Ikeh Darlington Ikeh (12:32:53): > @Preethi grace ManthenaWelcome onboard
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fetlework gubena arage (14:42:47): > @fetlework gubena arage has joined the channel
fetlework gubena arage (14:47:03): > Hello everyone, my name is fetlework from Ethiopia, excited to be here and learn from everyone here. hope to contribute under the guidance of@Svetlana Ugarcina Perovic
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anushka singh (15:38:59): > @anushka singh has joined the channel
Aleru Divine (15:39:58): > Hi@fetlework gubena arage@Flourish Ralph, welcome:hugging_face:Please join the#bugsigdbchannel, there are resources there and it is where everyone communicates, including the mentors and fellow contributors.
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2024-03-08
DataWithPrecision (00:08:42): > @DataWithPrecision has joined the channel
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Raihanat Adewuyi (04:56:11): > @Aleru Divineplease how do I curate and issue given to me.. > I have read and put down some point in Ms work how do I add it to bugsigdb
Aleru Divine (04:58:47): > @Raihanat Adewuyigo to the BugSigDB main page and click on the “+ Add a Study”https://bugsigdb.org/Main_Page - Attachment (BugSigDB): Main Page > … - File (JPEG): IMG_7766
Aleru Divine (04:59:02): > Have you requested an account already?
Raihanat Adewuyi (05:01:39): > I did that and in putted everything.. > But I was told that I do not have permission to edit the page and all my work disappeared
idiaru Angela (05:02:45) (in thread): > Do you have an account?
Raihanat Adewuyi (05:03:32) (in thread): > Yes I do and it was approved
Svetlana Ugarcina Perovic (05:24:08) (in thread): > Wrong channel. Please continue your discussion in#bugsigdb
Svetlana Ugarcina Perovic (05:24:46) (in thread): > Wrong channel. Please continue your discussion in#bugsigdb
Aleru Divine (05:25:34) (in thread): > My apologies
Svetlana Ugarcina Perovic (05:25:45) (in thread): > no worries
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acha rhaah (07:35:03): > Good afternoon everyone. My name is Acha Rha’ah and Im from Cameroon. I am super excited to be here to grow and make meaningful contributions:smiley:
Joan C. Chukwuemeka (09:15:16) (in thread): > Welcome@acha rhaahdo join#bugsigdbchannel for outreachy related discussions and resources
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Emem Eduoku (13:42:23): > If you’re just joining the channel today, join#bugsigdbtoo get more information on everything you’d be doing
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Evelyn Mary Attah (17:46:14): > Hello everyone, my name is Evelyn from Nigeria. I am excited to be here in this community and hoping to learn from everyone.
2024-03-09
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Ima-obong (Aimah) (01:47:21): > Hello everyone it’s a new day and if you’re new here please joing the#bugsigdbchannel to begin your contributions
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Peace Daniel (17:03:19) (in thread): > Hello Evelyn,welcome. Do join this group#bugsigdb
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2024-03-10
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2024-03-11
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Isha Kashyap (10:22:17): > Hello everyone, myself Isha from India. It is overwhelming as well as exciting to be here to work and grow in open source with the guidance and community help. I am relatively new, so I will be looking forward to talk to all of you. Thank you.
Michael Adekanye (11:41:40) (in thread): > Please join the#bugsigdbchannel and go through the pinned messages for a start.
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2024-03-12
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subhiksha sundaram (00:22:42): > hi all i am working with Medip-seq data. I tried using the MEDIPS-R package and followed the instructions in the manual. I have few doubts understanding the result. chr start stop mmp40.bam.counts s4dna.bam.counts mmp40.bam.rpkm s4dna.bam.rpkm MSets1.counts.mean MSets1.rpkm.mean MSets2.counts.mean MSets2.rpkm.mean edgeR.logFC edgeR.logCPM edgeR.p.value edgeR.adj.p.value 1_id 2_id 3_id > 1152833 chr1 115283201 115283300 66 0 569.06 0 66 569.06 0 0 9.38062365468903 3.74971858632751 1.21128729477115E-22 5.33563574335627E-17 ENSG00000285698 ENSG00000228035 NA > 1152834 chr1 115283301 115283400 123 0 1060.53 0 123 1060.53 0 0 10.2777407051359 4.65272618085034 9.17824982124343E-42 4.04295479850898E-36 ENSG00000285698 ENSG00000228035 NA > 1152835 chr1 115283401 115283500 175 0 1508.88 0 175 1508.88 0 0 10.7860919424516 5.16659956323243 5.12989637130111E-59 2.25968344228354E-53 ENSG00000285698 ENSG00000228035 NA > 1152836 chr1 115283501 115283600 215 0 1853.76 0 215 1853.76 0 0 11.0829216668553 5.46656728985704 2.36234658646107E-72 1.04059713491E-66 ENSG00000285698 ENSG00000228035 NA > 1152837 chr1 115283601 115283700 221 0 1905.5 0 221 1905.5 0 0 11.1226133197082 5.50666271626026 2.00704106996786E-74 8.84087542033354E-69 ENSG00000285698 ENSG00000228035 NA > 1152838 chr1 115283701 115283800 221 0 1905.5 0 221 1905.5 0 0 11.1226133197082 5.50666271626026 2.00704106996786E-74 8.84087542033354E-69 ENSG00000285698 ENSG00000228035 NA Can anyone explain what is the three id mentioned at the last. some have the ensembl id and few say NA. what significance does it have to that particular chromosome position?https://www.bioconductor.org/packages//2.7/bioc/vignettes/MEDIPS/inst/doc/MEDIPS.pdf this was the reference manual that i used. - File (PNG): image.png
Saasha Gupta (03:52:14): > @Saasha Gupta has joined the channel
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White Kiky (08:05:18): > @White Kiky has joined the channel
White Kiky (08:05:59): > :wave:Hello, team!
Mkpouto Shedrack (08:14:21): > @Mkpouto Shedrack has joined the channel
Adenike Oladimeji-Kasumu (08:49:01): > You’re welcome@White KikyDo join the#bugsigdbchannel and read the pinned messages to get started
Maria Doyle (08:59:18): > :wave:Welcome to all the Outreachy contributors and new members! We’re thrilled to have you join our community. A special thanks to members for helping guide our newcomers. As a friendly reminder, we encourage you to use the#introductionschannel for your introductions and the#bugsigdbchannel for discussions related to Outreachy and bugsigdb queries. This helps us keep our community organised and makes it easier for everyone to follow along and contribute effectively. Looking forward to your contributions and thank you for being part of our community!
Maria Doyle (09:16:22) (in thread): > Hi Subhiksha, it’s great you’ve sought help with MEDIPS at Bioconductor support site (https://support.bioconductor.org/p/9157065/ ). It’s the ideal spot for queries about using packages. Hopefully, someone there can help you!
Dima Lvovs (20:43:42): > Hi everyone, sorry if it’s obvious, I wasn’t able to find the answer fast: is it OK to leave Dockerfile in the branch that is pushed to the Bioconductor?
Guan Gui (22:14:57): > @Guan Gui has joined the channel
2024-03-13
Shila Ghazanfar (00:11:43): > Dear Bioconductor members - especially those in Australia who are not yet part of the ABACBS - Australian Bioinformatics and Computational Biology Societywww.abacbs.org :flag-au::kangaroo::coffee::sunny::beach_with_umbrella::parrot_aussie::flag-au:(Apologies for cross-posting) > > Next week we will have a specialABACBS Fellowships and Grants Panel shila.ghazanfar@sydney.edu.au . Be sure to check your spam folder for the registration confirmation.Date: Tuesday, March 19 2024 Time: 01:00 PM - 03:00 PM Canberra, Melbourne, Sydney (AEDT) https://uni-sydney.zoom.us/meeting/register/tZcvcOGgqDMsHdYgae3pANsb8QtLj0hN1Mtx After registering, you will receive a confirmation email containing information about joining the meeting. > > Best wishes, > on behalf of the ABACBS National Executive Committeewww.abacbs.org
assel (02:20:32): > @assel has joined the channel
Vince Carey (07:50:06) (in thread): > I’d say that the working approach is that any file not needed for the package should be excluded from the bioconductor branch. But I think you could leave it on the branch if you add it to .Rbuildignore. We might make the rules on this topic more specific.
Raony Guimaraes Corrêa Do Carmo Lisboa Cardenas (10:49:34): > @Raony Guimaraes Corrêa Do Carmo Lisboa Cardenas has joined the channel
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2024-03-14
Maria Doyle (05:11:17): > :mega:Reminder: BioC2024 Opportunities Abstract Submission: here .:art:Sticker Design Contest: here . > > Don’t miss out on these chances to contribute to BioC2024!
Vinay Mannam (10:31:19): > @Vinay Mannam has joined the channel
2024-03-15
Tung Trinh (02:22:56): > @Tung Trinh has joined the channel
subhiksha sundaram (07:28:29) (in thread): > Thanks
Mindy Kim Graham (18:05:58): > @Mindy Kim Graham has joined the channel
2024-03-17
Aananditaa (01:58:09): > Hii everyone!! > Could anyone please tell, how much time after requesting an account, we get the account access?
Taiwo Akinlagun (06:18:32): > @Taiwo Akinlagun has joined the channel
EBERE ADEKOGBE (12:14:31) (in thread): > @AananditaaIt does not take long. it only requires you to confirm your email address. Within 5-10mimutes should do
Aananditaa (13:39:40) (in thread): > @EBERE ADEKOGBEhave received now.. Thanks for responding :)
EBERE ADEKOGBE (14:31:46) (in thread): > You are welcome
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2024-03-18
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2024-03-19
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2024-03-20
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Praise Agbetuyi (19:38:44) (in thread): > It is good to know you have your account now. Welcome onboard@Aananditaa
2024-03-22
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Maria Doyle (10:47:40): > :loudspeaker:Good News!:rotating_light:We’ve extended the deadline! The BioC2024 call for abstracts and sticker contest entries now has a new submission deadline ofApril 1st https://www.bioc2024.bioconductor.org/ - File (PNG): BioC2024 Call For Abstracts (1).png
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Erica Feick (15:42:35): > To get all the updates on BioC2024, please join the new#bioc2024channel!
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2024-03-25
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2024-03-26
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Alex Mahmoud (15:31:33): > PSA: for anyone interested in WebR/RWASM developments related to Bioconductor, there is a#wasmchannel with more discussion. WebR is a client-side (running entirely in your browser with no server backing it) way of running R code. We now have an experimental repository for ~2100 Bioconductor packages for webR pushed tohttps://webr.bioconductor.org/3.18 . > > WebR team provides a testing environment athttps://webr.r-wasm.org/latest/ where you may use a combination of their repository (for CRAN packages) with our experimental repository for Bioconductor ones. Eg: > > webr::install("SingleCellExperiment", > repos=c("[https://repo.r-wasm.org/](https://repo.r-wasm.org/)","[https://webr.bioconductor.org/3.18](https://webr.bioconductor.org/3.18)")) > > Any feedback welcome for how useful this is and/or how to make it more useful!
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2024-03-27
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2024-03-28
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2024-03-29
Maria Doyle (08:07:15) (in thread): > :loudspeaker::alarm_clock:Final Call April 1st BioC2024 submissions for guidelines and to submit your work. Looking forward to your contributions!
2024-04-01
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2024-04-02
Leonardo Collado Torres (21:07:08) (in thread): > Sounds useful and definitely interesting!
2024-04-03
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Lu Zhou (07:41:45): > :wave:Hi everyone! Nice to meet you all
Maria Doyle (09:52:13) (in thread): > Welcome Lu!:wave:Nice to meet you too. Feel free to share about yourself in#introductionsif you want to. Looking forward to connecting with you!
Jenny Drnevich (10:08:35): > ~~~This is a ~****~warning ~****~to anyone using NCBI’s new mouse RS_2024_02 transcriptome that was released in Feb 2024.~~~Warning RETRACTED. Apparently it was in internal error of someone copying the file instead of re-downloading. I thought I had double-checked the error still persisted on a fresh download, but I think it’s not the case. Although it would help if NCBI versioned their gene annotation files in the name instead of just the genome version!
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2024-04-04
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2024-04-05
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2024-04-07
Givanna Putri (19:35:41): > hi guys, sorry i accidentally added a slack connect invite that meant to go to different a team but ended up here. please just reject it as i have no clue how to undo the request
Givanna Putri (21:03:20) (in thread): > sorted. thanks@Marcel Ramos Pérez
2024-04-08
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2024-04-09
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Ludwig Lautenbacher (12:28:45): > Hi everyone! I have a quick question that I hope you are able to help me with. I’m preparing to submit a package to Bioconductor. The package is a client for a web server, and its R code resides in a subdirectory of the main GitHub repository. Can I submit it from this subdirectory, or do I need to create a separate repository for the submission? I would prefer to have the client and server code in the same repo but if that is not supported I will seperate them.
Kasper D. Hansen (13:10:51): > You probably have to separate them. There is a part of the submission process where our build system pulls the code from the repos and builds it automatically, and that might be very hard to handle with your setup. I do get your point though.
Vince Carey (14:51:30): > Thanks@Kasper D. HansenI think you are right but@Ludwig Lautenbacherif u would like to get into details lets use#developers-forum
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2024-04-11
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2024-04-12
Maria Doyle (05:42:10): > :hourglass_flowing_sand:Just a friendly heads-up that there’s two weeks left until the abstract submission deadline for EuroBioC2024 onApril 26th EuroBioC2024 Submission Page - File (PNG): EuroBioC2023 Abstracts open (1).png
Gordon Zheng (12:16:11): > Hi, all. I was wondering if there is a support chat for FGSEA. I am having an issue with the coding.
Andres Wokaty (13:02:36) (in thread): > Have you tried asking onhttps://support.bioconductor.org/ if you’re having trouble using the package? > > If there is a problem with the fsgea code, you can make a bug report on their issue tracker athttps://github.com/ctlab/fgsea/issues .
Felipe ten Caten (13:22:58): > @Felipe ten Caten has joined the channel
2024-04-13
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2024-04-14
Shian Su (19:38:44): > Has anyone implemented a parquet/arrow equivalent of tabix yet? Last time I visited the idea, itwasn’tclear if it was possible to create an index (or two since we need chromosome and position). Most recent information I can find seems to be from 23andme using it for VCFs but their use case seems to be whole-column access.
Shian Su (19:40:30): > I’mdesperate for a compressed tabular data storage with fast random access to genomic regions thatisn’tbottlenecked by gzip.
Martin Morgan (23:06:04) (in thread): > Have you looked at duckdb, which can read csv (alsoparquet ) files (in parallel ) and has good range-based queries (outlined at the end ofthis section of the AlphaMissenseR vignette, and in thisduckdb blog post ). It integrates easily with R DBI / dbplyr, including through the even more efficientduckplyr package (I haven’t explored ranged queries in duckplyr). Also maybegdsfmt ? - Attachment (DuckDB): Reading and Writing Parquet Files > Examples – read a single Parquet file SELECT * FROM ‘test.parquet’; – figure out which columns/types are in a Parquet file DESCRIBE SELECT * FROM ‘test.parquet’; – create a table from a Parquet file CREATE TABLE test AS SELECT * FROM ‘test.parquet’; – if the file does not end in “.parquet”, use the read_parquet function SELECT * FROM read_parquet(‘test.parq’); – use list parameter to read 3 Parquet files and treat them as a single table SELECT * FROM read_parquet([‘file1.parquet’, ‘file2.parquet’, ‘file3.parquet’]); – read all files that match the glob pattern SELECT * FROM ‘test/.parquet’; – read all files that match… - Attachment (DuckDB): Reading Multiple Files > DuckDB can read multiple files of different types (CSV, Parquet, JSON files) at the same time using either the glob syntax, or by providing a list of files to read. See the combining schemas page for tips on reading files with different schemas. CSV – read all files with a name ending in “.csv” in the folder “dir” SELECT FROM ’dir/.csv’; – read all files with a name ending in “.csv”, two directories deep SELECT * FROM ’ // .csv’; – read all files with a name ending in “.csv”, at any depth in the folder “dir” SELECT * FROM ’dir/****/*.csv’;… - Attachment (mtmorgan.github.io): Accessing AlphaMissense Resources in R > AlphaMissenseR - Attachment (DuckDB): Range Joins in DuckDB > DuckDB has fully parallelised range joins that can efficiently join millions of range predicates. - Attachment (Bioconductor): gdsfmt > Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.
Shian Su (23:17:32) (in thread): > Thanks Martin, GDS might not be appropriate becauseI’mnot working with VCFs, but DuckDB might be exactly whatI’mlooking for. From further reading of parquet, it should be storing column ranges in metadata within each block. So in theoryI don’tneed any indexing for sorted columns and a direct query via DuckDB (via dbplyr?) would efficiently retrieve the range I want.
Shian Su (23:27:50) (in thread): > @Martin Morganwould you happen to have any opinions regarding using the native DuckDB format vs Parquet for genomic data?
2024-04-15
Michael Milton (00:48:04) (in thread): > ~If you’re after compression as well as range access, I believe you will still need to enforce a chunking pattern, but Parquet does support this.~DuckDB seems to automatically handle range queries using row groups, which are separately compressed:https://duckdb.org/2021/06/25/querying-parquet#automatic-filter–projection-pushdown
Michael Milton (00:52:50) (in thread): > If you intend to distribute the data then you should use Parquet and not the native format, since the native format changes between DuckDB versions. It also seems to be faster to process Parquet:https://github.com/duckdb/duckdb/discussions/10161
Shian Su (02:12:52) (in thread): > Now I remember what stopped me the last time I looked a this. The R API to Parquet does not to offer a way to write a single file without loading all the data into the memory first, thus negating the primary use-case I have, which is to work on data too-large-for-memory.https://github.com/apache/arrow/issues/32708 indicates this will not be a feature for R. - Attachment: #32708 [R] Add append option to write_parquet > Hi, parquet format helps a lot to handle data, I think would be great add an option to can write data appending it to a particular file, this is necessary when we works with a lot of data. > > https://arrow.apache.org/docs/r/reference/write_parquet.html > > Thx! > > Reporter : Lagu Watchers : Rok Mihevc / @rok Note : This issue was originally created as ARROW-17442 . Please see the migration documentation for further details.
Michael Milton (02:22:11) (in thread): > Can you explain your use case further? Do you have a source file that is too large for memory that you want to convert to parquet? You could try incrementally writing separate parquet files and then combine them using duckdb. Or alternatively you could incremental writes in Python/reticulate
Shian Su (02:25:12) (in thread): > I have a 1TB tsv file and would like to turn that into a single parquet file. I know I can have a hundred smaller parquet files but I’m not interested in implementing that in a way that’s constrained by system memory, any splitting implementation I would consider would be at the chromosome/sample or other meaningful level, not by system memory.
Shian Su (02:29:03) (in thread): > I believe might be a way to useopen_dataset()on a tsv file andwrite_dataset()to parquet. Unfortunatelyopen_dataset()appears to be broken on macOS basic installations for now.https://github.com/apache/arrow/issues/40667#issuecomment-2007942987 (should be fixed at next CRAN release) - Attachment: Comment on #40667 [R] arrow R package 15.0.1 missing dataset, parquet, etc. on Mac M2 > Hi all, sorry for the trouble. The most recent submission (15.0.1) ran into some trouble after acceptance when being built on macOS. This lead to the reduced feature-set. We’re actively working on preparing a new submission so the macOS version of the package has the usual feature-set but it may take some time. > > In the mean time, 15.0.1 is now on R-universe so you should be able to install a binary using: > > > install.packages('arrow', repos = c('[https://apache.r-universe.dev](https://apache.r-universe.dev)')) > > > @letitbk
Shian Su (02:34:26) (in thread): > I also won’t use Reticulate for a single feature because maintaining and debugging across R-Python doesn’t sound like it’s worth the trouble.
Michael Milton (02:37:25) (in thread): > You can probably do the whole operation using DuckDB. If you prefer you can use an R interface for it (for exampledbplyr). DuckDB can read directly from csv/tsv files and write to parquet:https://duckdb.org/docs/data/csv/overview.html
Michael Milton (02:41:18) (in thread): > The SQL would be something like:
FROM read_csv('input.tsv', delim = '\t', ... )
TO 'output.parquet' (FORMAT 'parquet', ...);
Shian Su (03:00:23) (in thread): > Thanks! That should be useful if I can’t get the *_dataset functions working.
Shian Su (03:20:47) (in thread): > Using nightly build for Arrow fixesopen_datasetandwrite_dataset, early results promising. A 68GB tsv compresses to 20GB under bgzip and only 5.1GB under parquet.
Shian Su (09:06:26) (in thread): > > library(arrow) > library(dplyr) > library(Rsamtools) > library(duckdb) > library(dbplyr) > > data_pq <- open_dataset("data/data.pq", format = "parquet") > > query_pq <- function(x, chr, start, end) { > x %>% > filter( > pos >= start & pos <= end > ) %>% > collect() > } > > query_tabix <- function(file, chr, start, end) { > scanTabix(file, param = GRanges(paste0(chr, ":", start, "-", end))) > } > > bm <- bench::mark( > pq_5k = query_pq(data_pq, "U00096.3", 2641650, 2641650 + 5000), > tb_5k = query_tabix("data/data.tsv.gz", "U00096.3", 2641650, 2641650 + 5000), > pq_10k = query_pq(data_pq, "U00096.3", 2641650, 2641650 + 10000), > tb_10k = query_tabix("data/data.tsv.gz", "U00096.3", 2641650, 2641650 + 10000), > pq_20k = query_pq(data_pq, "U00096.3", 2641650, 2641650 + 20000), > tb_20k = query_tabix("data/data.tsv.gz", "U00096.3", 2641650, 2641650 + 20000), > pq_40k = query_pq(data_pq, "U00096.3", 2641650, 2641650 + 40000), > tb_40k = query_tabix("data/data.tsv.gz", "U00096.3", 2641650, 2641650 + 40000), > check = FALSE, > min_iterations = 10 > ) > > bm[, 1:9] > > expression min median `itr/sec` mem_alloc `gc/sec` n_itr n_gc total_time > <bch:expr> <bch:tm> <bch:tm> <dbl> <bch:byt> <dbl> <int> <dbl> <bch:tm> > 1 pq_5k 51.57ms 53.06ms 18.8 3.65MB 0 10 0 530.93ms > 2 tb_5k 663.15ms 684.72ms 1.44 35.44MB 0.160 9 1 6.25s > 3 pq_10k 60.03ms 63.06ms 15.9 7.52MB 0 10 0 630.23ms > 4 tb_10k 1.26s 1.29s 0.767 60.36MB 0.192 8 2 10.43s > 5 pq_20k 76.97ms 82ms 11.9 14.12MB 0 10 0 837.93ms > 6 tb_20k 2.48s 2.51s 0.398 145.01MB 0.398 5 5 12.55s > 7 pq_40k 100.64ms 105.07ms 9.40 28.63MB 1.04 9 1 957.35ms > 8 tb_40k 4.27s 4.29s 0.233 276.39MB 0.932 2 8 8.59s > > Had to manually set a row-group size, the default seem to be only 10k rows, I set it to 300k which created ~800kb row groups (was aiming for 1MB). The performance seems to be very good, and scaling somewhat miraculously.
Shian Su (09:08:04) (in thread): > This is without using DuckDB, it wasn’t clear in R how to connect it to a parquet file.
