#bioc2018

2018-07-19

Martin Morgan (10:10:04): > @Martin Morgan has joined the channel

Martin Morgan (10:10:48): > set the channel description: General conversations about BioC 2018: Where Software and Biology Meet

Nitesh Turaga (10:14:08): > @Nitesh Turaga has joined the channel

Marcel Ramos Pérez (10:34:40): > @Marcel Ramos Pérez has joined the channel

Davide Risso (14:07:49): > @Davide Risso has joined the channel

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Aedin Culhane (16:49:12): > @Aedin Culhane has joined the channel

Qiang Hu (17:37:41): > @Qiang Hu has joined the channel

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2018-07-20

Charlotte Soneson (02:10:35): > @Charlotte Soneson has joined the channel

Diya Das (11:12:07): > @Diya Das has joined the channel

Diya Das (11:13:25): > Hello - I have a question about posters. Will they be displayed on July 25-27, or just for the main conference July 26-27? (I am trying to figure out whether I should expedite shipping)

Martin Morgan (11:31:57): > main conference only, July 26-27

Diya Das (13:59:11): > Thanks Martin!

Martin Morgan (14:33:28): > @Diya Dasdid you submit a poster abstracthttp://bioc2018.bioconductor.org/call-for-abstracts? No problem if not, but submitting an abstract will mean that the poster title etc. is listed in the program - Attachment (BioC 2018): BioC 2018: Where Software and Biology Connect > Where Software and Biology Connect. July 25 - 27, Toronto, Canada.

Diya Das (14:46:42) (in thread): > I filled out a poster submission form with an abstract on May 15, and I was notified it was accepted on May 31. Do I need to submit an abstract again for the program? (I assumed it would be taken from the form, but I can do it now.)

Martin Morgan (14:49:42) (in thread): > let me track things down…

Martin Morgan (15:21:28) (in thread): > ok, thanks for your patience; no need for you to submit a poster abstract !

Diya Das (15:33:26) (in thread): > Excellent, thank you!

2018-07-21

Matthew McCall