Shian Su (09:25:37) (in thread): > > query_duckdb <- function(file, chr, start, end) { > tbl(con, sprintf("read_parquet('%s')", file)) %>% > filter( > pos >= start & pos <= end > ) %>% > collect() > } > > I believe this is how it’s supposed to be done according tohttps://duckdb.org/docs/api/r.html , though I may be mistaken because there seems to be a pretty significant performance penalty > > expression min median `itr/sec` mem_alloc `gc/sec` n_itr n_gc total_time > <bch:expr> <bch:tm> <bch:tm> <dbl> <bch:byt> <dbl> <int> <dbl> <bch:tm> > 1 pq_5k 50.11ms 54.11ms 18.4 3.65MB 0 10 0 543.38ms > 2 dd_5k 215.54ms 227.24ms 4.41 43.29MB 0 10 0 2.27s > 3 tb_5k 766.67ms 784.51ms 1.27 35.44MB 0.141 9 1 7.11s > 4 pq_10k 56.97ms 62.27ms 15.9 7.52MB 0 10 0 627.35ms > 5 dd_10k 388.2ms 426.24ms 2.31 89.75MB 0.256 9 1 3.9s > 6 tb_10k 1.34s 1.34s 0.738 60.54MB 0.0820 9 1 12.2s > 7 pq_20k 73.8ms 81.37ms 11.8 14.12MB 1.31 9 1 761.02ms > 8 dd_20k 669.56ms 690.89ms 1.45 168.89MB 0.619 7 3 4.84s > 9 tb_20k 1.94s 2.48s 0.419 145.01MB 0.180 7 3 16.69s > 10 pq_40k 97.28ms 117.97ms 8.48 28.63MB 0 10 0 1.18s > 11 dd_40k 876.42ms 906.82ms 1.10 342.95MB 0.736 6 4 5.43s > 12 tb_40k 4.19s 4.19s 0.238 244.39MB 0.555 3 7 12.61s > - Attachment (DuckDB): R API > Installation duckdb: R API The DuckDB R API can be installed using install.packages(“duckdb”). Please see the installation page for details. duckplyr: dplyr API DuckDB offers a dplyr-compatible API via the duckplyr package. It can be installed using install.packages(“duckplyr”). For details, see the duckplyr documentation. Reference Manual The reference manual for the DuckDB R API is available at R.duckdb.org . Basic API Usage The standard DuckDB R API implements the DBI interface for R. If you are not familiar with DBI yet, see here for an introduction. Startup & Shutdown To use DuckDB, you must first create a connection object that represents…
Shian Su (09:32:27) (in thread): - File (PNG): image.png
Martin Morgan (12:02:51) (in thread): > That’s really helpful!@Michael Miltonmentioned that > > the native format changes between DuckDB versions > but that was only true before version 0.10;the format is now stable . > > Something like the following would create a DuckDB database from the parquet file(s) > > duckdb_dir <- tempfile() > duck_db <- dbConnect(duckdb(), dbdir = duckdb_dir, read_only = FALSE) > > DBI::dbExecute( > duck_db, > "CREATE TABLE test AS SELECT * FROM 'data/data.pq'" > ) > > and thentbl(duck_db, "test")provides dplyr access; I think it’ll be faster than using parquet-via-duckdb, though I don’t know about arrow directly. > > I did want to mention again therange joins in DuckDB (illustrated in theAlphaMissenseR vigentte ). It seems like a very common use case is basicallyfindOverlaps()between 100’s or 1000’s of genomic regions of interest and the data. The query in the benchmark would have to be repeated for each region of interest, so execution would scale linearly with number of regions. The range join (maybe it has to be written directly in SQL, rather than through dplyr syntax) is much better than this, maybe thesame order of magnitude assubsetByOverlaps()?
Michael Milton (19:14:29) (in thread): > I’m surprised that DuckDB is this much slower as well. Is your parquet dataset composed of multiple files?
Shian Su (19:14:57) (in thread): > Just a single one
Shian Su (19:17:28) (in thread): > Could just be a constant overhead that becomes negligible if queries take minutes, butI’mlooking for sub-second responses.
Shian Su (19:28:35) (in thread): > I think it’s also neat that arrowwrite_dataset()can automatically partition the data by specific columns. Could make it a lot easier to subset data for distribution.
Shian Su (19:28:51) (in thread): > i.e. at the sample or chromosome level
Shian Su (19:34:04) (in thread): > Also noticed that the parquet size shrunk further under the larger row-group size. It’s now 2GB. Also created the duckdb using Martin’s code. So we’re at > * raw: 68GB > * bgzip: 20GB > * duckdb: 12GB > * parquet: 2GB
Shian Su (21:39:16) (in thread): > > query_duckdb_dbplyr <- function(con, chr, start, end) { > tbl(con, "test") %>% > filter( > chr == chr & pos >= start & pos <= end > ) %>% > collect() > } > > query_duckdb_sql <- function(con, chr, start, end) { > dbGetQuery(con, sprintf("SELECT * FROM 'test' WHERE chr = '%s' AND pos >= %d AND pos <= %d", chr, start, end)) > } > > Tried out querying the DuckDB native database. - File (PNG): image.png
Shian Su (21:45:15) (in thread): > I’m looking to implement a new storage format for NanoMethViz which stores per read, per site methylation data (currently using tabix). The data will be read-only and I’m querying out particular regions to plot. So far arrow-parquet seems like the most efficient and simple solution, with the advantage that it’s extensible via DuckDB later on if I require more complicated queries.
2024-04-17
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Changqing (21:01:24): > Was wondering how one can create an alignment plot with reads colored by a bam tag / read ID / user provided vector like this: (Fig4c fromhttps://doi.org/10.1186/s13059-021-02505-w ) > I had a look with Gviz and it does not look like you can do it with Gviz::AlignmentsTrack - File (PNG): Screenshot 2024-04-18 at 10.57.02 am.png
2024-04-18
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Vince Carey (07:23:04) (in thread): > Did you post tosupport.bioconductor.org ? Lots more eyeballs there … If the underlying tooling is in python it might be worth building an interface. Check with the paper authors?
Changqing (08:37:51) (in thread): > Thanks, I’ll give it a try!
Jenny Drnevich (09:20:18) (in thread): > From the end of the methods: “A custom UCSC Track Hub displaying pseudobulk snATAC peaks per cluster, LR-Split-seq reads used for TSS calling per cluster, ENCODE cCREs, and GENCODE vM21 transcript models can be found athttps://github.com/erebboah/c2c12_trackhub .” > > Also in the methods: “Figure generation code can be found athttps://github.com/fairliereese/2021_c2c12 [52 ] or on Zenodo athttps://doi.org/10.5281/zenodo.5168059 . All code is available under the MIT open source license.” > > This is the kind of documentation I long for when someone asks me to make a figure from a paper!! - Attachment (BioMed Central): Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq - Genome Biology > The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells. - Attachment (Zenodo): fairliereese/LR-splitpipe: LR-splitpipe v1.0 > Code to demultiplex long-read Split-seq data
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Maria Doyle (06:29:17): > :tada:Announcing the BioC2024 Sticker Design Contest Winner: Farhan Ameen@Farhan Ameen! > > We’re thrilled to present Farhan’s winning design, which creatively draws inspiration from the Grand Rapids city logo, featuring the blue of the Grand River, the iconic red of La Grande Vitesse sculpture, and the bright yellow of the Michigan sun. > > Discover more about Farhan and his work: > Linkedin:http://linkedin.com/in/farhan-ameen-5913841b0 Github:https://github.com/fame2827 Join us in celebrating Farhan’s contribution and don’t forget to mark your calendars forBioC2024 , happening July 24-26! - File (PNG): Asset 8.png
Emil Funk (07:20:43): > @Emil Funk has joined the channel
2024-04-24
USLACKBOT (03:08:21): > This message was deleted.
Martin Grigorov (03:17:42) (in thread): > according tohttps://github.com/r-lib/actions/tree/v2/setup-r#inputs you could usedevelas a version too
Martin Grigorov (03:17:58) (in thread): > What issues do you face ?
Tuomas Borman (03:18:53) (in thread): > Also check rworkflows@Jacques SERIZAYis one of the contributors
Kristian Ullrich (03:19:55) (in thread): > The issue is related to one package of mine:https://github.com/kullrich/CRBHits . The problem in most cases is that the pipeline fails on every release-cycle because of building the vignettes and deploying the package pages with “pgkdown”.
Kristian Ullrich (03:21:40) (in thread): > Therefore I need to adjust the dependencies for each cycle, so that the community sees the flag “pipline passed”, which of course is a bit annyoing, but since most bioinformatician just rely on pipelines where people can see a green flag, I try to keep up-to-date with it.
Kristian Ullrich (03:24:25) (in thread): > Thx@Martin GrigorovI will have a look so that I can more easily switch between the cycles.
Martin Grigorov (03:34:51) (in thread): > How about having two Git branches athttps://github.com/kullrich/CRBHits -develandrelease. Each of them will have its own Github Actions workflow and its own version of DESCRIPTION so that you could install the dependencies withhttps://github.com/r-lib/actions/tree/v2/setup-r-dependencies ?
Kristian Ullrich (03:37:18) (in thread): > Hi, that might be a good soultion for CRBHits, I could not put it until now to bioc, since it so far compiled “last” and “dagchainer” within the pacakge, which works fine on linux/mac but fails on Windows, due to licence restrictions with “mingw”.
Kristian Ullrich (03:55:07) (in thread): > Also thx@Tuomas Bormanfor the suggestion
Alan O’C (04:25:35) (in thread): > You can submit to Bioc with windows builds disabled
Kristian Ullrich (04:35:46) (in thread): > Hi, thx, I know, anyhow I would like to provide it for any OS
Jacques SERIZAY (04:55:25) (in thread): > @Kristian Ullrichyou can userworkflows( ccing@Brian Schilderhere) as@Tuomas Bormanmentioned. You can set up a simplerworkflows.yml(e.g.https://github.com/js2264/tidyCoverage/blob/devel/.github/workflows/rworkflows.yml ) in your .github folder, which will trigger therworkflowGHA (https://github.com/marketplace/actions/rworkflows ). > You can tweak the configuration to run the checks on different configs in the matrix:https://github.com/js2264/tidyCoverage/blob/devel/.github/workflows/rworkflows.yml#L23-L39 . > > More to read on therworkflowspackage repo:https://github.com/neurogenomics/rworkflows Don’t hesitate to ask if smth is not clear!
Mike Smith (05:41:53) (in thread): > You could try the actions I provide athttps://github.com/grimbough/bioc-actions The intention is that you can specify e.g.bioc-version: develand the action will determine the version of R and Bioc you want etc. Assuming I keep the mapping file up-to-date you won’t need to worry about updating your workflow to specify that.
Kristian Ullrich (07:54:22) (in thread): > Thx@Jacques SERIZAYand@Mike SmithI will have a look
Lluís Revilla (08:11:58) (in thread): > There is also biocthis:https://bioconductor.org/packages/release/bioc/html/biocthis.html - Attachment (Bioconductor): biocthis > This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly.
Maria Doyle (09:26:40) (in thread): > :loudspeaker::alarm_clock:Final Call: The EuroBioC2024 abstract submission is this Friday April 26th 5pm BST. If you haven’t submitted yet, now’s the time! Please visitEuroBioC2024 submissions for guidelines and to submit your work. Looking forward to your contributions!
Lance Zhang (09:35:09): > @Lance Zhang has joined the channel
USLACKBOT (13:41:48): > This message was deleted.
Lance Zhang (13:58:07): > Hello, I am glad to join the community. May I know whether I could raise a question here or other channels?
Maria Doyle (14:32:44) (in thread): > Welcome to the Bioconductor community! Feel free to share your question here, and we’ll guide you to the right place for the best answer.
Hervé Pagès (18:10:47) (in thread): > Sorry for the bad timing. I’m in the process of fixing all affected packages. Yours was fixed yesterday. > Let’s please use the #developer-forum channel for this kind of conversation. 3312 people are on the general channel!
2024-04-25
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Lance Zhang (03:01:32) (in thread): > Thanks for your message, Maria.:+1:
Lance Zhang (03:02:20) (in thread): > I have one question about the GDCprepare, because I met one issue when I handle the TCGA-BRCA data.
Lance Zhang (03:03:41) (in thread): > Here is the link :https://www.biostars.org/p/9593443/ ,please take a look at it for your reference.
Hervé Pagès (03:42:02): > @Nan DengWhat’s the point of posting 5 full screens of HTML source code of zero interest in the general channel? Do you realize that there are 3000+ people following this channel? Please delete as soon as possible. Thanks!
Maria Doyle (05:00:52): > Hello all:wave:, > To keep our discussions clear, please consider using tools likegist for sharing longer content. Thank you,@Hervé Pagès, for helping us maintain efficiency.@Nan Deng, welcome to the community—please feel free to reach out if you need guidance on posting. > Thanks everyone!
Maria Doyle (05:02:50) (in thread): > Thanks for your question Lance! For issues related to using Bioconductor packages, our support site is the best place to get help. I see you’ve already posted here:https://support.bioconductor.org/p/9157973/ — please remember to add the package nameTCGAbiolinksto your post to tag the package authors. Here are our posting guidelines for more details:https://bioconductor.org/help/support/posting-guide/ . > > It’s generally best to avoid cross-posting across multiple forums as it can fragment community efforts and make it harder to track responses. Consider deleting the Biostars post to keep responses centralised. > > Hope this helps, and that your issue is resolved soon!
Kristian Ullrich (06:45:08) (in thread): > Thx again for fixing the issue so quickly.
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Nan Deng (09:17:08) (in thread): > Sorry. I have deleted the html. I know almost nothing about the web server, so I was hoping some information might help diagnose the problems. BTW: is there a specific bug report channel?
Lluís Revilla (10:48:38) (in thread): > Yes, on the landing page of the package you have: > > Bug Reportshttps://github.com/Bioconductor/S4Vectors/issues
Nan Deng (11:14:54) (in thread): > Thanks for your response! I believe the issue isn’t with the package itself, but rather the repository server. I encountered a “404 Not Found” error before even attempting the installation. This leads me to suspect a problem with how the server handles headless requests (such as those made by download.file, wget, and curl and I am not sure if I used the correct wording “headless” ). Interestingly, browsers seem to download the file just fine. My limited HTTP knowledge makes me unsure about the exact cause, but the discrepancy between browser and headless requests suggests a routing issue? That’s why I reached out here and included the full curl response for further analysis.
Lluís Revilla (11:21:14) (in thread): > It is good that you provided data for analysis, but it is also good to consider if the 3k people would need to know get notified about. Anyway, we all are learning in this quickly evolving online landscape:smile:
Nan Deng (12:03:56) (in thread): > I think it is something that should bring the user’s attention. S4Vectors, a crucial dependency for Bioconductor. Also it caused challenges when building my Docker container for distribution. Bioconductor is undeniably a vital package for many users, and I wouldn’t want anyone else to encounter the same issue (I also provided a temporary fix for this issue which might save others time). I apologize if my initial post was overly detailed. While including comprehensive information is encouraged in some other communities, I understand this might be more appropriate for a bug or issue channel. As a newcomer, I explored channels for sharing this information and I didn’t see any such channel on the list.@Maria Doylesaid in another thread that we could share any question here, thus I did so. I’ve since removed the extraneous details and offered my sincere apologies.
Hervé Pagès (12:31:31) (in thread): > Thanks for deleting the HTML content. The Bioconductor website and packages are served via Amazon CloudFront. It could be that the error you got yesterday (cannot open URLhttps://bioconductor.org/packages/3.19/bioc/src/contrib/S4Vectors_0.41.6.tar.gz ) was a CloudFront caching issue. I was myself victim of a very similar issue yesterday while trying to update thelimma
Nan Deng (12:41:40) (in thread): > Thank you so much for letting me the problem was fixed, it seems that now theBioManage::installpoints to version 0.41.7, and this morning it pointed to 0.40.xx. I don’t this info would help you identify the problem. Since this problem was fixed, I have deleted my original posts to keep the channel clean.
Maria Doyle (12:47:29) (in thread): > Thanks for your detailed feedback@Nan Deng. I’m sorry if my earlier message was unclear about where to post specific questions. We’re always striving to make things clearer and continuously improve. I’m taking this chance to review and enhance our posting guidelines to make sure they’re easy to understand for everyone. > > Feel free to reach out to me directly if you have more feedback or need any clarification on anything. We’re here to help and want to make sure everyone has a great experience in our community.
2024-04-26
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2024-04-28
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2024-05-01
Lori Shepherd (15:30:15): > Bioconductor Core Team is pleased to release Bioc3.19! Thank you to all developers and community members for contributing to the project. The full release announcement can be found at:https://bioconductor.org/news/bioc_3_19_release/
2024-05-02
Fabricio Almeida-Silva (02:56:05): > Hi, everyone. > Does anyone know if there’s any Bioc package that can take aSpatialExperimentobject and, for each spatial domain separately, aggregate spots (e.g., by summing counts for N neighboring spots) based on spatial coordinates? The functionMetaspotsByGroups()from the hdWGCNA (seehere ) doesexactly
Lambda Moses (02:59:51) (in thread): > I’m considering writing my own implementation of Moran’s I in place of that of spdep using matrix multiplication to see if it’s faster when run for thousands genes for the Voyager package. What you’re describing is closely related, to set all spatial weights to 1. Shouldn’t be difficult.
Fabricio Almeida-Silva (03:50:39) (in thread): > Yes, this doesn’t seem like something hard to implement from scratch, but I just wanted to avoid reinventing the wheel. > Actually, what hdWGCNA does seems even simpler: if I understood it correctly, they identify evenly spaced “central spots”, and then aggregate counts using the central spots and all their neighbors, so each “metaspot” (nearly) always has 7 spots combined (see the schematic figure in the vignette I mentioned above).
Alik Huseynov (06:11:00) (in thread): > aggregating spots into hexagonal large spots should easy.
Fabricio Almeida-Silva (06:48:16) (in thread): > Agreed. I’ll implement it myself, then, because I don’t think this is already implemented in other packages.
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Alik Huseynov (08:04:10) (in thread): > Support for aggression and spatial binning is on our todo list as@Lambda Mosessaid for SpatialFeatureExperiment & Voyager..
Fabricio Almeida-Silva (08:05:10) (in thread): > Amazing!
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2024-05-03
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Lance Zhang (08:05:22) (in thread): > Hello Maria,
Lance Zhang (08:06:17) (in thread): > thanks for your suggestions, I have already updated the content.
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2024-05-04
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2024-05-05
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2024-05-06
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Svetlana Ugarcina Perovic (03:55:21): > If you were an**** OUTREACHY applicant ****and contributed to any of the Bioconductor projects#BugSigDB #sweave2rmd #BSgenomeForge #miaverse , please help us in spreading the word about your amazing work. > > You can share your experience (anonymously) by filling in this short surveyhttps://forms.gle/brqH5M2uTYMKy23x7 Thank you! - Attachment (Google Docs): Outreachy-Bioconductor survey > Dear Outreachy-Bioconductor contributor, > Thank you for participating in the Outreachy-Bioconductor program. In order to improve the experience for future contributors as well as to spread the word about your amazing contribution to the Bioconductor projects in the form of a conference talk and publication, we would appreciate you taking just a few minutes to complete an online survey about your experience. > > All survey responses are collected anonymously. If you have any questions, please contact us. > > Many thanks in advance and best wishes, > Bioconductor team > Email address: mailto:jennifer.wokaty@sph.cuny.edu|jennifer.wokaty@sph.cuny.edu
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2024-05-07
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2024-05-08
Maria Doyle (08:26:59): > :bell:Just a quick reminder, 1 week left to apply forBioC2024 conference scholarships and nominate for BioC awards::small_blue_diamond:In-person Scholarships: Apply byMay 15 Scholarship Application :small_blue_diamond:BioC Award Nominations: Nominate byMay 15 Nominations Form :small_blue_diamond:Early Registration: Secure your spot! Early bird rates endMay 31 Registration Also, note that you can now support the scholarship fund by donating here:Support the Scholarship Fund :innocent:Thank you for your continued engagement and support!
Johannes Mayer (11:46:58): > @Johannes Mayer has joined the channel
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2024-05-09
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2024-05-10
Maria Doyle (07:57:03): > :trophy:Last Chance to Nominate for the Bioconductor Awards 2024!:trophy:Time is running out to recognise individuals who have made impactful contributions to our community. Don’t miss this opportunity to honour their hard work and achievements!:star2:Criteria: Significant contributions in one or more ways to the project:busts_in_silhouette:Selection: 4 awardees based on impact:alarm_clock:Deadline: 15th May 2024 > > Nominate Now:Nomination Form Learn More:Bioconductor Awards - File (PNG): BiocAwards.png
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2024-05-11
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2024-05-14
Maria Doyle (12:33:24): > :loudspeaker:Hi all, > A quick note to let you know: > * We’re cleaning up ourSlack channels channel directory where you can see a list of all channels, the date of the last message, and other details. This will make it easier to see what channels currently exist and find discussions you may want to join. The table updates automatically daily. > Thanks!
Kayleigh Ann (19:26:22): > @Kayleigh Ann has joined the channel
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2024-05-16
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2024-05-17
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Maria Doyle (07:30:30): > :loudspeaker:New Channel:
2024-05-20
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Maria Doyle (12:10:49): > :mega:BioC2024 Schedule Now Available Schedule Reminder: May 31 Mastodon Share onLinkedIn
2024-05-21
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2024-05-22
Maria Doyle (14:37:16): > :rocket:Boost Your Bioinformatics Skills! > Join us for theBioC2024 **** Bioconductor Carpentries RNA-Seq Workshop**!:date:July 22-23, 2024:round_pushpin:Grand Rapids, MI:mag:Who: Biologists and researchers with some R experience:bulb:Why: Hands-on Bioconductor training, expert instructors, networking opportunities:point_right:Register here For more details, check out our posts onMastodon andLinkedIn . > Please share with your networks or anyone who might be interested!
Will Hore-Lacy (20:06:10): > @Will Hore-Lacy has joined the channel
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2024-05-23
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Dag Stockstad (07:13:29): > We’re having issues with the Bioconductor R repository. Looks like it’s down: > > curl -L[https://bioconductor.org/packages/3.17/workflows/src/contrib/PACKAGES](https://bioconductor.org/packages/3.17/workflows/src/contrib/PACKAGES)curl: (28) Failed to connect to mghp.osn.xsede.org port 443 after 258368 ms: Connection timed out > > This is failing installs such as: > > BiocManager::install("mixOmics", dependencies = TRUE) > > Are others experiencing the same? Have confirmed this on 3 separate networks so believe it’s server side issue. Any advice?
Dag Stockstad (07:15:23) (in thread): > If there’s a better channel for this, please let me know and I’ll be happy to post there.
Lori Shepherd (07:18:40): > Yes we noticed this morning the location we store archived versions of Bioconductor is reporting an outage. I’m in process of temporarily changing the location to another backup archive. It should be active within the next 20 min or so.
Dag Stockstad (07:29:05): > Ah, great, thanks, Lori.
Lori Shepherd (07:31:57): > access should be restored via the secondary location now
Dag Stockstad (07:32:30): > Yeah, I can confirm it’s working. Thanks for the quick resolution.
Kelvin Muithya (09:55:20): > @Kelvin Muithya has joined the channel
Lori Shepherd (14:20:56): > Due to unforeseen circumstances, our daily builders and new submission builders are currently offline. We are sorry for the inconvenience and will restore as soon as possible
2024-05-24
Boyi Guo (08:56:16): > Question about the BioC 2024 In-person scholarship - The website (https://www.bioc2024.bioconductor.org/ ) says that the scholarship award notification will be given out on May 22. Is there a email going out to those who are not selected for the award? Thanks.
Maria Doyle (09:21:45) (in thread): > Thanks for asking!@Erica Feickwill be getting in touch with everyone about the scholarship notifications soon, if she hasn’t already. Appreciate your patience!
Boyi Guo (09:35:19) (in thread): > Thanks for coordinating! > Just curious, would the notification come out earlier than the early registration ends (May 31)? > I read from a previous email suggesting > > If you applied for a scholarship, please wait until we announce the recipients. You will receive a separate email about the decision.
2024-05-27
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2024-05-28
Maria Doyle (16:04:21) (in thread): > Just an update: Erica has sent out emails to those who applied for the scholarship. If you haven’t received an email, please check your inbox and spam folder.
Boyi Guo (16:31:19) (in thread): > Yes, I’ve received the notification. Thank you so much!
2024-05-29
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2024-05-31
Maria Doyle (04:48:36): > :mega:EuroBioC2024 Registration is Open! Register here Help spread the word!:pray: > * Share on LinkedIn > * Share on Mastodon
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2024-06-02
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2024-06-03
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Stevie Pederson (22:44:07): > Hi everyone. The BiocAsia conference organising group is currently being put together. We’d absolutely love for anyone who’s keen to help to be involved. The 2024 event is likely to be held in Sydney, this November. Please contact@stefano mangiola@Ellis Patrickor@Stevie Pedersonif you’re keen to help out. You can also just pop into the#biocasiachannel if you’d like as well.
2024-06-04
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Shraddha Pai (12:20:34): > Hi everyone. Not sure if this is the right forum to ask: > I’m trying to add a new mask to a BSgenome MaskedDNAString (specifically, Bismap mappability mask to chr1 of BSgenome.UCSC.hsapiens.hg38). > > When I try to add the mask to the sequence I get an error I don’t know how to overcome. I’ve tried to look at documentation forMaskedBSGenome,BSgenome,MaskedXStringbut cannot figure out how to fix this. > > Would appreciate guidance, thanks! > > EDIT - It looks like the problem comes with trying to assign theMaskedDNAStringto the BSgenome object. > > Browse[1]> masks(genome$chr1) <- curmsk > Error in `$<-`(`**tmp**`, chr1, value = new("MaskedDNAString", unmasked = new("DNAString", : > no method for assigning subsets of this S4 class > Browse[1]> class(genome) > [1] "MaskedBSgenome" > attr(,"package") > [1] "BSgenome" > Browse[1]> curmsk > MaskCollection of length 5 and width 248956422 > masks: > maskedwidth maskedratio active names desc > 1 18470101 7.419010e-02 TRUE AGAPS assembly gaps > 2 5309 2.132502e-05 TRUE AMB intra-contig ambiguities > 3 119060341 4.782377e-01 FALSE RM RepeatMasker > 4 1647959 6.619468e-03 FALSE TRF Tandem Repeats Finder [period<=12] > 5 30883473 1.240517e-01 TRUE BSMAP-UN Bismap S100 unmappable > all masks together: > maskedwidth maskedratio > 141695090 0.5691562 > all active masks together: > maskedwidth maskedratio > 30886323 0.1240632 >
Hervé Pagès (12:25:54) (in thread): > Any question about basic usage of the software should be asked on the support site. Thanks!
Shraddha Pai (12:27:47) (in thread): > Thanks Hervé, will do.
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2024-06-05
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2024-06-07
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Dima Lvovs (16:13:43): > Hello, seeking for wisdom: > > * Checking man page documentation... > * WARNING: Empty or missing \value sections found in man page(s). > > my confusion is that is that the .rd file that generates this is the package description .rd file, which does not describe any functions. Or is having a package description doc (using _PACKAGE) is not a good practice anymore?
Marcel Ramos Pérez (16:23:57) (in thread): > The man page for the package shouldn’t trigger the check. Can you open an issue with a reproducible example athttps://github.com/Bioconductor/BiocCheck/issues ? Thanks
Kasper D. Hansen (17:08:35) (in thread): > There is a way to specificy that a package Rd file is the special package type. Look in R-exts
Marcel Ramos Pérez (17:22:50) (in thread): > Yes, BiocCheck skipspackageandclassdocTypes when checkingvaluesections
Dima Lvovs (17:26:35) (in thread): > Maybe that’s the issue then, as docTypepackageis now deprecated in favor of _PACKAGE
Dima Lvovs (17:44:28) (in thread): > Hmm maybe I should try @aliases -package
2024-06-09
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2024-06-10
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Dima Lvovs (10:02:51) (in thread): > Hello, this was a false alarm due to outdated packages - after updating BiocCheck and roxygen2, the latter generatesdocType{package}and the former passes it correctly.
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2024-06-11
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Samuel Ortion (23:53:23): > bien dormi ?
2024-06-12
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Kailasadatta Boggaram (12:23:55): > Hello. I wanted to ask for help on changing the principal components (PCs) in the DESeq2 plotPCA function. It automatically sets to PC1 and PC2 but I don’t know how to look at the other PCs. Appreciate any help
Jenny Drnevich (12:36:02) (in thread): > If you look at the help for plotPCA?DESeq2::plotPCA, there is an argument > > pcsToUse = 1:2 >
Kailasadatta Boggaram (13:38:19) (in thread): > Thank you for responding. Which version of DESeq2 is that argument present? I don’t see it as an argument in the help for the function. My package is 1.40.2
Jenny Drnevich (13:45:36) (in thread): > I’m running 1.44.0. According to the news: > Changes in version 1.42.0 > * collapseReplicates() now noisier (warning) about other assays. > * plotPCA() prints out the ‘ngenes’ setting. > * Added pcsToUse for plotPCA (idea from Vince Carey) > * Added test that SE exist for lfcShrink (in case of glmGamPoi fitType).
Kailasadatta Boggaram (15:07:22) (in thread): > Got it. Thank you for letting me know
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2024-06-13
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Jane Lyon (09:32:42): > Hello. I am very new to using R and I am just using it to follow a specific protocol. > I have installed ‘BiocManager’ in R but R does not recognise the function ‘readBStringSet’. I tried to install ‘readBStringSet’ specifically to see if that would help but it’s not available for the version of R I have which is the most up to date version. Any ideas of what I might be doing wrong? I have already input the fasta file and the target name and the below code was the next step in the protocol. > > > target_fasta <- readBStringSet(fasta_file) > > Results: > Error in readBStringSet(fasta_file) : > could not find function “readBStringSet” > > > install.packages("readBStringSet") > > Results: > Installing package into ‘C:/Users/AppData/Local/R/win-library/4.4’ > (as ‘lib’ is unspecified) > Warning in install.packages : > package ‘readBStringSet’ is not available for this version of R > > A version of this package for your version of R might be available elsewhere, > see the ideas athttps://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages sessionInfo( )
Lori Shepherd (09:34:28): > You should install the specific package with that function which would be Biostrings > > BiocManager::install('Biostrings') # installs the package > library(Biostrings) # loads the package into R session with all available functions from that package >
Lori Shepherd (09:34:55): > readBStringSet is a function inside a package not a package itself.
Jane Lyon (10:00:57): > Thank you for the help. I do now seem to have Biostrings installed but now I’m getting another error message: > > > target_fasta <- readBStringSet(fasta_file) > Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") : > cannot open file './input/Dmel_cip4-exon.fa' >
Lori Shepherd (10:04:02): > And that file exists at that location./input/Dmel_cip4-exon.fa
Jane Lyon (10:20:53): > Ah thank you. That was the issue.
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2024-06-14
Joselyn Chávez (09:59:14): > Hi all, we are hosting a 3-day online workshop for doing spatial analysis with the Giotto package. Joins us! Feel free to reach out if you have any questions - File (PDF): giotto_flyer
2024-06-17
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2024-06-19
Dima Lvovs (14:23:07): > Hi everyone, looking for bioc package data structuring wisdom. We are using some internal data for unit tests, and we arestoring it insysdata.rda. The idea to reuse the same data for examples does not seem off, and it does seem that the user does not need this data so its OK to keep it internal. However, it has been pointed to us that the usage of:::to get the data for examples is a bad practice. What is the best way to store and access the minimal dataset for ruse both in tests and the examples? Or would it help to load the data via e.g.data <- get(name, envir=asNamespace(pkgName))instead of:::in the examples? - Attachment (contributions.bioconductor.org): Chapter 13 Package data | Bioconductor Packages: Development, Maintenance, and Peer Review > When developing a software package, an excellent practice is to give a comprehensive illustration of the methods in the package using an existing experiment data package, annotation data or data…
Kasper D. Hansen (15:28:07): > I would never put test data or example data insysdata.rda
Kasper D. Hansen (15:28:38): > I would put example data in/dataand test data - if it is only used in tests - inside a subdirectory ofinst
Dima Lvovs (15:39:20) (in thread): > Thanks! Is there any specific reason for this?
Kasper D. Hansen (15:41:02) (in thread): > First, I don’t think examples or tests follow the (admitted loose) criteria for being in sysdata, second because I think examples should always be accessible and documented and third because if it is for tests only, I think it should be kept to tests
Kasper D. Hansen (15:41:12) (in thread): > Not sure that is super understandable
Dima Lvovs (15:42:48) (in thread): > Makes sense to keep what’s needed only in tests close to tests. We wanted to avoid duplication, so tests and examples share objects.
Kasper D. Hansen (15:44:23) (in thread): > IMO the best thing for examples is to think about the didactic component of examples - you want examples that are worth understanding and inspecting
Kasper D. Hansen (15:44:36) (in thread): > (base R is sometimes not the best example of this)
Kasper D. Hansen (15:46:46) (in thread): > Likewise you want test data to be as small and specific as possible to cover exactly what you’re testing, no more.
Dima Lvovs (15:47:06) (in thread): > Right, so then the ‘bad practice’ refers to example data having to be available to the user, but accessing with:::means accessing the unavailable probably.
Kasper D. Hansen (15:49:07) (in thread): > Yes, I strongly believe example data should be either exported and documented or constructed on the fly as part of the example.
Kasper D. Hansen (15:50:05) (in thread): > Because example data should be played with by the user and everything the user is supposed to play with should be accessible without:::
Dima Lvovs (15:54:21) (in thread): > Ok, thanks for your pov!
Martin Morgan (16:58:32) (in thread): > Users don’t usually ‘start’ with an R data object, but rather a CSV or similar file. The convention is to put such files ininst/extdata/example.csvand to access the path to the file withpath <- system.file(package = "pkgName", "extdata", "example.csv"). The example is thenegdata <- read.csv(path)or whatever. Structuring folders underextdatacould make sense.
Hervé Pagès (18:35:05) (in thread): > Yes. to paraphrase@Kasper D. Hansen, anything that is exposed to the user (in the man page examples or in the vignettes) should be exported and documented. In other words, instead of usingdominoSignal:::pbmc_dom_built_tinyin your examples, export and documentpbmc_dom_built_tiny, and simply usepbmc_dom_built_tinyin your examples and unit tests. It’s also a good idea to link each man page wherepbmc_dom_built_tinyis used topbmc_dom_built_tiny’s man page. This is done by adding a\seealsosection that typically looks something like this: > > \seealso{ > \link{domino} objects. > > \code{\link{pbmc_dom_built_tiny}} for the toy domino object used in the examples below. > > etc... > } > > In the future please ask questions about the development of your package in the#developers-forumor#package-submissionchannels, or on the bioc-devel mailing list. Thanks!
Dima Lvovs (20:48:19) (in thread): > Thanks everyone for your valuable comments and directions.
Lambda Moses (23:35:37): > Also,R CMD checkwill give you a note or warning if your package’s installed size is too large, and the installed size includes data ininst. If you need larger example or test data, you should write a data package that your main package suggests and upload the data to Experiment Hub.
2024-06-20
Dima Lvovs (07:50:21) (in thread): > That’s right, and that is clearly communicated in the docs.
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2024-06-21
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2024-06-24
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2024-06-25
Alex Mahmoud (15:08:11): > PSA:workshop.bioconductor.org will be going down for a few days as I update the stack in preparation for the upcoming conference
2024-06-26
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2024-06-27
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Jasmine Daly (14:34:47): > :wave:Hi everyone, if you have R package development experience and would like to share your thoughts on the CRAN submission process - I’d greatly appreciate your feedback in thisbrief survey that will be used to provide feedback for theCRAN Cookbook project :fork_and_knife: - Attachment (Google Docs): CRAN Cookbook Survey #1 > Hello! > > We appreciate you taking a moment to participate in this survey about your experiences with CRAN and R package development. Your responses will contribute valuable insights to our project, “CRAN Cookbook: Improving the Skills of R Package Maintainers,” a 2024 Special Project Grant recipient from the R Consortium. Thank you for helping us enhance the tools and resources available to the R community.
Lluís Revilla (18:02:05) (in thread): > Does the experience in submitting or contributing to Bioconductor packages count? Note that the repository, reviewers, manual review, and checks are different…
2024-06-28
Jonathan Bobak (06:12:36): > @Jonathan Bobak has joined the channel
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Jasmine Daly (10:28:22) (in thread): > We are most interested in CRAN experience!
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2024-06-30
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2024-07-01
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2024-07-02
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stefano mangiola (08:48:38): - Attachment: Attachment > Join us Tuesday 16th of JULY for a #tidyomics Zoom celebration and open discussion about #future plans! > > 8.30AM US time (New York, EDT) > 1.30PM Europe time (London, BST) > 10.30PM Australia time (Sydney, AEST) > > Zoom: https://unimelb.zoom.us/j/88334039518?pwd=EU0W9q7OsMbSO27693Ka5raygBet99.1 > Password: 542990 > > #everyone welcome!
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2024-07-03
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2024-07-04
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2024-07-05
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Maria Doyle (07:55:00): > :mega:Reminder: BioC2024 in-person registration closes July 10! Register here Also, applications are open for the Bioconductor Carpentries RNA-seq Workshop, taking place on July 22-23, right before the main conference.Apply here ****.****Feel free to share! > * Share onMastodon > * Share onLinkedIn
Dominik Burri (09:09:09): > @Dominik Burri has joined the channel
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2024-07-08
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2024-07-09
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Maria Doyle (13:12:28): > :alarm_clock:Final reminder: BioC2024 in-person registration closes tomorrow. Don’t miss out
Vilhelm Suksi (18:25:57): > @Vilhelm Suksi has joined the channel
2024-07-10
Miha (04:54:05): > @Miha has joined the channel
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Maria Doyle (18:34:32): > :writing_hand:New Bioconductor blog post about the recently updated Slack welcome message. Check it outhere .
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2024-07-11
Maria Doyle (05:42:44): > :rocket:Join us for the EuroBioC2024 Carpentries Workshops! Workshops: Register here For more details, check out our posts onMastodon andLinkedIn . > Please share with your networks!
Hothri Moka (06:00:52): > @Hothri Moka has joined the channel
Vanessa Gonzalez Ribao (08:04:04): > :loudspeaker:Only 1 week left! Don’t miss Zuguang Gu’s seminar on July 18. Dive into advanced data visualisation techniques with R & #Bioconductor packages like ComplexHeatmap & InteractiveComplexHeatmap. Register now:https://t1p.de/rcptq - Attachment (ghga.de): GHGA Webinar: Biological data visualisation in R and Bioconductor > Join us for a practical introduction to biological data visualisation using R and Bioconductor.
Monthly general reminder (09:30:02): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush:
2024-07-12
Maria Doyle (14:08:15): > :writing_hand:New Bioconductor blog post about the CZI EOSS 6 grants. Check it outhere .
Camila Pereira Perico (15:05:43): > @Camila Pereira Perico has joined the channel
Martin Morgan (16:05:55) (in thread): > Impressive!Congratulations all!
Janani Ravi (17:12:26) (in thread): > Cross-posting w/#r-ladies#events#bioc-conference-everyoneWe’re getting together later this month for aBioconductor + R-Ladiesmeetup at Grand Rapids, MI! If you are an R-Ladies member/ally & are a computational biologist/bioinformatics developer/user, this could be for you!:point_right:RSVPhere on Meetup :parrotconga::writing_hand:As a reminder, virtual registration for BioC is still open:https://www.bioc2024.bioconductor.org/registration (especially affordable for trainees @$10) > Schedule:https://www.bioc2024.bioconductor.org/schedule See you soon!:raised_hands:[Please DM me if you have any questions! ]
2024-07-13
stefano mangiola (21:49:54) (in thread): > Beautiful, I love the map!
2024-07-14
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2024-07-15
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Maria Doyle (17:18:28): > :zap:BioC2024 Lightning Talks submission form for all the details you’ll need to get your talk ready.BioC2024 virtual registration is still open! register here.
2024-07-16
Hiru (06:53:40): > @Hiru has joined the channel
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2024-07-17
천유경 (02:25:45): > @천유경 has joined the channel
2024-07-18
Khang-Trang Hoang Jamieson (08:46:50): > @Khang-Trang Hoang Jamieson has joined the channel
2024-07-19
vivek pal (03:21:34): > @vivek pal has joined the channel
Maria Doyle (10:24:17): > :mega:Hi everyone! Just a quick reminder thatBioC2024 Virtual registration register here . It’s only $10 for students and postdocs! > > Also, note that virtual registrants can submitLightning Talk submission form for details. - File (PNG): BioC2024 Virtual Registration Open.png
Peter(Yizhou) Huang (10:51:02): > @Peter (Yizhou) Huang has joined the channel
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2024-07-21
Maria Doyle (05:07:13): > :writing_hand:New blog post announcing Bioconductor and R-Ladies collaboration. Check it outhere .
sofie shankar (05:43:52): > @sofie shankar has joined the channel
2024-07-22
Richard Dushime (03:47:31): > Hi Everyone, > > I thought you might find this interesting: > > TheRSE Asia Australia Unconference 2024 (RSEAA24) is happening from September 10th to 13th! This year’s theme is “Sharing tech architectures,” and we’re looking forward to another amazing event. > We’re excited to announce that thescholarship and micro-grant application deadline has been extendedEarly bird registration is open : - Deadline: 14th August 12pm UTC +10 (Wednesday). > Please check theRSEAA24 website for more details. - Attachment (RSE Asia Australia Unconference): RSEAA24 - A research software community event for Asia and Australia > Website for the RSE Asia Australia Unconference - Attachment (Google Docs): 2024 RSE Asia Australia Application form for Scholarships and Accessibility Micro-grant > We are committed to creating a safe, accessible, and inclusive environment for all participants. > To this end we are offering scholarships for staff or students to participate for free, as well as 10 accessibility micro-grants of $50 AUD to help with internet, headphones, childcare etc. > Eligibility for the scholarships will be based on prioritising and maximising the inclusion and participation of people who have been impacted due to the cumulative effects of discrimination on factors such as race, gender, disability, gender identity, financial status, and the intersectionality of that discrimination as well as others not mentioned here. > Eligibility for the accessibility will be based on a similar approach. Only participants from Asia and Australia are eligible for the micro-grant. > We encourage participants to apply even if they do not think they are eligible as this will allow us to prioritise and maximise diversity and inclusion. All information will be treated in a confidential manner. > All successful recipients of scholarships and accessible micro-grants are expected to submit a poster for the event after they have been notified of their conditional success. Once the poster has been accepted, the scholarship/micro-grants will be processed. > Only one poster per person is necessary. > Submissions close 17th July 12pm UTC +10 (Wednesday) See in your time zone - Attachment (events.humanitix.com): RSE Asia Australia 2024 (RSEAA24) | Humanitix > We invite you to join us for the third online Research Software Engineer (RSE) Asia Australia Unconference from the 10th to the 13th of September 2024. - File (JPEG): Extended.jpeg
Stevie Pederson (03:56:20) (in thread): > Thanks Richard. Are you also in the ABACBS slack? Might be a good one to share there as well!
Richard Dushime (03:57:53) (in thread): > I am Not > Please Help Share > Thanks > Or you can get me an invite too
Stevie Pederson (03:59:38) (in thread): > I think anyone is free to joinabacbs.slack.com . Just added the links to my group’s slack as well. Looks like a really good event
Richard Dushime (04:01:24) (in thread): > Thank you:raised_hands:
Richard Dushime (04:11:24) (in thread): > Unable to join the slack , may be if you can create an invite link
Stevie Pederson (04:12:19) (in thread): > DM sent
Meghana GC (09:49:36): > @Meghana GC has joined the channel
Maria Doyle (14:11:23) (in thread): > :earth_africa:Virtual scholarships are available for BioC2024, happening this week! Free registration is available to underrepresented minorities and individuals from low to middle-income countries, including students, fellows, and early career investigators from regions such as Africa, Latin America, and Asia. > > To apply, please fill out the BioC2024 Scholarship Application formhere . > > Feel free to share this information: > Share onLinkedIn Share onMastodon
2024-07-23
Jamie Park (11:56:09): > @Jamie Park has joined the channel
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2024-07-24
Gigi (08:39:45): > @Gigi has joined the channel
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Maria Doyle (11:49:20): > :star2:Annual Nominations Open for CAB & TAB! Community Advisory Board (CAB) Technical Advisory Board (TAB) Apply by Aug 31: CAB Application Form > * TAB Application Form > Don’t miss this opportunity to impact Bioconductor’s future! > > Feel free to share this onLinkedIn orMastodon
Kavya Ayalasomayajula (12:46:04): > @Kavya Ayalasomayajula has joined the channel
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2024-07-25
Maria Doyle (09:57:48): > :writing_hand:New Bioconductor blog post on highlights from the CZI Open Science meeting. Check it out here:https://blog.bioconductor.org/posts/2024-07-24-czi-os-meeting-highlights/ - Attachment (Bioconductor community blog): Bioconductor highlights from the CZI Open Science Meeting – Bioconductor community blog > A blog for the Bioconductor community!
brian capaldo (12:33:15): > Apologies if this is the wrong channel for this, but I’m running into an install error on my windows machine, but not on my HPC, is this something related to crowdstrike? > > > BiocManager::install("DEXSeq") > 'getOption("repos")' replaces Bioconductor standard repositories, see > 'help("repositories", package = "BiocManager")' for details. > Replacement repositories: > CRAN:[https://cran.rstudio.com/](https://cran.rstudio.com/)Warning: unable to access index for repository[https://bioconductor.org/packages/3.18/bioc/src/contrib](https://bioconductor.org/packages/3.18/bioc/src/contrib): > cannot open URL '[https://bioconductor.org/packages/3.18/bioc/src/contrib/PACKAGES](https://bioconductor.org/packages/3.18/bioc/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://bioconductor.org/packages/3.18/data/annotation/src/contrib](https://bioconductor.org/packages/3.18/data/annotation/src/contrib): > cannot open URL '[https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PACKAGES](https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://bioconductor.org/packages/3.18/data/experiment/src/contrib](https://bioconductor.org/packages/3.18/data/experiment/src/contrib): > cannot open URL '[https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PACKAGES](https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PACKAGES)' > Warning: unable to access index for repository[https://bioconductor.org/packages/3.18/workflows/src/contrib](https://bioconductor.org/packages/3.18/workflows/src/contrib): > cannot open URL '[https://bioconductor.org/packages/3.18/workflows/src/contrib/PACKAGES](https://bioconductor.org/packages/3.18/workflows/src/contrib/PACKAGES)' > Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31 ucrt) > Installing package(s) 'DEXSeq' > Warning: unable to access index for repository[https://bioconductor.org/packages/3.18/bioc/src/contrib](https://bioconductor.org/packages/3.18/bioc/src/contrib): > ... > Warning messages: > 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : > there is no package called 'DRIMSeq' > 2: package 'DEXSeq' is not available for Bioconductor version '3.18' > > A version of this package for your version of R might be available elsewhere, > see the ideas at[https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages](https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages)3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : > there is no package called 'DRIMSeq' > Loading required package: DRIMSeq >
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Kerry (13:20:37) (in thread): > I get this error when R is out of date.https://cran.r-project.org/bin/windows/base/ https://cran.r-project.org/bin/macosx/ The other reason could be not having Rtools installed (Windows) orXQuartz on mac.
brian capaldo (13:35:11) (in thread): > I have successfully installed packages from bioconductor before on this machine, and I have the same version of R on my HPC. I’d rather not do a fresh R install unless I have to as I’m trying to keep the R environments the same between the HPC and my local machine
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Lori Shepherd (15:11:15) (in thread): > Are you behind a proxy?
Anh Nguyet Vu (15:12:10): > @Anh Nguyet Vu has joined the channel
brian capaldo (15:14:10) (in thread): > yes, I’m on VPN
Lori Shepherd (15:14:49) (in thread): > maybe check out this support site post:https://support.bioconductor.org/p/131736/
brian capaldo (15:15:20) (in thread): > diasbled VPN and it worked
brian capaldo (15:15:21) (in thread): > thanks
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2024-07-26
Robert Shear (11:32:27): > Bioconductor Package Download Rate Limitation (HTTP 429) Applicability www.bioconductor.org are subject to a rate limit. Specifically, no more than 3,000 packages can be downloaded directly in any 10-minute period from a single IP address. If this limit is reached, the server will returnan HTTP 429 Too Many Requestsclient error response status code. > > Most 429 response codes will arise from systems that have a very high-speed link (cloud-to-cloud) and that (a) perform bulk downloads of the complete Bioconductor library for more than one version or (b) loop on requesting the same package or set of packages repeatedly with faulty retry count logic. > > If you have encountered a 429 while downloading packages fromwww.bioconductor.org , then read on.Background Understanding Rate-Limiting (Status Code 429) IETF RFC 8516 proposes a solution to this problem in the form of HTTP status code 429 that signals the client that it has issued too many requests over some period of time and optionally advises the client how long it should wait before resuming requests. The implementation of status code 429 processing is becoming more common to address the issue of very high demand from anonymous data consumers. It is also a useful adjunct to the protection of sites from hostile use. Some newer HTTP clients automatically support 429 processing.Our Implementation Details www.bioconductor.org . This rule only applies to URLs that are in the form of a package download. After modeling the expected behavior of this implementation over a month of traffic from April 2024, we chose parameters that would almost never affect typical users. Our parameters are as follows:Look-back window Rate limit Handling 429 Responses Simple Workaround
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2024-07-27
Lluís Revilla (04:40:50) (in thread): > Some websites have reported that some users making many requests are from AI bots scraping content. Do you have some list of user agents/IP and resources requested? Are manuals and vignettes also affected or this is just CI machines installing again and again the same packages?
Lluís Revilla (04:42:19) (in thread): > Maybe announcing this to the mailing list will help to share it in the open, it is the official place that packages developers must register and use (I mean besides the forum post:https://support.bioconductor.org/p/9159338/ )
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2024-07-29
Steffen Neumann (08:11:01): > Hi, I am looking for some cool data analysis packages, that leverage SummarizedExperiments as input data.
Steffen Neumann (08:12:33) (in thread): > You could say the SummarizedExperiment is a data matrix with beefed-up rowdata and coldata. I am looking for e.g. Shiny Apps that take (nearly) whatever SummarizedExperiment and nicely and generically allow to use the rowdata / coldata for various axes, legends, labels etc.
Steffen Neumann (08:14:40) (in thread): > In addition to generic and versatile consumers of SummarizedExps, I am looking for conventions for coldata and rowdata, maybe via ontology terms, that help such an e.g. visualisation to select suitable and sane defaults.
Charlotte Soneson (08:23:58) (in thread): > I would say that iSEE fits this description pretty well:slightly_smiling_face:
Maria Doyle (11:00:10): > :writing_hand:New Bioconductor blog post on the inaugural Bioconductor Athena Award winner, Beatriz Calvo-Serra. Check it out here:https://blog.bioconductor.org/posts/2024-07-29-athena-award/ - Attachment (Bioconductor community blog): Beatriz Calvo-Serra: inaugural Bioconductor Athena Award winner – Bioconductor community blog > Celebrating Bea’s contributions, resilience, and the inaugural Athena Award in her honor.
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2024-07-30
Li-Fang Yeo (02:42:29): > @Li-Fang Yeo has joined the channel
Rishi (02:52:58) (in thread): > You may have a look inbroadSeq package which helps exploring colData and rowData easily but it is not a shiny app like iSEE - Attachment (Bioconductor): broadSeq (development version) > This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.
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2024-07-31
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2024-08-01
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NABISUBI PATRICIA (11:03:35): > Hello all.
NABISUBI PATRICIA (11:04:16): > Where can i get global AMR metadata that is not from humans?
Janani Ravi (11:25:02) (in thread): > Did you try NCBI NDARO and BV-BRC?
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2024-08-02
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2024-08-04
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2024-08-05
NABISUBI PATRICIA (03:45:04) (in thread): > yes I did try NCBI
2024-08-06
WJ P (01:18:01): > @WJ P has joined the channel
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Yanina Bellini Saibene (11:27:54): > No se lo pierdan Carolina es quien mantiene el paquete eph y una de las campeonas de rOpenSci. > > Estará charlando sobre diferentes aspectos de desarrollar paquetes en 40 minutos. (En inglés). > > Más info aquí:https://hachyderm.io/@rOpenSci/112915708542202869 #RStats - Attachment (Hachyderm.io): rOpenSci (@rOpenSci @hachyderm.io ) > rOpenSci Coworking and Office Hours coming up in an hour! > > Today’s Theme: Building your first R package with cohost @caro_pradier @twitter.com > > Tuesday August 6th 09:00 Americas Pacific (16:00 UTC) > > https://ropensci.org/events/coworking-2024-08 > > #RStats > @rstats @a.gup.pe
2024-08-07
Maria Doyle (08:47:30): > :dna:Join us for the EuroBioC2024 Carpentries Workshops! Workshops: Register here For more details, check out our posts onMastodon andLinkedIn . > Please share with your networks!
2024-08-08
Zhu Yujia (01:29:30): > @Zhu Yujia has joined the channel
Atte Lihtamo (03:38:27): > @Atte Lihtamo has joined the channel
stefano mangiola (03:53:42) (in thread): > Looking forward to meeting you all!
Cedric Dewas (04:41:32): > @Cedric Dewas has joined the channel
Maria Doyle (09:41:49): > ️:zap:EuroBioC2024 Flashtalks & Birds-of-a-Feather Sessions conference schedule for session date and time andsubmit here . > > * Birds-of-a-Feather: Propose your interactive discussion sessions on GitHub by September 5.See last year’s examples and more details here . > Join us in Oxford & share your ideas with theEuroBioC2024community! > > Share onMastodon andLinkedIn .
Varun Kumar Kesherwani (10:01:52): > @Varun Kumar Kesherwani has joined the channel
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Hayden Spence (12:19:21): > Hello, does anyone have any information on what process bioconductor uses to determine the next R devel version?
Lori Shepherd (12:23:51): > The version of R that Bioconductor users on the devel branch changes per release. From the release of the new version of R in April/May to the Bioconductor release in Oct/Nov, Bioconductor uses the current R release (or patched version) on the devel branch. After the Oct/Nov release until the following R release, Bioconductor uses R-devel to prep for the release of R. We try to update the builders to the current R-devel version every 4-6 weeks during this time.
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2024-08-09
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Maria Doyle (10:14:18): > :star2:Reminder: Annual Nominations Open for CAB & TAB! Community Advisory Board (CAB) Technical Advisory Board (TAB) Apply by Aug 31: CAB Application Form > * TAB Application Form > Don’t miss this opportunity to impact Bioconductor’s future! > > Feel free to share this onLinkedIn orMastodon
2024-08-11
Lu Yang (13:28:42): > @Lu Yang has joined the channel
Enrique Mondragon (20:12:27): > @Enrique Mondragon has joined the channel
2024-08-13
Mike Smith (05:10:55): > Hi all, we’re going through some changes at EMBL and I’m curious about how other institutes support working with R. Here at EMBL we have had an RStudio Server Pro instance running for 5-6 years on a large, shared memory, machine, with a licence that lets anyone in the institute use it at anytime. Since it’s a centrally managed resource it gives easy access to institute level storage, and the licences means it’s been pretty flexible at meeting the needs of both ‘novice’ users who want to look at their data occasionally and bioinformaticians that are doing analysis tasks everyday. > > In the near future we will be required to move to a per-user licence which will massively exceed the current budget if we try to accommodate everyone, so there’s no possibility to continue providing the same access to all users we currently do. We’re canvassing other options e.g. Jupyter hub, free RStudio Server instances via Kubernetes, no central solution at all - just use your laptop or the cluster, …. None of these are a direct replacement or as convenient as our existing implementation. I was curious to know if any has experience with these options or any other that are working in your institutes.
Hans-Rudolf Hotz (07:08:44) (in thread): > At the FMI (https://www.fmi.ch/ ), we have the free RStudio Server running on four kind of “large, shared memory, machines” each with access to the institute storage. This has worked very well so far - though, the free server version does lack some nice features included in the paid option…
Stevie Pederson (08:49:26) (in thread): > I’m currently trialling a JupyterHub RStudio setup at an HPC provider we use. They’ve set that end up for us and after a slightly glitchy start, it’s been running OK. A clear downside is that for this specific setup, I reserve an entire node for an interactive session. This means I have a stupid number of cores that I don’t really need (Intel Knights Landing with 68 cores usually) but it’s a node setup for parallel computing & isn’t great for rendering figures etc with a single core. Running things likeedgeR::estimateDisp()is horrifyingly slow, but setting up well thought outmclapply()operations is pretty good. From a data security perspective, it’s also pretty watertight.
Jared Andrews (09:03:21) (in thread): > At St. Jude, we have Singularity images and associated launch scripts with the free RStudio server that are easily run. We also use OnDemand to allow users to launch an HPC job running it with the click of a button. It works well and allows variable resources to be requested since it’s just run from an interactive job.
Jared Andrews (09:04:05) (in thread): > It’s probably not quite so convenient as your current option, but it’s not far off.
Jared Andrews (10:09:08) (in thread): > Our latest Singularity image definition file and launch script, if interested. Spits out an IP address running RStudio that the user can plug into the browser. Occasionally, we have to update with a system dependency of a package, but it’s pretty low maintenance and easy to update with each version of R. - File (Plain Text): rstudio_r_4.4.0-1.2004.0.def - File (Shell): rstudio_launch.r_4.4.0.sh
Jenny Drnevich (10:50:11) (in thread): > @Chris FieldsGood information here for us. Our HPC currently has a Juypter Hub interface where we can run Python/Bash/R notebooks but having RStudio Server would be awesome.
Jenny Drnevich (10:50:51) (in thread): > Also tagging@Alex Mahmoudto the thread as he’s running the Bioconductor Galaxy interface we’ve been using for conference workshops
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Maria Doyle (11:15:09) (in thread): > This is very useful info, thanks everyone! Do you think it’d help to have a dedicated channel for discussing multi-user setups on HPC/servers? It might be a good way to keep all this valuable info from getting lost and make it easier to share tips, troubleshoot, and swap resources. If there’s interest, I can set it up, and we could look into linking it to a page on the Bioconductor website down the line so others can find it. What do you think?
Chris Fields (11:41:00) (in thread): > A separate channel focusing on infrastructure would be great! We’ve discussed having RStudio Server on our local HPC but currently using Jupyter + R kernel (can adjust mem and CPU).
Chris Fields (11:42:26) (in thread): > Thx for including me in this BTW@Jenny Drnevich!
Chris Fields (11:42:27) (in thread): > I think the option that Jared mentions would be great based on the way our local cluster is set up
Maria Doyle (11:48:08) (in thread): > Great to hear! I’m thinking of calling the channel****#research-computing-infrastructure**to cover all the HPC/server discussions and setups. Does that work for everyone, or do you have other suggestions? Let me know, and I can get it set up!
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Peter Hickey (17:29:48) (in thread): > At WEHI it was also initially a RStudio Server instance running on a large, shared memory, machine (or virtual machine?). This is still available (as posit workbench, I’ve not kept up to date with product name changes) but IT then set up and encouraged us to move to OnDemand, which runs via SLURM on our broader HPC with ability to specify memory, CPU etc. requirements AFAIU
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2024-08-14
Konstantinos Geles (Constantinos Yeles) (04:03:28) (in thread): > just use nvim
Chris Fields (09:38:01) (in thread): > https://xkcd.com/378/ - Attachment: Real Programmers > [Title text] “Real programmers set the universal constants at the start such that the universe evolves to contain the disk with the data they want.”
xueyao (11:38:26): > @xueyao has joined the channel
2024-08-15
Monthly general reminder (06:00:02): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush:
Maria Doyle (06:43:36): > :sparkles:EuroBioC Updates: Important Deadlines Final Week to Register for EuroBioC 2024 Aug 21st Register now :wrench:Carpentries Workshops Aug 23rd Sign up :mega:Host EuroBioC 2025 Aug 31st Apply here Feel free to share theLinkedIn orMastodon post to help spread the word!
Maria Doyle (09:20:14) (in thread): > Thanks for all the great input so far! I don’t want to split the conversation in the middle, so we’ll keep it here in general for now. Feel free to keep adding any thoughts or ideas. In a few days, or when the conversation here winds down, I’ll set up a dedicated channel for infrastructure setups so you can continue sharing resources and ideas, and I’ll link back to this thread so nothing gets lost. I’ll keep you posted!
2024-08-17
Konstantinos Geles (Constantinos Yeles) (02:22:48) (in thread): > There is a well made module with neovim that turns it more or less like Rstudio. I have been using it for more than 5 months now and If only I knew before I would have never used Rstudio. > Here:https://github.com/R-nvim/R.nvim
ari-ds_8bioc (14:10:49): > @ari-ds_8bioc has joined the channel
Sounkou Mahamane Toure (21:04:32) (in thread): > In my company we use Vscode + remote-ssh (https://code.visualstudio.com/docs/remote/ssh ) + R-vscode extension (https://code.visualstudio.com/docs/languages/r ) . This has the advantage of using a more mainstream and polyglot IDE which is going to be maintained for a long time unlike Rstdudio by Posit - Attachment (code.visualstudio.com): Developing on Remote Machines using SSH and Visual Studio Code > Developing on Remote Machines or VMs using Visual Studio Code Remote Development and SSH - Attachment (code.visualstudio.com): R in Visual Studio Code > Learn about working with the R programming language in Visual Studio Code.
2024-08-19
Angelique Trusler (09:01:09): > @Angelique Trusler has joined the channel
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2024-08-20
Aaishah Mahadeo (06:51:47): > @Aaishah Mahadeo has joined the channel
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Maria Doyle (08:57:21): > :hourglass_flowing_sand:**** Final Reminder: EuroBioC2024 in-person registration closes tomorrow!****Don’t miss out—register here
Krithika Bhuvanesh (16:38:58): > Hi everyone. Question related to 3D genomics space. Can anyone recommend a tool for running differential loops on either .hic or .cool file format that actually works ? I’ve tried the following already - Hiccups-diff, hictoolsr, and mariner, but haven’t had any luck . thanks.
Vince Carey (17:53:25): > @Jacques SERIZAY^^ (who I think is on vacation but should, I think, have some advice)
Krithika Bhuvanesh (19:45:09): > Thank you
2024-08-21
Angelique Trusler (05:01:39): > [Cross posting]The Fellowship Capacity Accelerator Network (CAN) initiative develops data science talent for climate and health impact across Africa. The CAN Fellowship provides emerging data science professionals with the skills needed to address challenges at the intersection of climate and health and make a positive impact on lives across the continent. > During the program, participants collaborate with host institutions and mentors on projects to share their data skills, encourage innovative solutions, and build a network of data professionals committed to sustainable development. The fellowship includes practical project work, media training, and opportunities for fellows to present their work at local, regional, and international events.https://www.data4sdgs.org/about-can-data-science-fellowship
Eric Davis (07:18:21) (in thread): > @Krithika Bhuvaneshare you having trouble using mariner for differential loop analysis? There is a Bioc workshop that shows how to do this:http://ericscottdavis.com/Bioc2023mariner/ Here is a link to Jacques’ OHCA book also:https://bioconductor.org/books/devel/OHCA/ ThoughI’mnot sure if it covers differential looping analysis specifically. - Attachment (ericscottdavis.com): Bioc2023mariner > BioC2023 workshop using mariner and > plotgardener for analyzing and visualizing Hi-C genomic data.
Maria Doyle (08:08:30) (in thread): > Hi Angelique, > This is great—thanks for sharing! It would be fantastic if you could also post this in the#bioc_africachannel. We’re hoping to revive that channel with the Bioconductor workshops being planned for Africa, and your post would be a perfect fit for that community.
Krithika Bhuvanesh (08:15:34) (in thread): > @Eric DavisThank you for sharing the links ! I ran Juicer on the hic data to get .hic files. Trying to get some downstream tools to work. I was able to run Hiccups and Mustache to get the loops and looking to run diff-loops. Will try out the links you shared and see if i can get it to work. Thanks !
Maria Doyle (14:35:07): > :writing_hand:New Bioconductor blog post on an Outreachy internship experience by@Scholastica Urua, mentored by@Svetlana Ugarcina Perovic, and supported by the#bugsigdbteam. Check it out here:https://blog.bioconductor.org/posts/2024-08-15-OutreachyInternshipExperience/ - Attachment (Bioconductor community blog): Outreachy May 2024 – Bioconductor community blog > Bioconductor participated in the Outreachy Internship program for the May 2024 cohort. In this post, our intern shares her journey, detailing her experience working on the Microbiome Study Curation project and Bioconductor in general.
2024-08-22
Maria Doyle (04:49:56): > :mega:BioCAsia 2024 Abstract Deadline - August 26th this Monday, August 26th, at 11:59 PM (AEST) BioCAsia 2024 Submission Page . > > Looking forward to seeing your contributions!
2024-08-23
Dario Strbenac (22:00:00): > Any way to easily loadgzipped RData files from GEO Browser for a reproducible example? I tried > > load(gzcon(url("[https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE188737&format=file&file=GSE188737%5Fhnscc%5Fseu%2ERData%2Egz](https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE188737&format=file&file=GSE188737%5Fhnscc%5Fseu%2ERData%2Egz)")) >
2024-08-26
Maria Doyle (10:25:27): > :bell:Reminder: Tidyomics meeting is tomorrow! https://x.com/steman_research/status/1826059124091793867 orhttps://bsky.app/profile/stemang.bsky.social/post/3l26vts4aak26
Peter Hickey (17:51:19) (in thread): > download.file()to a temp location, unzip, and load would be my approach
2024-08-27
Maria Doyle (08:06:11): > :mega:𝗥𝗲𝗴𝗶𝘀𝘁𝗿𝗮𝘁𝗶𝗼𝗻 𝗳𝗼𝗿 𝗕𝗶𝗼𝗖𝗔𝘀𝗶𝗮 𝟮𝟬𝟮𝟰 𝗶𝘀 𝗻𝗼𝘄 𝗼𝗽𝗲𝗻! > > Join a key event connecting the bioinformatics community.:point_right:Register here:https://buff.ly/4cEmcIj Note: BioCAsia registration is available separately if you’re not attending ABACBS. If attending ABACBS, select ‘ABACBS Full’ or ‘ABACBS Student’ to add BioCAsia during the process. Feel free to share theLinkedIn orMastodon posts.
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Gordon Zheng (13:29:09): > Hi, All I have a question regarding to the DSEQ w/ RNA data: dds <- DESeqDataSetFromMatrix(countData = counts2, colData = coldata, design = ~condition) > dds <- DESeq(dds) > vsdata <- vst(dds, blind = FALSE) > res <- results(dds, name=“condition_S_vs_C”) > res <- results(dds, contrast = c (“condition”, “S”, “C”)) > res > write.csv(res, “test_before_apeglm.csv”) > resLFC <- lfcShrink(dds, coef=“condition_S_vs_C”, type=“apeglm”)
Gordon Zheng (13:29:30): > Did I do 2 lfcshrinkage or one?
Marcel Ramos Pérez (13:32:23) (in thread): > Hi Gordon! Please ask software-use questions on thesupport.bioconductor.org site. Make sure to tag the appropriate package. Thanks!
Gordon Zheng (13:45:01) (in thread): > okay thank you for the direction
Artür Manukyan (14:21:50) (in thread): > It looks to me that you did only once, what makes you think that it might be twice ?
2024-08-28
NABISUBI PATRICIA (04:45:03): > Hello all. > I am doing a study on metagenomics to assess people’s understanding of metagenomics in health care. > I request you help me participate and also share in your other networks. > This is the link to the questionnaire:https://forms.gle/5NR1WhNB9znT8DDA9 - Attachment (Google Docs): Understanding the Knowledge and Attitudes Towards Metagenomics in Clinical Care > This study aims to assess the knowledge, perceptions, and attitudes of healthcare professionals in Uganda towards the use of metagenomics in clinical care. Metagenomics, the study of genetic material obtained directly from environmental or biological samples, holds significant potential for revolutionizing diagnostics, disease surveillance, and antimicrobial resistance detection. > The study seeks to identify gaps in knowledge, explore attitudes towards integrating metagenomics into clinical practice, and assess the perceived benefits, barriers, and opportunities. By understanding these factors, the study aims to inform the development of training programs, policies, and infrastructure that could facilitate the adoption of metagenomics in Uganda’s healthcare system. The findings will also provide insights into how metagenomics can be used to improve patient outcomes and address public health challenges, including antimicrobial resistance.
Maria Doyle (06:53:27) (in thread): > :money_with_wings:Just a heads-up! The “Conference Access Award” is available to help cover your BioCAsia registration fee. If you’re presenting or participating and need support, consider applying here:https://biocasia2024.bioconductor.org/submissions/
Angelique Trusler (09:48:00): > Hello, Community! > > We’re thrilled to invite you to our next quarterlyGlosario CodeFes t co-working event on4 September at 15:00 UTC! find your time and toadd it to your calendar ). Let’s come together tocelebrate diversity, break language barriers, and empower learners around the globe! > > During the event, community members will have another opportunity to co-work on increasing the number of languages supported in Glosario byadding, reviewing and translating English ). > > - Here is acontribution guide to Glosario. > - Here is a quickguide in English on how to contribute to Glosario . > - And here is theGlosario contribution guide in Spanish . > - Not comfortable with GitHub? You can submit your contribution using thisGoogle Form . > > Sign up here:https://pad.carpentries.org/Glosario_Codefest_2024 . We look forward to having you join us! - Attachment (The Carpentries): Breaking Language Barriers in Data Science: Glosario Codefest Event > Let’s celebrate diversity and break language barriers. - Attachment (timeanddate.com): Event Time Announcer - CarpentriesWelcome > Event Time Announcer shows time for CarpentriesWelcome in locations all over the world. In UTC it happens on Wednesday, September 4, 2024 at 3:00:00 pm. - Attachment (Google Workspace): Google Calendar - Easier Time Management, Appointments & Scheduling > Learn how Google Calendar helps you stay on top of your plans - at home, at work and everywhere in between. - Attachment (YouTube): Glosario Contribution Instructions in English
2024-08-29
melissa hahn (07:16:15): > @melissa hahn has joined the channel
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2024-08-30
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2024-09-04
Angelique Trusler (03:29:03): > Join us TODAY to Attachment > Hello, Community! > > We’re thrilled to invite you to our next quarterly Glosario CodeFes t co-working event on 4 September at 15:00 UTC! :earth_africa: (Don’t forget to find your time and to add it to your calendar ). Let’s come together to celebrate diversity, break language barriers, and empower learners around the globe! > > During the event, community members will have another opportunity to co-work on increasing the number of languages supported in Glosario by adding, reviewing and translating data science terms included in the glossary in various languages (including English ). > > - Here is a <https://docs.google.com/document/d/18oxYd6D9heESqw2gw9cbtxiCfkb4wlxazERFBIDCoeM/edit#heading=h.wsi1psxc3n64|contribution guide> to Glosario. > - Here is a quick guide in English on how to contribute to Glosario . > - And here is the Glosario contribution guide in Spanish . > - Not comfortable with GitHub? You can submit your contribution using this Google Form . > > Sign up here: https://pad.carpentries.org/Glosario_Codefest_2024 . We look forward to having you join us!
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2024-09-06
gilda williams (00:00:55): > @gilda williams has joined the channel
Lori Shepherd (07:13:40): > The 3.20 release schedule has been announced. Please be aware of important deadlines:https://bioconductor.org/developers/release-schedule/
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2024-09-07
Maria Doyle (06:16:11): > :star2:Save the date for EuroBioC2025 Barcelona, September 17-19, 2025 LinkedIn andMastodon for more details, and stay tuned for a recap of EuroBioC2024! - Attachment (linkedin.com): Bioconductor on LinkedIn: #eurobioc2024 #eurobioc2025 > :star2: Thank you to all our amazing sponsors, organisers, presenters, and attendees for making #EuroBioC2024 a success! Stay tuned for a recap blog post, and save…
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2024-09-08
Federica Gazzelloni (11:15:27): > #generalquestion for anyone who knows where I could find ALSFRS-R Datasets. I am looking at various articles, but wondered if any specific source is available for downloading data. Thanks in advance (any input would be much appreciated)
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2024-09-09
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2024-09-10
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2024-09-11
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2024-09-12
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2024-09-14
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2024-09-15
Monthly general reminder (06:00:03): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush:
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2024-09-16
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2024-09-17
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2024-09-18
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2024-09-19
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2024-09-21
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2024-09-23
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2024-09-24
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Maria Doyle (11:07:41): > FYI - Attachment: Attachment > :rocket: Starting in one hour!! > > Navigating the R ecosystem using R-universe. > > Jeroen Ooms will share details on what R-Universe is and an update on what you can do with it today. He will also discuss the future of R-Universe and how it can be used to navigate the R ecosystem. > > Link to join + add to your calendar: https://ropensci.org/commcalls/nov2024-r-universe/
Jasmine Baker (12:48:28): > @Jasmine Baker has joined the channel
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Wes W (21:54:35): > Hey everyone! > > I am hosting a 3-day livestream this week, Sept 26-28th, to raise money for the Fuck Cancer charity. Fuck cancer works to support advancing health equity through early detection and prevention programs, and by providing resources to navigate, manage, and cope with cancer at all stages. > > We are trying to raise $2500 and would be fantastic if you could share in your networks! > > If you work in cancer research, would be keen to have you on Friday or Saturday (Thursday schedule is full) and have you on to chat about your work! > > Donate ->https://tilt.fyi/4EROG67Tfn Campaign ->https://tiltify.com/@tumortalk/fcancer … Our livestream (on 26th-28th) ->https://www.youtube.com/tumortalk/live - Attachment (Tiltify): Tiltify - Tumor Talk F Cancer > TumorTalk is fundraising for F Cancer September 2024 on Tiltify - File (MPEG 4 Video): 3. Full - 2nd.mp4
2024-09-25
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Maria Doyle (06:58:31): > :mortar_board:Exciting opportunity for Carpentries Instructors! 2025 Bioconductor African Courses Interested? Complete ourexpression of interest form by Oct 21, 2024 ** - Attachment (Google Docs): Bioconductor African Courses 2025 - Instructor Expression of Interest > We are excited to announce the upcoming Bioconductor African Courses scheduled for 2025. The first course will take place in Nairobi, Kenya in March/April, with a second course planned for West Africa a few months later. These courses aim to build local capacity and foster a strong network of learners and instructors across Africa. > Course Structure: > Each weeklong course consists of two teaching modules and a BYO data day: > Monday & Tuesday: bioc-intro module (Introduction to genomic data analysis with R and Bioconductor) > Wednesday & Thursday: bioc-rnaseq module (Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor) > Friday: Bring your own (BYO) data day > What We’re Looking For: > We are seeking Carpentries-certified instructors to teach these modules. Each module will be taught by a pair of instructors—one international and one based in Africa. Additional local instructors may be included to provide more teaching opportunities. > Instructors will teach one module (either bioc-intro or bioc-rnaseq) but are expected to stay for the full week to assist as a helper in the other module and the final BYO data day. This fosters collaboration and community-building among participants and instructors. You can express interest in teaching either the Nairobi course, the West Africa course, or both. > Funding: > Thanks to funding from the Chan Zuckerberg Initiative (CZI), travel and accommodation expenses will be covered for instructors. For more details on this and other CZI-funded Bioconductor projects, please check out our blog post. > > How to Express Interest: > Please complete our expression of interest form by Monday, October 21st, 2024. The form will ask for your certification status, area of expertise, and preferred module and location. > We are considering the following dates for the Nairobi course: > March 24-28, 2025, or > March 31-April 4, 2025 > Dates for the West Africa course will be confirmed later. We aim to finalise the instructor line-up for Nairobi by the end of the year and will follow up regarding West Africa soon after. > Should you have any questions, feel free to reach out to us directly. > Thank you for your interest in contributing to this important initiative. We look forward to hearing from you! > Maria Doyle > Bioconductor Community Manager > Email: mailto:maria.doyle@ul.ie|maria.doyle@ul.ie
Imran Khan (08:55:27): > @Imran Khan has joined the channel
2024-09-26
rohitsatyam102 (07:26:23): > Hey Everyone. Is there an R package to quickly get pathways and corresponding genes from BioCyc. I see that in the package vignettes like Brenda, they mentioned that we now require an account with BioCyc, login in it and then use SmartTables to download it.
Vince Carey (07:37:42) (in thread): > > BioCyc Academic/Non-Profit Subscriptions > > Academic/Non-Profit subscriptions provide unlimited, unrestricted access to all of the BioCyc databases, which currently number over 20,000. > Purchase an Academic/Non-Profit Subscription for an Individual or Lab > Purchase a subscription by credit card -- provides one year of access to BioCyc by a single person or lab. > > Contact your institution's library -- in many cases libraries will purchase a subscription for the entire institution (see below) at no cost to you. > > Purchase for Academic/Non-Profit 2024 (USD) > Individual $375 > Student $175 > Lab ≤ 5 people $675 > Lab ≤ 10 people $850 > Lab ≤ 15 people $1,025 >
rohitsatyam102 (07:43:15) (in thread): > Hi Carey. I read this. I have actually more than 50 organism and I was writing a function to automatically fetch it from BioCyc if possible.
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Vince Carey (09:58:46) (in thread): > so you would like code that works after authenticating to BioCyc?
Vince Carey (09:59:33) (in thread): > I suspect you might have better luck atsupport.bioconductor.org where someone may have already done that. Or speak to the BrendaDb developers.
2024-09-27
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2024-09-29
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Stevie Pederson (23:10:00): > Hi everyone. We’ve recently received some fantastic applications for presentations at BiocAsia (Sydney, Australia, Nov 7-8). However, every application was from a researcher based in Australia, and we’re very keen to ensure that members of the BiocAsia community located in other regions are given every opportunity to present. If you’re from elsewhere in the region and would like to present remotely, we’re specifically re-opening talk applications for remote presentations, and we’d love to hear from you. Please visithttps://forms.office.com/pages/responsepage.aspx?id=DQSIkWdsW0yxEjajBLZtrQAAAAAAAAAAAAN__jdh18tUNFhMRzBWOTVBQzY4MUdHTU9DVFJBWTJWVi4u&route=shorturl
2024-09-30
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2024-10-01
Anna Quaglieri (she/her) (05:02:36): > Bioconductor Code of Conduct Committee Elections https://forms.gle/DPxyubQotSsd3iD1A .What level of commitment is expected if I apply? The CoC only meets 3 to 4 times per year, and always for a good reason. This allows members to also participate across other boards of the consortium. > If you want more information feel free to contact the current chairs of the committee@Anna Quaglieri (she/her)(anna.quaglieri@gmail.com ) and@Gerry Tonkin-Hill(g.tonkinhill@gmail.com ). You can find all current committee members here:https://www.bioconductor.org/about/code-of-conduct/ . - Attachment (Google Docs): Bioconductor Code of Conduct Committee Elections 2024 > The Bioconductor Code of Conduct Committee updates, disseminates, upholds and enforces the Code of Conduct (http://bioconductor.org/about/code-of-conduct/ ) across all platforms of the Bioconductor project. Each year the Code of Conduct Committee invites applications to become a new member of the committee. If you are interested in becoming a member of the committee, please fill out the following short application. The applications are then voted on by the current committee. The Bioconductor Code of Conduct Committee strives for a diverse and inclusive committee and thus encourages applications from members of underrepresented groups. > > If you want to find out more about serving on the Bioconductor Code of Conduct Committee, see the following presentation (https://docs.google.com/presentation/d/1VdcmY1bs0vIYQ2kegxDt0SqN7oaCeU5-gbkU_sTHD60/edit?usp=sharing ). > > Applications close 31st of October. > > If you have any questions regarding serving on the Bioconductor Code of Conduct Committee or the application process, please contact Anna Quaglieri (mailto:anna.quaglieri16@gmail.com|anna.quaglieri16@gmail.com ). - Attachment (bioconductor.org): Bioconductor - Code of Conduct Policy > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
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Aidan Lakshman (12:27:19): > is there a way to report comments/posts onsupport.bioconductor.org ? for example,this comment seems to be spam with a potentially unsafe link (note: link here goes to the comment itself, not to the link in the comment)
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Marcel Ramos Pérez (12:41:24) (in thread): > Thanks for pointing it out. I’m not sure there is a way to report comments@Lori Shepherd? I’ve marked it as spam.
Aidan Lakshman (12:42:26) (in thread): > i couldn’t find one myself–doesn’t seem like a huge issue, but it would be a nice addition. Thanks for flagging it.
Lori Shepherd (12:43:07) (in thread): > thank you for letting us know. You can message in the dedicated#support-sitechannel or open an issue but not directly on the site.
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Maria Doyle (10:51:31): > :wave:Welcome to all the new Outreachy contributors! We’re delighted to have you in our community. > To help you get started, please use these channels: > * #introductionsfor your intros (or the project-specific channels#molevolvr/#bugsigdb) > * #outreachyfor general Outreachy questions. > * #molevolvrfor Molevolvr project questions. > * #bugsigdbfor BugSigDB project questions. > This will help keep things organised and make it easier for everyone to engage.
Mildred Anashie (10:55:27) (in thread): > Thank you@Maria Doyle
Aleru Divine (10:56:44) (in thread): > Thank you so much@Maria Doyle
Adeshile Oluwatosin (10:59:39) (in thread): > Thank you:hugging_face:@Maria Doyle
Maria Doyle (10:59:55) (in thread): > You’re all very welcome!:blush:If you have any questions or need help getting started, feel free to reach out in the above channels!
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2024-10-08
Zelal Özgür Durmuş (01:29:47): > Hello. I am Zelal from Türkiye. I am a developmental biologist working with ants. I am trying to run Deseq2 for my transcriptome data. I am not a specialist in this field and have some questions about the process. What channel is appropriate to ask those questions?
Robert Castelo (04:25:52) (in thread): > Hi Zelal, the recommended way to find help is: > 1. consult the available documentation, in this case DESeq2 is very well documented, go to the landing page of the package athttps://bioconductor.org/packages/DESeq2 and read through the vignette entitled “Analyzing RNA-seq data with DESeq2”. > 2. another important source of documentation are workflows, there’s at least one using DESEq2 athttps://bioconductor.org/packages/release/workflows/html/rnaseqGene.html > 3. you can find further sources of documentation (courses, videos, etc) athttps://bioconductor.org/help > 4. for specific questions on the use of the software, go to the Bioconductor support site athttps://support.bioconductor.org please try first searching for your question, just in case it has been already answered, and if you don’t find any such question and want to formulate your own, please read first the Bioconductor Posting Guide athttps://www.bioconductor.org/help/support/posting-guide with tips on how to write a question, in general, only good questions attract good answers! - Attachment (Bioconductor): DESeq2 > Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. - Attachment (Bioconductor): rnaseqGene > Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results. - Attachment (bioconductor.org): Bioconductor - Help > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists. - Attachment (bioconductor.org): Bioconductor - Posting Guide > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
Zelal Özgür Durmuş (05:07:17) (in thread): > Thank you for answering…
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rohitsatyam102 (07:35:11): > Hi everyone! Is there a Package size limit when thinking of submitting to Bioconductor(I know there is 10 MB for CRAN).
rohitsatyam102 (07:35:30): > Also how big can data packages be?
Lori Shepherd (07:38:44): > Seehttps://contributions.bioconductor.org/general.html#package-size andhttps://contributions.bioconductor.org/non-software.html#non-software . We encourage large data to not be directly stored in a package and instead hosted on something like zenodo and accessed through the ExperimentHub interface
Lori Shepherd (07:45:57) (in thread): > justification also being often large example files and data files are not needed to show package functionality; smaller can do just as well. And end users do not need large example data as they have their own to analyze and could potentially run into space limitations if utilizing shared resources with limited capacity. If providing useful experiment data or annotation data then hosting the data elsewhere (like zenodo or if necessary a Bioconductor default location on Microsoft data lake) also keeps the package lightweight and will only be downloaded when necessary.
rohitsatyam102 (09:37:25) (in thread): > Thanks@Lori Shepherd. Let me give it a read.
2024-10-09
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Steffen Neumann (09:59:40): > Hi, I have a non-BioC package that depends on other packages, including BioC ones. In my Dockerfile, I want to install all dependencies, and then install my own package.
Lori Shepherd (10:05:37): > are the non-BioC packages on CRAN or github? if CRAN , BiocManager::install will install any CRAN and Bioconductor package
Steffen Neumann (10:07:34) (in thread): > The Dockerfile is based on rocker/shiny, which currently uses R-4.4.1. > So far, I useddevtoolsto install the dependencies: > > library(devtools); install_deps("/tmp/mypackage") > > Recently, installation of S4Vectors chokes witherror: format not a string literal and no format argumentsbecauseinstall_depsgrabsS4Vectors_0.40.2.tar.gz from BioC 3.18, which is too old forgcc (Ubuntu 11.4.0-1ubuntu1~22.04). > When installing BiocManager, I get the expectedS4Vectors_0.42.1.tar.gz which compiles nicely.****=> How do I install build dependencies of my package and benefit from BiocManager ?****
Steffen Neumann (10:10:29) (in thread): > See the thread above for more details. My package is currently on GitHub only. And, because I have a Base Dockerimage with all the (rarely) changing dependencies, I don’t want to install my package in that base image. In the past, I had manually coded theinstall(...)and used BiocManager. Now I fell in love withinstall_deps(...)
Lori Shepherd (10:12:41) (in thread): > You could add BiocManager::repositories() , I assume install_deps has a repository argument that could be passed
Steffen Neumann (10:13:50) (in thread): > Cool, let me check …
Steffen Neumann (11:01:08) (in thread): > cool, worked !
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2024-10-12
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Vince Carey (07:39:48): > Looking for folks interested in discussing the processing of Illumina EPIC arrays. I have been working with wateRmelon and find that IlluminaHumanMethylationEPICv2anno.20a1.hg38, essential for the import process, takes inordinately long to install, presumably because of the mass of Rda files in the annotation data. Once it is installed, it is fine, so maybe it is a non-issue. methylumiSet is a derivative of eSet, and a SummarizedExperiment approach could be beneficial. Quantifications/annotations could be managed out of memory, rowRanges and tidySE processes might be valuable, etc. In short, does the toolchain for EPIC arrays with Bioconductor need some community attention, and if so, would interested parties add some comments on desirable steps forward?@Kasper D. Hansen@Tim Triche@Zuguang Gu… a slack channel might be warranted
Kasper D. Hansen (09:40:13): > This is long overdue and a bit of public shaming / reflection might help on this. The main issue here is that the annotation system is long overdue for a complete re-design.
Kasper D. Hansen (09:40:20): > Here are the main issues as I see them
Kasper D. Hansen (09:42:12): > 1. the crazy install time, package size and ram consumption at installation. This is caused by the SNP annotation and the solution is to remove the SNP annotation to a different package, > 2. the reported (and somewhat fixed) error with a row mismatch between the manifest package and the annotation package (reported and fixed by your group). This is caused by having a separate annotation and manifest package and the solution is to merge the two packages into one.
Kasper D. Hansen (09:43:28): > 3. (enhancement) We need a robust system to map probes to the genome, so we can provide annotation packages for both hg19, hg38 and t2t genomes. Multiple people I have spoken to over the years say they have done this (and it is not super difficult in principle). We should have a set of tested scripts which does this.
Kasper D. Hansen (09:45:12): > 4. (enhancement) We should provide better annotation that we actually understand. For example, the CpG Island annotation should not be grabbed from Illumina’s files but should be generated by some code which takes CpG locations and intersects it with (say) UCSC CpG Islands.
Kasper D. Hansen (09:45:41): > 3 and 4 are optional, but I strongly feel that 3 is long overdue as well. I am very interested in people who have trustworthy scripts for this.
Kasper D. Hansen (09:46:10): > So now I’ll transition from listing the issues and provide a deeper analysis of the issues
Jared Andrews (09:51:15): > For what it’s worth, SeSAME has done an admirable job supporting the newer arrays, and I felt the docs were more comprehensive/easier to follow than minfi, conumee, and co. I’d suggest getting them involved if possible, they also have done work on the annotations and such.
Kasper D. Hansen (10:01:51): > The main design issues are the following > 1. A long time ago I decided it would be convenient to have an easy way to filter for probes with SNPs in them. To this end, we provide a number of objects containing the intersection between probes and SNPs from various versions of dbSNP. These interestions are large and because there are multiple versions (the package Vince refers to have 7 different versions) they are large. In addition, there seems to be a weird issue in R related to package installation. The design is that we have data files with different names, each containing an object with the same name (soSNPs.v2.rdaandSNPs.v1.rdaeach has an object inside which is named (say)snps.) For some reason that I never managed to track down, this creates some kind of issue during package installation where the data objects are listed in a central location (I think). The solution is to remove all of these objects and create a new package. I don’t think they are used a lot. > 2. Originally, I choosed a design with two separate packages, a “manifest” package and an “annotation” package. The idea was that the design would stay fixed (manifest package) and the annotation would change. This never really happened and Illumina messed it up by releasing multiple subtle different manifests which tends to drop a few probes. And the drawback of this design - a not perfect link between the two packages - led to the possibility of an error reported and fixed by Vince’ group. > So two fix this, the best solution is a complete redesign, which is a fair amount of work. But there are also a fair amount of people depending on this stack.
Kasper D. Hansen (10:02:40) (in thread): > SeSAME has done a good job yes. The main issue is that we have a lot of packages which are built on the minfi infrastructure so in a perfect world, it should get fixed.
2024-10-13
Vince Carey (05:42:05): > Thanks for all this feedback. Just a few reactions. 1) The error fix attributed to my group was work of Jonathan LeFaive at U Mich, I played a role in communicating the finding but it was not work of my group. 2) it is disconcerting to me that a) a google search of “analyze EPIC arrays with Bioconductor” does not return information about SeSAME, b) searching “EPIC arrays” in the search box atBioconductor.org does not return information about SeSAME:@Tim Trichewhat can we to to elevate visibility? 3) I am not raising the question to shame or to ask for more effort from any particular lab, but to get community input on a road map to improving scalability of best-in-class approaches to annotation and analysis of this cumbersome data type. I can imagine some simple modifications to the annotation packages that – at least – install with reasonable rapidity. Then there are questions about out-of-memory representations of quantifications that may not have been addressed yet … and then tidyverse concepts that may play a role. We cannot expect labs that pioneered methods 13 years ago (that’s the age tag for minfi; SeSAME is a pre-teen 6 yo) to keep incorporating new concepts especially in the face of backward-compatibility expectations and other limitations arising from tradition and ecosystem stability constraints (I know this is vague). I want to view these concerns as opportunities for collaboratively streamlining the user experience, and, I hope, enhancing developer support so that changes can be explored and verified in a timely manner. Maybe we should make a channel or continue in developers forum?
Kasper D. Hansen (13:06:46): > The first quick fix would be to drop the SNP annotation from the packages. This will result in reduced functionality, but I don’t think that many people use that right now.
2024-10-14
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Tim Triche (13:10:51) (in thread): > Yes
Tim Triche (13:14:24) (in thread): > This is what sesameData already does
Tim Triche (13:14:45) (in thread): > This too is handled by sesameData
Tim Triche (13:15:54) (in thread): > This has never been a showstopper until Lori requested that Wanding remove the sesamize() function that turns sesame objects into minfi objects (RGSet, GRSet) and back
Tim Triche (13:16:25) (in thread): > So interop died at that point in order to make the package import fewer dependencies.:man-shrugging:
Tim Triche (13:17:22) (in thread): > It’sfixable, relax the methods to query a SummarizeExperiment-derived object and we can work from there
Tim Triche (13:17:56) (in thread): > Sesame’s issue is that itdoesn’treally use an expressionSet/SummarizedExperiment at its heart
Tim Triche (13:18:12) (in thread): > These two issues are why interop is hard
Tim Triche (13:20:08) (in thread): > Arguably the SNP annotation is superseded by detection-based thresholding anyways.It’swhy sesame exists (to avoid artifacts) and I remember that minfi has something similar (gapFinder?) to flag high-MAF suspicious sites
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Jenny Drnevich (18:02:53) (in thread): > @Chris Fields:arrow_up:
2024-10-15
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Monthly general reminder (06:00:05): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush:
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Maria Doyle (09:50:04): > :mortar_board:Exciting opportunity in Brazil 2025 Brazilian Genetics Society co-teach a Bioconductor workshop symposia roundtable Interested? Complete theexpression of interest form by Oct 26, 2024 *! - Attachment (Google Docs): Brazilian Genetics Meeting 2025 - Bioconductor Instructor Expression of Interest > We are excited to invite expressions of interest for a Carpentries-certified instructor to represent Bioconductor at the Brazilian Genetics Society Meeting, to be held in Belém do Pará, Brazil, from August 13-16, 2025. This is the largest national scientific event in Brazil, attracting over 1,500 attendees including graduate, undergraduate, and post-doc researchers. While many researchers in Brazil may use Bioconductor packages, awareness of the broader Bioconductor ecosystem and community is still growing. This event offers a significant opportunity to raise awareness and showcase Bioconductor’s rigorous science, first-class software, and community-driven education efforts, particularly in the Latin American (LATAM) bioinformatics and genetics communities. > We are primarily seeking a Carpentries-certified instructor to co-teach a beginner/intermediate Bioconductor Carpentry workshop in English, alongside Izabela Mamede, a Bioconductor Carpentry instructor from Brazil. There is also an optional opportunity to lead a symposia or roundtable session on Bioconductor (its software principles, education, outreach, or specific packages). A symposia is a 45-minute talk, and a roundtable consists of 20-minute talks for 3 researchers. > We welcome applications from those interested solely in presenting a symposia or roundtable, but please note that travel support from Bioconductor is prioritized for the instructor role. If the instructor has access to grant funding or support from their employer, it would be reasonable for part of the airfare to be covered through those means. The conference will cover food and accommodation for workshop, symposia, or roundtable presenters. > Please note that this is for a proposal submission to the Brazilian Genetics Society, and it is not guaranteed to be selected by the conference organizers. > Key Dates: > Application Deadline (to apply in this form): October 26, 2024 > Proposal Submission Deadline (to the Brazilian Genetics Society): October 30, 2024 > Contact for questions: > Maria Doyle, Bioconductor Community Manager (mailto:maria.doyle@ul.ie|maria.doyle@ul.ie ) > Izabela Mamede (mailto:iza.mamede@gmail.com|iza.mamede@gmail.com )
2024-10-19
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2024-10-20
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2024-10-22
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Ramon Massoni-Badosa (03:49:56): > Hi, I just posted in#proteomics, but I’m not sure if that channel is active anymore. Is there any site or channel that I can use to post these kind of questions? Thank you
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2024-10-25
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Maria Doyle (11:00:15): > :art:Enter the GBCC2025 Logo Contest! Deadline: Prizes: https://forms.gle/mZFEhevYU4cccbUv8
2024-10-26
Chris Fields (13:37:26) (in thread): > @Negin Valizadegansee above discussion
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2024-10-27
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2024-10-28
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2024-10-29
Steffen Neumann (03:56:35): > Hi, for years, and on multiple installations, I have an issue where on LinuxR CMD INSTALL somepackagegives***** caught segfault ***** address (nil), cause 'memory not mapped', > butdevtools::install("somepackage")works as expected.
Steffen Neumann (03:59:01) (in thread): > This is on Ubuntu 20.04, 22.04 and several 24.04 on my laptop. The package is MSnbase, checked out fromhttps://github.com/lgatto/MSnbase.git Over time, there were certainly multiple versions of R, gcc etc. > So while I have a workaround withdevtools, I wouldn’t mind getting down to the cause. Maybe I can make something more robust.
Steffen Neumann (03:59:35) (in thread): > => Has anyone ever experiencedsegfaultuponR CMD INSTALLwith any package as well ?!
Shian Su (04:05:32) (in thread): > R CMD INSTALLis for installing packages from local source, were you using it in that way?
Steffen Neumann (04:07:23) (in thread): > Yes, I have a locally checked out version. > While digging down and retracing every step, I checked out a clean copy from git, and voila, issue gone.git statusin the broken copy didn’t reveal anything that shouldn’t be there, but if it is my borked working directory, there is no way anyone can reproduce, and I can happily use the working fresh checkout onwards. > Sorry for wasting peoples time, sometimes writing issues help to resolve them yourself …
Lluís Revilla (09:14:39) (in thread): > If it helps in the future, the r-hub has some containers to check for memory and segfaults as CRAN does. They are helpful for this kind of problems.
Leonardo Collado Torres (10:43:21): > Hi! > > Ishttps://bsky.app/profile/bioconductor.bsky.social a legit account? Or is it someone else who took over the @Bioconductor username? - Attachment (Bluesky Social): Bioconductor (@bioconductor.bsky.social ) > Bioconductor: Free, open-source software for rigorous, reproducible biological data analysis with R. Join our diverse community of developers and data scientists. > https://bioconductor.org/
Marcel Ramos Pérez (10:46:43) (in thread): > @Maria Doyle^^
Svetlana Ugarcina Perovic (10:46:50) (in thread): > It’s legit!@Maria Doylecan confirm it.
Svetlana Ugarcina Perovic (10:47:32) (in thread): > See in#social-mediahttps://community-bioc.slack.com/archives/C04BXB04V96/p1729798436711389 - Attachment: Attachment > Thanks, everyone! Buffer added Bluesky support back in July, and with the growing interest from the community (such as here), I’ve gone ahead and set it up as an additional platform for Bioconductor announcements (alongside LinkedIn and Mastodon). You can find us now here: https://bsky.app/profile/bioconductor.bsky.social . First post goes out tomorrow at ~11am ET for the GBCC2025 logo design contest :slightly_smiling_face:
Stevie Pederson (11:08:36) (in thread): > Great! Thanks Maria. I began putting together a Bioconductor Starter Pack too. Let me know if anyone wants to be added.https://bsky.app/starter-pack/smped.bsky.social/3l7n3557j742v - Attachment (Bluesky Social): Bioconductor Starter Pack > Join the conversation
Travis Blimkie (11:17:19): > @Travis Blimkie has joined the channel
Leonardo Collado Torres (13:33:50) (in thread): > Thanks for the confirmation of its legitimacy!
2024-10-30
Maria Doyle (06:42:49) (in thread): > Hi all! Thanks for checking in about the Bluesky account—it was a soft launch on Friday before we officially announced, so it’s great to see it was found and there’s already interest!:slightly_smiling_face:Yes, it’s an official account managed by me, and it’s also linked from theBioconductor.org homepage under “Connect with the Community” and in the footer.
Inge R Holtman (09:16:53): > @Inge R Holtman has joined the channel
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Lori Shepherd (16:31:05): > Bioconductor 3.20 is released! Thanks to all developers and community members for contributing to the project! Please see full release announcement:https://bioconductor.org/news/bioc_3_20_release/ - Attachment (bioconductor.org): Bioconductor - Bioconductor 3.20 Released > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
Stephanie Hicks (21:06:49): > That is wonderful news!
Chen Zhan (21:35:44): > @Chen Zhan has joined the channel
Hervé Pagès (21:45:27) (in thread): > It’s important to realize thatdevtools::install()likeinstall.packages()useR CMD INSTALLbehind the scene to install packages. Note thatR CMD INSTALLcan be used on a folder containing a package source tree (e.g. on a local git clone) or on a package source tarball. If used on a folder, you have to be careful to make sure that the folder doesn’t contain stale stuff like stale.oor.sofiles. The typical scenario where one ends up with these stale files is the following: > 1. A while ago you’ve installed the package withR CMD INSTALL mypackage/wheremypackage/is the path to a local git clone. Nowmypackage/src/contains.o/.sofiles. > 2. In the meantime someone made changes to the package. > 3. Today you’re going to work again on the package so yougit pullwhile insidemypackage/to get the latest changes. Note that now your old.o/.sofiles inmypackage/src/might be stale. > 4. Bad things could happen if you runR CMD INSTALL mypackage/again without cleaningmypackage/first. > This is why personally I don’t want*.oor*.soin my.gitignorefiles, so I can quickly get rid of potentially stale files by just doinggit clean -iright aftergit pull.
2024-10-31
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2024-11-02
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2024-11-04
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2024-11-05
Steffen Neumann (06:47:20): > Please confirm / correct this sentence: [https://bioconductor.org/biocLite.R](https://bioconductor.org/biocLite.R)was removed in 2024.
Steffen Neumann (06:48:22) (in thread): > Seems like it was removed last month:https://web.archive.org/web/20240000000000*/https://bioconductor.org/biocLite.R
Steffen Neumann (07:09:59) (in thread): > Was there an announcement of the biocLite.R removal ? It was the right thing to do, but I only found out through the 404:slightly_smiling_face:
Chris (09:16:56): > @Chris has joined the channel
Lluís Revilla (11:06:39) (in thread): > I thought it was removed several years ago. When BiocManager was announced I think that biocLite was announced as deprecated or directly removed (after a study about how unsafe that was due to typos from users).
Lulevere Beqiri (12:21:39): > @Lulevere Beqiri has joined the channel
2024-11-06
Mike Smith (03:33:19) (in thread): > It was deprecated, but remained available for those who wanted/needed to use older version of R/BioC. There’s still instructions on how to use it in the “Legacy and Older R Versions” section ofhttps://www.bioconductor.org/install/
Lluís Revilla (03:43:55) (in thread): > Wow! More than 6 years ago deprecated and it was still being maintained!!
Mike Smith (03:49:35) (in thread): > My interpretation was more “not being removed” than “maintained”, but I never actually checked that.
Ethan (13:17:37): > @Ethan has joined the channel
Kristian Ullrich (13:49:23): > Hi, I have a general question and might have missed the reason. In the latest Bioc-release 3.20, for all packages, the macOS Binary (arm64) version is still behind the version of macOS Binary (x86_64) and Windows Binary (x86_64). Can someone please explain? Thank you in anticipation
Andres Wokaty (15:08:30) (in thread): > There hasn’t been an announcement, but we’ve been having an issue with the machine so it has been removed from daily building.
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Ellis Patrick (21:39:00): > If anyone wants to eavesdrop or participate in BioCAsia, you can join via this link (now:slightly_smiling_face:)https://uni-sydney.zoom.us/j/87583095352
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2024-11-07
Kristian Ullrich (00:26:40) (in thread): > OK, thank you for the information
Angelique Trusler (01:21:16): > The Carpentries seeks up to six individuals to serve on our Board of Directors for a 3-year term beginning February 2025. Learn more andnominate yourself . I’m happy to answer questions as well. Thank you all for continuing to invest in our organisation! - Attachment (carpentries.org): The Carpentries > The Carpentries is a fiscally sponsored project of Community Initiatives, a registered 501(c)3 non-profit organisation based in California, USA. We are a global community teaching foundational computational and data science skills to researchers in academia, industry and government.
Cecilia M (07:12:32): > @Cecilia M has joined the channel
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2024-11-08
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Launlab (07:33:29): > Hi! Has anyone analyzed data quality (flowAI, flowcut, PeaQC) fcs files generated from samples that were processed with Euroflow protocols?
David Rach (09:22:49) (in thread): > I have used all three and tinkered with how they were different in context of my panel/experiments, but haven’t quantified extensively past that.
Launlab (23:43:26) (in thread): > Thank you. Ihadn’t noticed that my question was incomplete. It was about analysis of FSC files derived from Euroflow protocols.
2024-11-10
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2024-11-11
Josh Steier (12:24:29): > @Josh Steier has joined the channel
Josh Steier (12:27:05): > Hi everyone, > I have a background in computational biology(MS applied math and stats degree from Stony Brook University), and a strong background in machine learning, where I currently work as a machine learning engineer. > I’ve been working in machine learning for roughly 3-4 years, including my educational background, and programming in Python since I was younger. > I’m eager to contribute to Bioconductor and don’t know where to start, can someone help me with that? > Thank you!
Lori Shepherd (12:38:35) (in thread): > welcome! You might check out the#biocpythonand#machine-learningslack channels:slightly_smiling_face:
Josh Steier (14:18:19) (in thread): > Thank you!!
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2024-11-14
Svetlana Ugarcina Perovic (02:38:07) (in thread): > @Kasper D. Hansengreat sharing, thanks! I will add all to my github learning diary.
Svetlana Ugarcina Perovic (03:49:36) (in thread): > Added, thanks
Maria Doyle (05:57:04) (in thread): > Great suggestions! There’s also a new preprint from the Bioconductor Training group,Learning and teaching biological data science in the Bioconductor community , with a table of resources that might be handy:Preprint link . You can find the same table on our training site:Bioconductor resources . For more, the#education-and-trainingchannel has updates and discussions. - Attachment (arXiv.org): Learning and teaching biological data science in the Bioconductor community > Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and best practices available within the Bioconductor project - an open-source software community focused on omics data analysis. This guide serves as a valuable reference for both learners and educators in the field.
Louis Le Nézet (08:07:05): > Hi, > I’ve performed some GWAS using plink on a binary traits (affected vs unaffected) on 5 populations. > I would like now to go a bit deeper on the analysis of the lead loci and would like to know if there is a dedicated package to do so. > Do you have any suggestions ? > I was thinking oftopRorgeneHapR. As I’m working in dogs a library working with any species out of the box would be nice.
Lillian Dillard (10:49:51): > @Lillian Dillard has joined the channel
2024-11-15
Chioma Onyido (03:11:13) (in thread): > Thank you for sharing,@Svetlana Ugarcina Perovic:cherry_blossom:
Monthly general reminder (06:00:02): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush: - Attachment (bioconductor.org): Bioconductor - Code of Conduct Policy > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
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2024-11-16
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2024-11-17
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2024-11-18
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2024-11-19
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2024-11-20
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Y. Schumann (04:03:37): > Dear all, > > I am maintainer and developer of the BERT Bioconductor package. I have recently changed my affiliation to another institution and would like to continue to maintain my package from there. What do I need to transfer (e.g., bioc-devel mailing list, SSH certificates for git etc.) to make this work? Is there a tutorial for this? > > Best regards > Yannis > > PS: I am quite new to Bioconductor and hope this is the correct forum to ask.
Vince Carey (06:04:24): > @Lori Shepherd^^
Lori Shepherd (07:16:39) (in thread): > We don’t have a tutorial but that is a great idea! I can make one up. Places it will likely have to change > 1. bioc-devel mailing list (new sign up with new email fine if there is not an option to update) > 2. support site (if you do not have access to the old one to change yourself we can assist) > 3. BiocCredentials account used for managing package access (again if you do not have access we can assist if neceesary) > 4. package DESCRIPTION (you should do this yourself with a valid version bump)
Lori Shepherd (07:19:01) (in thread): > Once the package description is updated it will update on the package landing pages on the website and we will use that for any communication from the core team (just make sure to do the version bump with it).
Emanuele Pitino (10:30:07): > @Emanuele Pitino has joined the channel
Y. Schumann (10:45:15) (in thread): > @Lori ShepherdThanks a lot for the instructions! I have followed them closely and think that I managed to solve all problems. I have pushed the updated package DESCRIPTION with a version bump to bioconductor/devel. > > Is there any way to check that everything is now working properly (especially the CI is still passing with the modified email address)? > > Again, thank you so much for your help!:slightly_smiling_face:
Lori Shepherd (10:46:35) (in thread): > if you can log into BiocCredentials that is enough for that..same for the support site… but I can check registration on bioc-devel if you share the new email you are using
Y. Schumann (10:51:22) (in thread): > Ah, that would be great, thanks a lot! I will send the email in a direct message to you.
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2024-11-21
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Meg Urisko (17:35:41): > :wave:Hi! I’m Meg, a user researcher at the Chan Zuckerberg Initiative:wave:I am running a survey to understand how folks usethe CZ CELLxGENE Discover Census . We want to learn more about what data you’re interested in and how you download it.:arrow_right:We would appreciate it if you could take our survey :link::arrow_left::point_up_2:It should take about 10 minutes to complete, and we can offer you $10 Amazon eGift card as a thank-you for filling it out. We’d love to hear from as many Census users as possible, so please feel free to share this link with anyone you know who is using the Census:gratitude-thank-you:
Maria Doyle (17:50:22) (in thread): > Thanks for sharing this, Meg. Looking forward to the findings!
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2024-11-22
Maria Doyle (04:08:28) (in thread): > :bell:Just a quick reminder: the GBCC2025 Logo Contest is still open! Submit your design byDecember 8 submission form .
Maria Doyle (04:35:14) (in thread): > Hi Meg, given the specific focus of your survey on single-cell tech, you might consider posting it in the#singlecell-querieschannel too for visibility, especially if the general channel gets a bit busy.
2024-11-23
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2024-11-24
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2024-11-25
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rohitsatyam102 (06:48:27): > Hi everyone. I have RNASeq data for a gene that was Knocked out at multiple time points. For every time point we have control and KO samples (3 reps each). Any suggestion how to perform GSVA on such dataset where everytime-point has it’s own control sample? We want to see genes that were switched on/off during the different time point.
Robert Castelo (10:45:21) (in thread): > Hi, GSVA serves the purpose of analyzing the data using gene sets. Why do you want to use GSVA if you want to see genes (not gene sets) that were switched on/off during different time points?
rohitsatyam102 (12:50:18) (in thread): > I am sorry, I meant genesets. It must have been a typo.
rohitsatyam102 (12:51:15) (in thread): > I have custom genesets and I wish to see how they vary across different timepoints
Robert Castelo (12:57:50) (in thread): > Ah ok, 3+3=6 samples are too few for the GSVA algorithm to reliably estimate an expression statistic, but you may try with the ssGSEA algorithm. Please consult the help page ofssgseaParam()to learn how to use it.
rohitsatyam102 (13:00:37) (in thread): > Thanks a lot. I will shift my focus on ssgsea
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2024-11-26
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Steffen Neumann (10:00:23): > Hi@Alex Mahmoud, I saw that you put quite some effort into the bioconductor docker images
Steffen Neumann (10:00:51) (in thread): > I am looking for a version of the bioconductor_docker which has nvidia/cuda stuff enabled.
Steffen Neumann (10:05:50) (in thread): > Would thehttps://hub.docker.com/r/bioconductor/ml be a drop-in replacement forbioconudtcor_docker? I.e., it has everything, but is based on therocker/mlinstead ofhttps://github.com/Bioconductor/bioconductor_docker/blob/388f24b7d92cc15068bf95a0424984148bffbc29/Dockerfile#L2 rocker/rstudio? > I also saw that it has onlydevelavailable, onRELEASE_X_Y. So that I’d need to build myself inhttps://github.com/Bioconductor/bioconductor_docker/blob/388f24b7d92cc15068bf95a0424984148bffbc29/Dockerfile#L19 - Attachment (hub.docker.com): Attachment
Alex Mahmoud (10:38:27) (in thread): > We only started buildingmlflavor this devel cycle, so release versions for it won’t be available. However,bioconductor/ml-verse:3.20exists for the latest release, which is roughly themlimage + tidyverse packages. Fordevelyou have options ofcuda(just R) orml(RStudio)
Ben Valderrama (11:20:56): > @Ben Valderrama has joined the channel
Steffen Neumann (16:44:00) (in thread): > May I ask a question about installation ? I have our rstudio container built on top ofbioconductor_docker, where tensorflow installation works, and therocker/mlwhere the same does not: > > docker run --rm -it rstudio-ipb:RELEASE_3_19 R -e 'remotes::install_github("rstudio/tensorflow", upgrade="never"); library(tensorflow); install.packages("keras"); library(keras); install_keras(); model.sla <- keras_model_sequential(input_shape = c(NULL, 12906, 1))' > > docker run --rm -it rocker/ml R -e 'remotes::install_github("rstudio/tensorflow", upgrade="never"); library(tensorflow); install.packages("keras"); library(keras); install_keras(); model.sla <- keras_model_sequential(input_shape = c(NULL, 12906, 1))' > > In the second case withrocker/mlthe R/tensorflow does not find the python venv with the python/tensorflow. > > => Ideas ?!
Alex Mahmoud (16:50:18) (in thread): > Off the top of my head, I think our 3.19 container is ubuntu 22 while rocker/ml might be ubuntu 24, which is what our 3.20 containers are iirc. I assume you see the same issue if you build your container on top ofbioconductor/ml-verse:3.20instead?
Steffen Neumann (16:50:50) (in thread): > mom, trying as we speak …
Steffen Neumann (17:08:01) (in thread): > Hm, different error. I am trying in parallel bioc:ml:devel and bioc/ml-verse:3.20, same issue. > Installation of python stuff fails in the first place due to unmet dependencies, as no tf-2.15.* is available: > > ... > Using virtual environment 'r-tensorflow' ... > + /root/.virtualenvs/r-tensorflow/bin/python -m pip install --upgrade --no-user 'numpy<2' 'tensorflow==2.15.*' tensorflow-hub tensorflow-datasets scipy requests Pillow h5py pandas pydot > Collecting numpy<2 > Downloading numpy-1.26.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) > ERROR: Ignored the following versions that require a different python version: 1.21.2 Requires-Python >=3.7,<3.11; 1.21.3 Requires-Python >=3.7,<3.11; 1.21.4 Requires-Python >=3.7,<3.11; 1.21.5 Requires-Python >=3.7,<3.11; 1.21.6 Requires-Python >=3.7,<3.11 > ERROR: Could not find a version that satisfies the requirement tensorflow==2.15.* (from versions: 2.16.0rc0, 2.16.1, 2.16.2, 2.17.0rc0, 2.17.0rc1, 2.17.0, 2.17.1, 2.18.0rc0, 2.18.0rc1, 2.18.0rc2, 2.18.0) > ERROR: No matching distribution found for tensorflow==2.15.* >
Alex Mahmoud (17:10:11) (in thread): > That seems like a python version mismatch issue. Somewhere in the stack there are hardcoded versions that only work for older python. Or at least that is my naive interpretation
Steffen Neumann (17:11:22) (in thread): > rocker/mlis indeed 22.04, and has python 3.10.12 > So for that I’ll contact the rocker guys. Thanks for listening. I’ll keep you posted
Steffen Neumann (18:18:33) (in thread): > https://github.com/rocker-org/rocker-versioned2/issues/880 good night for now. - Attachment: #880 rocker/ml:latest fails to install tensorflow due to not finding its own venv > Container image name > > rocker/ml:latest > > Container image digest > > rocker/ml@sha256:327295f35a097a7ee2fec46804e0a285057c9918df1e4e12470e915e29e7de40 > > What operating system are you seeing the problem on? > > Linux > > System information > > Docker version 24.0.7-ce, build 311b9ff0aa93openSUSE VERSION = 15.5 > > Bug description > > Hi, I am installing keras/tensorflow in rocker/ml. Installation runs fine,/root/.virtualenvs/r-tensorflow and python can import tensorflow, and even shows some GPUs.library(tensorflow), because ModuleNotFoundError: No module named 'tensorflow'. > > On an older rocker/rstudio based container with R-4.4.1 I get > > > R version 4.4.1 (2024-06-14) -- "Race for Your Life" > ... > > library(tensorflow) > > reticulate::py_config() > python: /root/.virtualenvs/r-tensorflow/bin/python > ... > tensorflow: /root/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflo > NOTE: Python version was forced by import("tensorflow") > > > > while the non-working rocker/ml also installed into /root/.virtualenvs/r-tensorflow > > > Virtual environment 'r-tensorflow' successfully created. > Using virtual environment 'r-tensorflow' ... > + /root/.virtualenvs/r-tensorflow/bin/python -m pip install --upgrade --no-user 'numpy<2' 'tensorflow[and-cuda]==2.15.*' tensorflow-hub tensorflow-datasets scipy requests Pillow h5py pandas pydot > ... > Successfully installed MarkupSafe-3.0.2 Pillow-11.0.0 absl-py-2.1.0 array-record-0.5.1 astunparse-1.6.3 cachetools-5.5.0 certifi-2024.8.30 charset-normalizer-3.4.0 click-8.1.7 dm-tree-0.1.8 docstring-parser-0.16 etils-1.11.0 flatbuffers-24.3.25 fsspec-2024.10.0 gast-0.6.0 google-auth-2.36.0 google-auth-oauthlib-1.2.1 google-pasta-0.2.0 grpcio-1.68.1 h5py-3.12.1 idna-3.10 immutabledict-4.2.1 importlib_resources-6.4.5 keras-2.15.0 libclang-18.1.1 markdown-3.7 ml-dtypes-0.3.2 numpy-1.26.4 nvidia-cublas-cu12-12.2.5.6 nvidia-cuda-cupti-cu12-12.2.142 nvidia-cuda-nvcc-cu12-12.2.140 nvidia-cuda-nvrtc-cu12-12.2.140 nvidia-cuda-runtime-cu12-12.2.140 nvidia-cudnn-cu12-8.9.4.25 nvidia-cufft-cu12-11.0.8.103 nvidia-curand-cu12-10.3.3.141 nvidia-cusolver-cu12-11.5.2.141 nvidia-cusparse-cu12-12.1.2.141 nvidia-nccl-cu12-2.16.5 nvidia-nvjitlink-cu12-12.2.140 oauthlib-3.2.2 opt-einsum-3.4.0 packaging-24.2 pandas-2.2.3 promise-2.3 protobuf-3.20.3 psutil-6.1.0 pyarrow-18.1.0 pyasn1-0.6.1 pyasn1-modules-0.4.1 pydot-3.0.3 pyparsing-3.2.0 python-dateutil-2.9.0.post0 pytz-2024.2 requests-2.32.3 requests-oauthlib-2.0.0 rsa-4.9 scipy-1.14.1 simple-parsing-0.1.6 six-1.17.0 tensorboard-2.15.2 tensorboard-data-server-0.7.2 tensorflow-2.15.1 tensorflow-datasets-4.9.7 tensorflow-estimator-2.15.0 tensorflow-hub-0.16.1 tensorflow-io-gcs-filesystem-0.37.1 tensorflow-metadata-1.16.1 termcolor-2.5.0 tf-keras-2.15.1 toml-0.10.2 tqdm-4.67.1 typing-extensions-4.12.2 tzdata-2024.2 urllib3-2.2.3 werkzeug-3.1.3 wrapt-1.14.1 zipp-3.21.0 > creating symlinks: > - '/root/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/libcublasLt.so.12' -> '../nvidia/cublas/lib/libcublasLt.so.12' > - '/root/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/libcublas.so.12' -> '../nvidia/cublas/lib/libcublas.so.12' > ... > Installation complete. > > > > but a different python venv /opt/venv/ is used when I then want to load the library: > > > R version 4.4.1 (2024-06-14) -- "Race for Your Life" > ... > > library(tensorflow) > > reticulate::py_config() > python: /opt/venv/bin/python > libpython: /usr/lib/python3.10/config-3.10-x86_64-linux-gnu/libpython3.10.so > pythonhome: /opt/venv:/opt/venv > version: 3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0] > numpy: [NOT FOUND] > tensorflow: [NOT FOUND] > > NOTE: Python version was forced by VIRTUAL_ENV > > > > => How to inform reticulate/tensorflow to use the correct venv ?reticulate from 1.37 -> 1.40 which is the one in the working installation, same error.How to reproduce this bug? > > docker run –rm -it rocker/ml R -e ‘remotes::install_github(“rstudio/tensorflow”, upgrade=“never”); library(tensorflow); install.packages(“keras”); library(keras); install_keras(); model.sla <- keras_model_sequential(input_shape = c(NULL, 12906, 1))’ > > Full build log: > > ``` > docker run –rm -it rocker/ml R -e ‘remotes::install_github(“rstudio/tensorflow”, upgrade=“never”); library(tensorflow); install.packages(“keras”); library(keras); install_keras(); model.sla <- keras_model_sequential(input_shape = c(NULL, 12906, 1))’ > > ========== > == CUDA == > ========== > > CUDA Version 11.8.0 > > Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved. > > This container image and its contents are governed by the NVIDIA Deep Learning Container License. > By pulling and using the container, you accept the terms and conditions of this license: > https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license > > A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience. > > WARNING: The NVIDIA Driver was not detected. GPU functionality will not be available. > Use the NVIDIA Container Toolkit to start this container with GPU support; see > https://docs.nvidia.com/datacenter/cloud-native/ . > > > R version 4.4.1 (2024-06-14) – “Race for Your Life” > Copyright (C) 2024 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type ‘license()’ or ‘licence()’ for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type ‘contributors()’ for more information and > ‘citation()’ on how to cite R or R packages in publications. > > Type ‘demo()’ for some demos, ‘help()’ for on-line help, or > ‘help.start()’ for an HTML browser interface to help. > Type ‘q()’ to quit R. > > > remotes::install_github(“rstudio/tensorflow”, upgrade=“never”); library(tensorflow); install.packages(“keras”); library(keras); install_keras(); model.sla <- keras_model_sequential(input_shape = c(NULL, 12906, 1)) > Downloading GitHub repo rstudio/tensorflow@HEAD > Installing 3 packages: config, tfautograph, tfruns > Installing packages into ‘/usr/local/lib/R/site-library’ > (as ‘lib’ is unspecified) > trying URL ‘https://p3m.dev/cran/linux ’ > Content type ‘binary/octet-stream’ length 102935 bytes (100 KB) > ================================================== > downloaded 100 KB > > trying URL ‘https://p3m.dev/cran/linux ’ > Content type ‘binary/octet-stream’ length 162247 bytes (158 KB) > ================================================== > downloaded 158 KB > > trying URL ‘https://p3m.dev/cran/linux ’ > Content type ‘binary/octet-stream’ length 1486076 bytes (1.4 MB) > ================================================== > downloaded 1.4 MB > > * installing binary package ‘config’ … > * DONE (config) > * installing binary package ‘tfautograph’ … > * DONE (tfautograph) > * installing binary package ‘tfruns’ … > * DONE (tfruns) > > The downloaded source packages are in > ‘/tmp/RtmpFTTYLw/downloaded_packages’ > ── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── > :heavy_check_mark: checking for file ‘/tmp/RtmpFTTYLw/remotes12c84dcc0/rstudio-tensorflow-e26a203/DESCRIPTION’ … > ─ preparing ‘tensorflow’: > :heavy_check_mark: checking DESCRIPTION meta-information … > ─ checking for LF line-endings in source and make files and shell scripts > ─ checking for empty or unneeded directories > ─ building ‘tensorflow_2.16.0.9000.tar.gz’ >
2024-12-05
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2024-12-06
Steffen Neumann (05:31:18) (in thread): > Side-comment: I suggest keeping the tag consistent between flavours, so move fromml-verse:3.20toml-verse:REEASE_3_20
Alex Mahmoud (09:46:45) (in thread): > Both tags exist and point to the same container:slightly_smiling_face:We’ve been using the newx.yyformat as well (for the past ~2 years) to make it easier to type. Having to writeRELEASE_was a personal pet peeve, but it was kept (and will remain) for backwards compatibility
Steffen Neumann (09:47:48) (in thread): > Ic, so the other way around :-) will adapt.
Maria Doyle (10:53:37) (in thread): > :art:Final Reminder: The GBCC2025 Logo Contest closes in2 days Deadline: Prizes: submission form .
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2024-12-08
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Dinesh Sharma (23:49:48): > Hey hi everyone, > To introduce myself I am Dinesh Sharma (final year PhD Student at IIT Delhi, India). My research area is focused onon computational genomics and > bioinformatics, particularly in understanding the physicochemical properties of DNA. I am developing a universal genome annotation software pipeline using machine learning and deep learning techniques to efficiently identify and characterize genome elements such as promoters and exon-intron boundaries. Additionally, I am interested in applying these methods to better understand genomic diseases and related ailments. > > I am looking for some postdoc opportunities (preferably USA) to carry forward my research in Genomics and Bioinformatics. I will be grateful for any sort of leads and help. > > Thank you and sorry for any inconvenience. >
2024-12-13
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Maria Doyle (06:55:35) (in thread): > Hi Dinesh, thanks for sharing your research and goals! It’s always great to hear from members of the community. For better visibility and to keep things tidy, posts like this might fit better in our#introductionschannel—feel free to cross-post there! Also, be sure to keep an eye on the#jobschannel for opportunities.
Dinesh Sharma (06:56:37) (in thread): > Thank you:relaxed:
Tehniyat zahra (07:43:31): > Hi everyone, > I’m an undergraduate student studying Bioinformatics, and I’m interested in publishing my research paper. I would really appreciate any guidance on how to get started with the process, from choosing the right journal to preparing and submitting the manuscript.
Maria Doyle (08:32:46) (in thread): > Hi Tehniyat, this general channel is primarily for questions and discussions about Bioconductor and its tools. For broader topics like publishing, you might find more relevant guidance in#introductionsor through resources at your university. Best of luck with your research and publication!
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Monthly general reminder (06:00:03): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush: - Attachment (bioconductor.org): Bioconductor - Code of Conduct Policy > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
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Stephanie Hicks (12:49:34) (in thread): > @stefano mangiolathank you! I wanted to know if you could comment a bit more on the CTP guidelines. Is this being submitted somewhere or what kind of feedback are you looking for? Thanks!
2025-01-04
stefano mangiola (18:50:02) (in thread): > Hello@Stephanie Hicks! Sure, I made this commentary, reflecting on our experience with tidyomics open collaborationhttps://docs.google.com/document/d/1oSGcYLG9E4BWuRxzVFW8sNKJdI09n9tsRzQABNbL-IU/edit?usp=sharing Now under review at CACM. > > The intention was to do a campaign/initiative of open review with them, but turned out to be difficult. Then I thought that an aspect of practical utility of this effort would be guidelines for the community (putting aside my editorial piece) to how to implement from the ground up a open collaboration initiative with the crowd-to-paper model for any project (computational in nature for now), taking as a foundation our successful implementation for tidyomics. > > The goal is to make these guidelines robust and applicable to computation-oriented communities, such as biology, physics, information science, ecology, phycology, … > > So I invite feedback at all levels, from very fundamental (e.g. some principles are not valid for some, or I am missing some important sections), to very detailed (e.g. typo).
2025-01-05
Stephanie Hicks (06:35:18) (in thread): > ah, thanks! That’s helpful
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stefano mangiola (19:57:40) (in thread): > Thanks@Stephanie Hicksfor your contribution! You are always very generous and proactive! > > If anyone wants to add to some of the discussion points that@Stephanie Hicksstarted on the document, this is the right time! :)
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Maria Doyle (06:07:17): > :writing_hand:New Bioconductor blog post on the SpatialData hackathon and workshop held in November in Switzerland, organised by scverse with Bioconductor participation. Check it out here:https://blog.bioconductor.org/posts/2025-01-08-bioc-in-scverse-workshop/ Thanks,@Artür Manukyan! - Attachment (Bioconductor community blog): 2024 SpatialData Workshop – Bioconductor community blog > R/Bioconductor developers participating in the 1st scverse SpatialData Workshop
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2025-01-15
Monthly general reminder (06:00:04): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush: - Attachment (bioconductor.org): Bioconductor - Code of Conduct Policy > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
2025-01-16
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2025-01-27
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Ouma Ronald (06:24:43): > Hi @team . I am seeking for help about this error message that am getting while opening a project using RStudio. I have tried this on several projects and its the same issue. I have tried to cross check if the issue was being brought up by firewals or even R/Rw permissions but it seems to be another problem . I have been working on the project using VS Code but its a challenging environment there while working with R projects. Could anyone be knowing how to get rid of this error message such that i am able to open the project in RStudio.@Levi Waldron,@Marcel Ramos Pérez,@C . Mirzayi (please do not tag this account). Thank you - File (Matroska Video): vokoscreenNG-2025-01-27_10-41-34.mkv
Taofeecoh Adesanu (06:55:02) (in thread): > Hi@Ouma Ronald, have you tried opening the project directly from its directory on your desktop? > > Also for R projects, there should be a file “.rproj”, if you open that, all the files created in the folder will be loaded in R studio.
Ouma Ronald (07:28:41) (in thread): > thank you@Taofeecoh Adesanu,The project is written in Rm. I have tried opening the project directly from its directory but its the same error message and keeps exiting the it does in the video. The .Rproj can’t be located anywhere in the project
Liz Ing-Simmons (08:09:24) (in thread): > I don’t think this is the best forum for this question, as it’s not directly related to Bioconductor. I’d recommend trying the Posit forum:https://forum.posit.co/ (makers of RStudio) > > Having said that, the message in your console suggests your RStudio installation is having trouble finding your R installation, even outside of the project. If you haven’t already, I would definitely try reinstalling both R and RStudio. - Attachment (forum.posit.co): Posit Community > A community for all things Posit
Vince Carey (09:36:01): > Is there a representation of the DNA Methylation atlas suitable for use with Bioconductor?https://www.nature.com/articles/s41586-022-05580-6 - Attachment (Nature): A DNA methylation atlas of normal human cell types > Nature - We describe a human DNA methylome atlas based on deep whole-genome bisulfite sequencing, allowing fragment-level analysis of cell-type-specific markers and providing an essential resource…
Vince Carey (09:36:33): > Is there a package, database, or API available that we should wrap?
Vince Carey (10:29:37): > Licensing may be unfavorable? “Your Research Use only”
Kasper D. Hansen (11:24:27): > This appears to be on GEO. To make this really accessible, someone would need to host it, I think.
Kasper D. Hansen (11:24:46): > The data seems pretty big; I am wondering how bad it is when you reduce it.
Kasper D. Hansen (11:25:19): > This is a good example of what I think we should support in ExperimentHub 2.0: the ability to have indexed data which is hosted “elsewhere”.
Kasper D. Hansen (11:25:38): > If you want a lot of methylation data we also have recount-methylation, but that is only arrays
Kasper D. Hansen (11:26:10) (in thread): > Where is this? I couldn’t see this for example in the GEO records, but I also looked very quickly
Vince Carey (11:27:10) (in thread): > Maybe irrelevant … I was looking athttps://github.com/nloyfer/meth_atlas/blob/master/LICENSE.md
Lori Shepherd (11:27:22) (in thread): > if the data has a url to download it already is supported in the current hub. We want to encourage listing in the hub but hosting elsewhere.
Kasper D. Hansen (11:52:13) (in thread): > yeah, that seems to be their deconvolution software
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2025-01-28
Susan (01:19:53): > @Susan has joined the channel
Maria Doyle (09:19:39): > :earth_africa:Bioconductor Course, Kenya 2025 March 24–28, 2025 Apply now :information_source:More details We’ve also shared this announcement onLinkedIn ,Mastodon andBlueSky . Feel free to check them out and share if you’d like to help highlight this opportunity!:star2:
Nazgul (11:14:47): > @Nazgul has joined the channel
Devon Kohler (12:48:35): > The May Institute on Computation and Statistics for Mass Spectrometry and Proteomics, taking place on April 28 – May 11, 2025 on the campus of Northeastern University in Boston MA, is now accepting applications. The application deadline is March 5, 2025. > > Instructors are leading experts, who contributed numerous experimental and computational methods and software. The target audiences are both beginners and experienced scientists, with both experimental and computational expertise. > > New this year is a “Future developers meeting”, a 2-day program that brings together developers (and aspiring developers) of computational and statistical tools for mass spectrometry, proteomics and metabolomics. We invite you to submit an abstract and present your research. > > Participants can select a subset of the following programs: > > * April 28 - April 30, Quantitative proteomics with Skyline. Lead instructors: Susan Abbatiello, Brendan MacLean and Lindsay Pino > * April 30 – May 2, Beginners R and beginners statistics. Lead instructor: Ryan Benz > * April 30 – May 2, Intermediate R, data visualization and statistics. Lead instructor: Kylie Bemis > * April 30 – May 2, Intermediate Python, data visualization and statistics. Lead instructors: Ben Gyori, Arzu Tuğçe Güler, and Jeremy Muhlich > * May 5 – May 7, Statistics for quantitative mass spectrometry: methods and case studies. Lead instructors: Olga Vitek and Devon Kohler > * May 7 – May 9, Interpretation of proteomic experiments in the context of biomolecular networks with INDRA. Lead instructor: Ben Gyori > * May 9, Analysis of mass spectrometry images with Cardinal. Lead instructor: Kylie Bemis > * May 10 - May 11, Future Developers Meeting > > A limited number of registration fee wavers will be available for students and postdocs affiliated with academic or nonprofit institutions in the US. > > Please share this widely. More information is athttps://computationalproteomics.khoury.northeastern.edu/
Laina Mercer (16:29:15): > @Laina Mercer has joined the channel
2025-01-29
Amin Zadenoori (05:23:25): > @Amin Zadenoori has joined the channel
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2025-01-30
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Maria Doyle (14:22:39): > :tada:Announcing the GBCC2025 Logo Design Winner! GBCC2025-winner_Marie-Jossé.png - File (PNG): GBCC2025-runner-up_Charlie-Bayne
2025-01-31
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2025-02-02
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2025-02-03
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2025-02-05
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2025-02-06
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2025-02-07
Louis Le Nézet (04:38:32): > Hi everyone, > I’m currently writing a paper to present “Pedixplorer” package. > I’m planning to submit to Bioinformatics as an application note. > I was wondering if any of you would be interested to be listed as potential reviewers ? > The package is about a new Pedigree S4 class, filtering and improved visualisation of large pedigree. > I’ve also added a nice shiny application to interactively draw them. > Thanks for your help !
Taha Ahmad (14:52:18): > @Taha Ahmad has joined the channel
2025-02-09
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2025-02-10
Maria Doyle (07:39:37): > :art:**** Announcing the EuroBioC2025 Sticker Design Contest!****We invite you to design the official sticker forEuroBioC2025 How to Enter: this form by March 10, 2025.Prize: P.S. Abstract submissions for EuroBioC2025 will be opening soon—stay tuned for details!
Kevin (20:34:43): > @Kevin has joined the channel
2025-02-11
Juliana Kentomahun Mautin (07:42:20): > @Juliana Kentomahun Mautin has joined the channel
Carlo Pecoraro (08:21:32): > Online Course: R/Bioconductor for Mass Spectrometry & Proteomics! March 17-19 hands-on course mass spectrometry (MS) data Basic R knowledge required Course details & registration: Course Website - Attachment (physalia-courses): R/Bioconductor for Mass Spectrometry and Proteomics > Dates 17-19 March 2025 To foster international participation, this course will be held online
Maria Doyle (17:11:09): > :mega:GBCC2025 Abstracts & Registration Now Open! Abstract Deadline: Register/Submit gbcc2025.org
2025-02-12
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2025-02-13
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2025-02-14
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2025-02-15
Monthly general reminder (06:00:03): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush: - Attachment (bioconductor.org): Bioconductor - Code of Conduct Policy > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
2025-02-16
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2025-02-17
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2025-02-19
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2025-02-20
Maria Doyle (04:10:44): > :mega:**** EuroBioC2025: Abstract Submissions Open! ****Join us in Barcelona, Spain:es:, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster.:spiral_calendar_pad:Abstract Deadline: Register/Submit https://eurobioc2025.bioconductor.org/
Georgia Whitton (06:45:01): > @Georgia Whitton has joined the channel
Steffen Neumann (06:57:07): > Hi, I really like the idea of AnnotationHub and ExperimentHub, but in the past I was super annoyed that I couldn’t find any public interface/frontend to send URLs to people who might not be R wizards.
Steffen Neumann (06:57:57) (in thread): > Today I discoveredhttps://bioconductor.org/packages/devel/bioc/vignettes/AnnotationHub/inst/doc/AnnotationHub.html#interactive-retrieval-of[…]urces-with-biochubsshiny > > BiocHubsShiny::BiocHubsShiny() > > => Is there a public instance of that somewhere ?
Steffen Neumann (06:59:17) (in thread): > Ah, found it:https://shiny.sph.cuny.edu/BiocHubsShiny/
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2025-02-21
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2025-02-22
Levi Waldron (02:19:48) (in thread): > @Marcel Ramosyour app is being used!
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2025-02-25
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2025-02-28
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Maria Doyle (06:52:26): > :date:Hi everyone, just a heads-up that theuseR! 2025 submissions deadline is March 10th https://user2025.r-project.org/call
Maria Doyle (10:15:59): > :art:Reminder thatEuroBioC2025 Sticker Contest Deadline March 10th https://buff.ly/42JiCLN Abstracts are open for submission too!
2025-03-02
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2025-03-04
Maria Doyle (10:47:22): > :date:Thetidyomics **** group’s next meeting is on Wednesday, March 12th**at 4 PM NY / 9 PM London / 8 AM (Thursday) Melbourne. They will discuss improving the way they abstract and display SummarizedExperiment and get feedback on their recent package tidyprint. For more details and to join, please check@stefano mangiola’s message in#tidiness_in_biocchannelhere . All welcome!
Gabriela Santos (14:17:53): > @Gabriela Santos has joined the channel
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2025-03-05
Maria Doyle (09:59:57): > :memo:**** New Bioconductor Blog Post on CAB and its new co-chair**! > Stevie Pederson introduces themselves and shares insights about the Community Advisory Board (CAB). > Check it out here:https://blog.bioconductor.org/posts/2025-03-05-CAB/ Thanks@Stevie Pederson! - Attachment (Bioconductor community blog): Bioconductor Community Advisory Board – Bioconductor community blog > An introduction to the new Co-Chair
Lluís Revilla (10:31:40) (in thread): > :wave:Current CAB member. Feel free to ask anything about the CAB on#community-advisory-boardor here!
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Jennifer Velez (13:49:29) (in thread): > Why is there no one from Latin America?:sob:
Maria Doyle (14:05:36) (in thread): > Great question,@Jennifer Velez! There used to be a rep from Latin America, but no one volunteered from that region last year.:pensive:We did some outreach through Slack, LinkedIn, Mastodon, and our mailing list, but maybe we need to do more. This year, we’re also on Bluesky. > If anyone has ideas on how we can better reach out to potential volunteers in Latin America, please let us know. Or if you know someone who might be interested, it would be great if you could encourage them to volunteer in the annual call for new members around August.
Jennifer Velez (14:39:16) (in thread): > We have a great community, currently we have Hispanic Simposum and RSG initiatives. I will talk with chairs may be they unknown the proyect
Lori Shepherd (15:40:32): > Bioconductor 3.21 Release Schedule:https://bioconductor.org/developers/release-schedule/
Ritika Giri (16:33:00): > :loudspeaker:USRSE’25 is Calling for Participation USRSE’25 conference in:eagle:Philadelphia , 2025). > > Whether you’re a data scientist, bioinformatician, digital humanist, scientific programmer, software developer, or research software user - US-RSE is where code and research meet. If you write code for research or are curious about computational research careers , this is the event for you. It’s your chance to connect with peers, mentors, and experts in the growing research software community. > > This year’s theme: *** Code, Practices, and People*****:female-technologist::books::handshake:Submit your work via BoFs, workshops, short talks, or posters.:date:Key deadlines: Volunteer by April 1st! > Visit thewebsite for more details, check outlast year’s program , or emailusrse2025@easychair.org with questions. > Not a US-RSE member?Join for free & join our Slack community! - Attachment (USRSE’25): Participate > USRSE 2025 Conference
Lluís Revilla (17:05:59) (in thread): > It is not only a matter of volunteering: the serving committee needs to see which candidates are best suited for the existing openings. I don’t know who volunteered, but it could be that someone did but weren’t selected on the last round.
Lluís Revilla (17:06:06) (in thread): > But not being on the CAB doesn’t mean that people from Latin America doesn’t help/contribute to the project.
Stevie Pederson (20:12:21) (in thread): > Hi Jennifer. Thanks for speaking up & I’d noticed that as well. There were no nominees from the region last year and we’d love for that region be better represented. Going by some of the people I’ve met at conferences, there’s definitely some great work going on in Latin America (& South America too). We’d all be really delighted if someone with a knowledge or understanding of those regions were able to join so that’s really encouraging to hear you’ll reach out through your networks. Do keep us posted and stay in touch on here, either by DM or using the#community-advisory-boardchannel. The main qualifications for CAB membership are enthusiasm and a willingness to get involved so if you’re even considering it yourself, we’re always here for a chat too
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2025-03-06
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2025-03-07
Maria Doyle (14:24:11): > :mortar_board:GBCC2025 Training Topics:star2:The Galaxy and Bioconductor Community Conference (GBCC2025 ) is coming soon! We want to hear from you: > > - Topics you’re interested in learning about > - Interest in leading a session > > Fill out the formby Friday, March 21st https://forms.gle/i34Ag8SHMtBAmpPh7 Thanks!:pray: - Attachment (Google Docs): Expression of interest for GBCC2025 training topics > GBCC2025 is coming up soon and we’d like to hear from you! This year, we’re doing things a little differently with our joint conference between Galaxy and Bioconductor. There will be 10 training sessions, each lasting 1.5 hours. > > Please fill out this form to: > Indicate the topics you are interested in learning about at GBCC this year. > Express your interest in leading a training session (optional). > Note: This year, there are no abstract submissions for package demos or workshops, only talks and posters. If you want to lead a training session, please use this form. If you’re interested in giving a talk or presenting a poster, please submit through the conference abstract submission page. > Fill out this form by Friday, March 21st, so that we can create a training schedule that better serves all of us in the Galaxy and Bioconductor community. > > Thanks! > GBCC2025 Organizing Committee
2025-03-09
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2025-03-10
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2025-03-11
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2025-03-12
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2025-03-13
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2025-03-14
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2025-03-15
Monthly general reminder (07:00:04): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush: - Attachment (bioconductor.org): Bioconductor - Code of Conduct Policy > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
Vish Nair (21:29:15): > @Vish Nair has joined the channel
2025-03-16
RITU VERMA (10:14:23): > i am looking for opportunities related to beginner level bioinformatics any leads would be highly appreciated and helpful for me
Svetlana Ugarcina Perovic (11:26:14) (in thread): > Hi Rita, I see that you asked some time ago something similarhttps://community-bioc.slack.com/archives/C35G93GJH/p1731495278066419 What I would add is that most lab or project leaders would be happy to hear from you: write an emailwith a proposal of your contribution Attachment > i have post graduate degree in marine biotechnology ..can anyone tell or suggest me how should i transition myself from wetlab to dry lab
RITU VERMA (14:01:16) (in thread): > i did but no reply i am having basic knowledge (beginner level ) about bioinformatics
Svetlana Ugarcina Perovic (17:26:27) (in thread): > This list might help you to find an appropriate internship:https://www.geeksforgeeks.org/best-open-source-programs-for-students-to-participate/ Some projects within these programs do welcome beginners in bioinformatics. - Attachment (GeeksforGeeks): Best Open Source Programs For Students to Participate - GeeksforGeeks > A Computer Science portal for geeks. It contains well written, well thought and well explained computer science and programming articles, quizzes and practice/competitive programming/company interview Questions.
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2025-03-17
Angelique Trusler (03:29:06): > :loudspeaker:**** Help Us Improve Glosario – Share Your Feedback! ****:earth_africa:At The Carpentries, we’re working to make data and computing more accessible to everyone throughGlosario , our multilingual glossary of key terms. To improve its accessibility and usability, we needyour input! take our short survey **** (10 minutes or less!)****to share your experience and help us make Glosario even better. Whether you’re a frequent user, occasional contributor, or just interested in multilingual programming, we want to hear from you!:link:Click here **** to take the survey– open until 31 March (anywhere on Earth)! :bulb:Want to contribute beyond the survey? Join ourGlosario co-working session ** on 7 May @ 15:00 UTC**to help with translations, suggest new terms, or support development. > > Thank you for helping us build an open, inclusive, and accessible resource for the global community!:rocket:Read more here:https://carpentries.org/blog/2025/03/help-us-improve-glosario/ - Attachment (The Carpentries): Help us Improve Glosario: Share Your Feedback! > At The Carpentries, we are committed to building a more inclusive and accessible world for learners and researchers working with data and computing. One of our initiatives in this effort is Glosario, a multilingual glossary developed to help individuals understand key computing and data science terms in their preferred language. > To ensure Glosario meets the accessibility needs of our global community, we are surveying to gather feedback from current and potential users. Your insights will help us understand how to improve accessibility and enhance usability.
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2025-03-18
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2025-03-19
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2025-03-20
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2025-03-22
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2025-03-24
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2025-03-25
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Maria Doyle (09:31:17): > :hourglass_flowing_sand:Just a quick reminder ofapproaching deadlines for the Galaxy and Bioconductor Community Conference 2025 (GBCC2025) Early Bird Registration: March 31st Register Now . > * Abstract Submission April 1st Submit Abstract . > * Scholarships Available: April 1st Apply Here . > * Sponsorship Opportunities: Learn More . > We hope to see you at GBCC2025!
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2025-03-26
Angelique Trusler (02:29:49) (in thread): > Hey everyone! This is a quick reminder to take ourGlosario feedback survey 31 March (anywhere on Earth Survey link: https://docs.google.com/forms/d/e/1FAIpQLSfRad4PbscQ2USdvL73NQosDSyPb2nzVcFPKKRVNywKdTb58Q/viewform ] (Takes 10 minutes or less!) > > Thanks for helping us build an open, inclusive resource!:rocket:
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2025-03-27
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2025-03-28
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2025-03-29
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2025-03-30
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2025-03-31
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Maria Doyle (14:35:47): > :tada:Announcing the EuroBioC2025 Sticker Design Winner!:tada::trophy:Winner: LinkedIn post here . - Attachment (linkedin.com): #eurobioc2025 #bioconductor #bioinformatics #rstats #stickercontest | Bioconductor > :tada: Announcing the EuroBioC2025 Sticker Design Winner! :tada: > > :trophy: Winner: Chaima Hkimi > > :art: Chaima’s design draws on some of Barcelona’s most iconic landmarks… - File (PNG): EuroBioC2025 sticker_rev_CYMK.png
Vince Carey (14:56:46): > <!here>Sorry to interrupt but this is an important message for community-bioc. The Slack Pro support for this community has cost the Bioconductor Foundation $10,000.00 or more for each of the past few years. This cannot be sustained and we are planning to terminate the Pro plan some time in April. Slack free will remain available, but access to old messages will be lost. We are working on a plan to capture the historical public content and provide an archive for searching. Private channels and private DMs will become inaccessible once we terminate the Pro plan. If you would like to archive some private material used on the Pro plan, please do so. > > I have made limited inquiries towards establishing industry sponsorship, with no success. If you have thoughts about how to continue this service, through sponsorship or other means, please DM me.
Pariksheet Nanda (14:59:54) (in thread): > ~If we’re considering self-hosting~, I know the ImageJ people have a nice Zulip server that is similar to Slack but not proprietary and I think does the topic organizing better:https://imagej.net/discuss/chat#zulip - Attachment (ImageJ Wiki): Chat > The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants, including ImageJ2, Fiji, and others.
Pariksheet Nanda (15:01:30) (in thread): > Also has mobile and desktop apps:https://en.wikipedia.org/wiki/Zulip#Official_client_apps - Attachment: Zulip > Zulip is an open source chat and collaborative software created by Jeff Arnold, Waseem Daher, Jessica McKellar, and Tim Abbott in 2012. Today, it is one of the free and open source alternatives to Slack, with over 60,000 commits contributed by over 1000 people.
Laurent Gatto (15:19:59) (in thread): > I use Zulip for my lab (not self-hosted though), and I’m very happy with it..
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Moritz E. Beber (16:12:35) (in thread): > Slack is unsustainable for open communities. I can completely understand. I would strongly encourage you to move out the content while you can and move it somewhere else. Where depends on your ambition for the community. Is it a place to chat with occasional Q&A? Zulip has my vote, too. Do you mainly want a Q&A thendiscourse is a better fit. - Attachment (Discourse - Civilized Discussion): Discourse is the place to build civilized communities > Discourse is modern forum software for your community. Use it as a mailing list, discussion forum, long-form chat room, and more!
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Pariksheet Nanda (18:37:07) (in thread): > @Moritz E. BeberI also really like Discourse and wonder ifsupport.bioconductor.org is more similar to Discourse than Slack? My understanding is some people feel that a “chat” interface like this is less formal / high stakes than a forum or mailing list. Then again, Discourse could include separate Q&A like the support site as well as the various channels Slack has. I agree about making a backup of the Slack content though presumably someone with admin rights needs to do it (I as a member can only export the workspace analytics):https://slack.com/help/articles/201658943-Export-your-workspace-data - Attachment (Slack Help Center): Export your workspace data > With Slack, you can export data from your workspace or Enterprise Grid organization. Depending on your plan, you may have a few options for data exports: Free Pro Business+ Enterprise Grid …
2025-04-01
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Jenny Drnevich (11:31:27): > Update on GBCC2025, the joint conference between Galaxy & Biocluster held at Cold Spring Harbor: > 1. Abstract submission deadline for ~10 min TALKS is extended to April 8 https://gbcc2025.netlify.app/abstracts/submission_guidelines/ > 2. People interested in leading a ~1.5 hr TRAINING DEMO https://forms.gle/i34Ag8SHMtBAmpPh7 . This deadline is also in the process of being extended to April 8. > 3. Anyone who wants to see particular trainings should also fill out the above form, as this will help us decide what topics have the highest demand for trainings. - Attachment (Google Docs): Expression of interest for GBCC2025 training topics > GBCC2025 is coming up soon and we’d like to hear from you! This year, we’re doing things a little differently with our joint conference between Galaxy and Bioconductor. There will be 10 training sessions, each lasting 1.5 hours. > > Please fill out this form to: > Indicate the topics you are interested in learning about at GBCC this year. > Express your interest in leading a training session (optional). > Note: This year, there are no abstract submissions for package demos or workshops, only talks and posters. If you want to lead a training session, please use this form. If you’re interested in giving a talk or presenting a poster, please submit through the conference abstract submission page. > Fill out this form by Friday, April 11th, so that we can create a training schedule that better serves all of us in the Galaxy and Bioconductor community. > > Thank you for your input! > The GBCC2025 Organizing Committee
Janani Ravi (12:09:18): > Awesome,@Charlotte Soneson@Lori Shepherd@Marcel Ramos@Kevin Rue-Albrecht@Johannes Rainer@Hervé Pagès@Vince Carey!:raised_hands:Eleven quick tips for writing a Bioconductor package https://doi.org/10.1371/journal.pcbi.1012856 Soneson et al., PLoS Comp Bio. 2025 - File (PNG): image.png
Maria Doyle (14:23:08) (in thread): > @Alex Mahmoudhas been looking at Discourse as an alternative for our support site. Given the need to replace Slack Pro, it would be great if Discourse could also serve as our primary communication platform to consolidate the multiple tools Bioconductor currently uses. Discourse has a chat feature—does anyone have experience with it? > > If Discourse Chat meets our needs, we can streamline our communication and reduce costs. Otherwise, Zulip seems a strong alternative for real-time chat. Your feedback and experiences with these platforms would be greatly appreciated!
Pariksheet Nanda (15:21:53) (in thread): > @Maria DoyleWhoa! I would really like the idea of Discourse chat because one of the things I dislike about applications like Slack is their lack of web searchability. And it says here their chat feature can be quoted in topics (https://discourse.org/features ). I’m able to try out the chat feature fromhttps://try.discourse.org but you first have to login to be able to see the chat; after you login there is a chat bubble on the top-right and on the left-side bar there are “channels” that also appear like Slack. Not bad. - Attachment (Discourse - Civilized Discussion): Discourse features > Discover features your community will love. - Attachment (try.discourse.org): Discourse Demo > Demonstration sandbox for Discourse
2025-04-02
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Robert Castelo (09:48:29) (in thread): > Hi, I also use Zulip with my research group and my students (the cloud hosted version, not self-hosted) and I’m very happy with it. For my research group I did the transition from Slack to Zulip two years ago and I could export from Slack all the messages from non-private conversations and channels and import them into Zulip, preserving the whole history. Of course, the Bioconductor Slack is at another scale in the amount of message that one would have to move, but maybe it would work.
Pariksheet Nanda (11:59:20) (in thread): > @Robert Castelothat’s really good to know. It’s unclear how well the Slack history could be imported into the Discourse chat plugin. The Discourse chat plugin is more minimal than Zulip and moving to Zulip would presumably be a closer experience to Slack. To see how well the Discourse chat plugin works on mobile I tried the DiscourseHub app on Android, but from what I can tell all it does is add bookmarks to open in your mobile browser so DiscourseHub is not much of a mobile app at all?
Pariksheet Nanda (12:04:42) (in thread): > I just tried the Zulip app on mobile and like it better for chat. It’s also available on fdroid. Edit: Oooh, I like the combined feed on zulip.
Robert Castelo (12:15:44) (in thread): > I use the Zulip app on an android phone and works fine, as well as on macOS and Ubuntu, haven’t tried Windows. By the way, the info about transferring an entire workspace from Slack to Zulip is athttps://zulip.com/help/import-from-slack I haven’t read this page again in detail but two years ago, once I downloaded the Slack data, I had to send an email tosupport@zulip.com with a that data and a “Bot User OAuth Token” and in less than a week it was imported. By the way, this may interest@Vince Carey, since I’m using Zulip for a research group, I was eligible for having my Zulip organization as “sponsored for Zulip Standard”, you can find details about what that means athttps://zulip.com/for/research this was also arranged in the email exchange I had for the import. - Attachment (Zulip): Import from Slack | Zulip help center > You can import your current workspace into a Zulip organization. It’s a great way to preserve your workspace history when you migrate to Zulip, and to make the transition easy for the members of your organization. | The import will include your organization’s: | To import your Slack organization into Zulip, you will need to take the following steps, which are described in more detail below: | Slack’s data export service allows you to export all public channel messages, including older messages that may no longer be searchable under your Slack plan. - Attachment (Zulip): Zulip for researchers and academics > Make Zulip the communication hub for your research > group, department or scientific field. Organized team chat ideal for both > live and asynchronous conversations.
Laurent Gatto (12:19:29) (in thread): > I had the same experience as described by Robert, including benefitting the Zulip sponsoring.
Vince Carey (12:26:36) (in thread): > Thanks for all this input. We have slack, bioc-devel mailing list, and the biostars-basedsupport.bioconductor.org . Do you feel that zulip could be used to consolidate all those vehicles for project communication?
Laurent Gatto (12:33:42) (in thread): > Zulip is a great replacement for slack. I don’t think it should be used in addition to slack, as they cater essentially for the same type of communication.
Robert Castelo (12:39:59) (in thread): > As Laurent says, I also think that it’s a great replacement for Slack, probably also for the bioc-devel mailing list, because I’d say that since we have the#developers-forumSlack channel, the traffic on bioc-devel has reduced, but I’m less confident for the support mailing list, because like with Slack, it will not be searchable by Google, and this is a great feature to harness the knowledge base that the support site accumulates.
Robert Castelo (12:41:59) (in thread): > I also think that the traffic on the support site has reduced in favor of conversations through GitHub issues on public repos, which are also searchable by Google. I’d say that lately I’m answering more questions on GitHub issues about my packages than on the support site.
Laurent Gatto (12:44:39) (in thread): > I would keep bioc-devel - mailing lists have stood the test of time, and will most likely still be there by the time the next cool tech pops up and dies.
2025-04-04
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2025-04-07
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Maria Doyle (11:46:05): > :alarm_clock:Last Call for Abstract Submissions for GBCC2025!
Maria Doyle (12:36:47) (in thread): > I believe we do have that discount
Vince Carey (12:53:02) (in thread): > me too
Vince Carey (12:53:20) (in thread): > but i am getting update from sales
2025-04-08
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Maria Doyle (12:49:57): > :rotating_light:Today’s the Deadline for GBCC2025 Scholarship Applications! https://jxtxfoundation.org/news/2025-2-27-gbcc/ - Attachment (JXTX Foundation): JXTX + GBCC 2025 Scholarships > JXTX + GBCC 2025 Scholarships
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2025-04-09
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2025-04-10
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USLACKBOT (08:10:35): > This message was deleted.
Taofeecoh Adesanu (08:12:39) (in thread): > Hello@AmakaSeems you are in the wrong channel, please use#bugsigdb
Mildred Anashie (08:13:33) (in thread): > Hi@AmakaAsk on#bugsigdb
Amaka (08:13:51) (in thread): > Okay thanks
Aedin Culhane (12:17:22): > Anyone have a workaround for AACR Genie going down?
2025-04-11
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2025-04-12
Vince Carey (10:58:37) (in thread): > @Tim Trichethat might be in your wheelhouse?
Tim Triche (11:44:39) (in thread): > Oof I can look.I think we still have dbGaP access for it
2025-04-13
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2025-04-14
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2025-04-15
Monthly general reminder (06:00:03): > Hi everyone, > > Just a quick reminder to check out ourCode of Conduct . It helps keep our community welcoming and inclusive.:handshake:Also, don’t forget to explore ourSlack channel directory and join in on the conversations. If you have any ideas for new channels, feel free to drop them in#channel-requests.:speech_balloon:You can add topics and descriptions to channels to help improve the directory.:memo:Thanks for being a part of our community!:blush: - Attachment (bioconductor.org): Bioconductor - Code of Conduct Policy > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
2025-04-16
Lori Shepherd (15:21:17): > Bioconductor 3.21 is released! > Thanks to all developers and community members for contributing to the project! > Please see the full release announcement:https://bioconductor.org/news/bioc_3_21_release/ - Attachment (bioconductor.org): Bioconductor - Bioconductor 3.21 Released > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
2025-04-17
dhvani solanki (16:07:35): > @dhvani solanki has joined the channel
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Khanh (16:38:02): > Hi, here is data science and AI engineer
Khanh (16:38:21): > is there anyone looking for a developer? if you are, please send dm me
Pariksheet Nanda (17:13:08): > @Khanhyou can also check in#jobs- good luck!
2025-04-18
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D. Taylor (11:07:48): > I’m a retiree that refuses to stop. > My main interests are in Micro-Biology. Mycologie - Fungi, Virus research with Phages. Any local ( to me in Stuttgart, Germany. ) individuals or groups would be ideal.
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2025-04-20
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2025-04-21
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2025-04-22
Maria Doyle (06:07:10): > :hourglass_flowing_sand:Just a reminder —EuroBioC2025 abstract submissions close on 24 April! Barcelona https://eurobioc2025.bioconductor.org/pages/submissions.html We’ve shared the call on socials too — feel free to reshare if you’d like: > * LinkedIn > * Mastodon > * Bluesky
Maria Doyle (06:07:55) (in thread): > Hi@D. Taylor! Welcome to the community. We have a dedicated#introductionschannel for intros, and I see you found it.:blush:Feel free to share more about your interests there!
Maria Doyle (06:11:57) (in thread): > Hi Khanh, welcome! Just a quick reminder that job-related messages are best posted in the#jobschannel. This helps keep our#generalchannel focused on broader community discussions. Thanks for understanding and good luck with your search!:blush:
D. Taylor (09:11:29) (in thread): > Thank You for the welcome. > > –
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2025-04-23
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Maria Doyle (07:18:03): > :pencil:New Bioconductor blog post on Outreachy internship experience https://blog.bioconductor.org/posts/2025-04-23-outreachy-interns-experience/ - Attachment (Bioconductor community blog): Outreachy December 2024 Interns with Bioconductor – Bioconductor community blog > Bioconductor participated in the Outreachy Internship program for the December 2024 to March 2025 cohort. Our interns share their experience working on their various projects and Bioconductor in general.
Pariksheet Nanda (11:39:13) (in thread): > This is very cool! Nice to read that Divine will be starting graduate school this fall. I was curious if the Software Freedom Conservancy / Outreachy or Bioconductor has processes for Divine and Kate to pursue their maintainer interests in BugSigDB they mention about in the blog post or perhaps assist mentoring the cohort for the coming year assuming BugSigDB is on the docket?
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2025-04-24
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Maria Doyle (04:44:46) (in thread): > :alarm_clock:Final Reminder —**** EuroBioC2025 abstract submissions close today, 24 April**! Don’t miss the chance to share your work in Barcelona this September. Submit your abstract here:https://eurobioc2025.bioconductor.org/pages/submissions.html
Maria Doyle (04:52:36) (in thread): > Thanks, Pariksheet! I believe some mentees continue contributing to BugSigDB and even mentoring. For example, Chioma, Peace, and Esther were mentors of Divine and Kate in this cohort and were previous mentees. See all Outreachy posts here:https://blog.bioconductor.org/#category=Outreachy @Svetlana Ugarcina Perovicfrom the BugSigDB team may have more to add.
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2025-04-25
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Maria Doyle (14:26:41): > :mega:GBCC2025 Poster Abstracts https://gbcc2025.bioconductor.org/abstracts/submission_guidelines/
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2025-04-27
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2025-04-29
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2025-04-30
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2025-05-01
Pariksheet Nanda (10:58:28): > I’m trying to report an issue for a package that has no BugReports URL onsupport.bioconductor.org but when I hit “Submit” for the post I keep getting “Server Error > We apologize! A server error has occurred. If the problem persist please contact us.”
Pariksheet Nanda (11:00:24) (in thread): > In any case, here’s the post because I have a deadline at noon: > > Post Title: Three samples in GSE145926 cause DropletUtils::read10xCounts() to throw error gene information differs between runs > > Post Type: ask a question > > Post Tags: DropletUtils > > Three of the 12 samples in a published 10x Genomics dataset have inconsistent genes annotations: literally one gene missing from those 3 samples. But that throws the “gene information differs between runs” error. Which is great that it’s catching that inconsistency. I feel like providing the genome argument to read10xCounts() should maybe fix that? But I’m not clear on how I should provide the genome with Ensembl annotations to read10xCounts()? Code to reproduce is below: > > library(GEOquery) > library(DropletUtils) > > if (! exists("params", mode = "list")) { > params <- list(dir_data = "~/data") > } > > ## Reference ExpressionSet. > dir_gse <- file.path(params$dir_data, "GSE145926") > if (! dir.exists(dir_gse)) { > dir.create(dir_gse, recursive = TRUE) > } > es <- getGEO("GSE145926", destdir = dir_gse)[[1]] > experimentData(es) > > ## Download the supplementary files. > df_file_supp_tar <- > getGEOSuppFiles("GSE145926", > makeDirectory = TRUE, > baseDir = params$dir_data, > fetch_files = TRUE) > files_supp <- > untar(rownames(df_file_supp_tar), exdir = path.expand(dir_gse), list = TRUE) > files_supp > files_supp_exist <- file.exists(file.path(dir_gse, files_supp)) > if (! all(files_supp_exist)) { > untar(rownames(df_file_supp_tar), exdir = path.expand(dir_gse)) > } > > ## How one imports the data depends on the technology used to create the > ## dataset. Boyd 2020 used 10X Genomics. > paths_molecule_info <- > grep("*.h5", files_supp, value = TRUE) |> > (function(x) file.path(dir_gse, x))() |> > (function(x) setNames(x, sub("_.*", "", basename(x))))() > > debugonce(read10xCounts) > sce <- read10xCounts(paths_molecule_info) > > sessionInfo( ) > > > > Browse[1]> n > debug: if (nsets > 1 && length(unique(gene_info_list)) != 1L) { > stop("gene information differs between runs") > } > > Browse[1]> n > debug: stop("gene information differs between runs") > > Browse[1]> table(elementNROWS(gene_info_list)) > > 33538 33539 > 3 9 > > > > R version 4.5.0 (2025-04-11) > Platform: x86_64-pc-linux-gnu > Running under: Ubuntu 24.10 > > Matrix products: default > BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0 > LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > time zone: America/New_York > tzcode source: system (glibc) > > attached base packages: > [1] stats4 stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocParallel_1.42.0 DropletUtils_1.28.0 SingleCellExperiment_1.30.0 > [4] SummarizedExperiment_1.38.0 GenomicRanges_1.60.0 GenomeInfoDb_1.44.0 > [7] IRanges_2.42.0 S4Vectors_0.46.0 MatrixGenerics_1.20.0 > [10] matrixStats_1.5.0 GEOquery_2.76.0 Biobase_2.68.0 > [13] BiocGenerics_0.54.0 generics_0.1.3 > > loaded via a namespace (and not attached): > [1] tidyselect_1.2.1 dplyr_1.1.4 R.utils_2.13.0 > [4] XML_3.99-0.18 lifecycle_1.0.4 statmod_1.5.0 > [7] magrittr_2.0.3 compiler_4.5.0 rlang_1.1.6 > [10] tools_4.5.0 data.table_1.17.0 knitr_1.50 > [13] askpass_1.2.1 S4Arrays_1.8.0 dqrng_0.4.1 > [16] curl_6.2.2 DelayedArray_0.34.1 xml2_1.3.8 > [19] abind_1.4-8 HDF5Array_1.36.0 withr_3.0.2 > [22] purrr_1.0.4 sys_3.4.3 desc_1.4.3 > [25] R.oo_1.27.0 grid_4.5.0 beachmat_2.24.0 > [28] Rhdf5lib_1.30.0 edgeR_4.6.1 cli_3.6.5 > [31] crayon_1.5.3 remotes_2.5.0 httr_1.4.7 > [34] tzdb_0.5.0 DelayedMatrixStats_1.30.0 scuttle_1.18.0 > [37] rhdf5_2.52.0 parallel_4.5.0 BiocManager_1.30.25 > [40] XVector_0.48.0 vctrs_0.6.5 Matrix_1.7-3 > [43] jsonlite_2.0.0 hms_1.1.3 credentials_2.0.2 > [46] h5mread_1.0.0 locfit_1.5-9.12 limma_3.64.0 > [49] tidyr_1.3.1 snow_0.4-4 glue_1.8.0 > [52] codetools_0.2-20 UCSC.utils_1.4.0 tibble_3.2.1 > [55] pillar_1.10.2 rappdirs_0.3.3 rhdf5filters_1.20.0 > [58] openssl_2.3.2 GenomeInfoDbData_1.2.14 httr2_1.1.2 > [61] R6_2.6.1 sparseMatrixStats_1.20.0 gert_2.1.5 > [64] rprojroot_2.0.4 evaluate_1.0.3 lattice_0.22-6 > [67] readr_2.1.5 rentrez_1.2.3 R.methodsS3_1.8.2 > [70] Rcpp_1.0.14 SparseArray_1.8.0 whisker_0.4.1 > [73] xfun_0.52 fs_1.6.6 usethis_3.1.0 > [76] pkgconfig_2.0.3 >
Lori Shepherd (11:03:27) (in thread): > Could it be related to special characters as posts don’t support non-ASCII characters? > Also you might want to post this question in a non thread so more people will see it quickly rather than hidden in a thread.
Pariksheet Nanda (11:04:13) (in thread): > I’ll troubleshoot later in the afternoon; have to send my PI a figure before noon.
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That was fun to check out! - Attachment (f1000research.com): F1000Research Article: BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem. > Read the latest article version by Shian Su, Vincent J. Carey, Lori Shepherd, Matthew Ritchie, Martin T. Morgan, Sean Davis, at F1000Research.
- Attachment (twitter): Attachment > BioCAsia is coming to Sydney on Dec 5-6! > Dec 5 we’ll bring together researchers with an interest in @Bioconductor & #rstats to exchange ideas & expertise. > Dec 6 we’re teaming up with @Bioinfosummer (Dec 2-6) to run hands on bioinformatics training featuring Bioconductor software. https://pbs.twimg.com/media/D80D6x2UcAAZxIQ.png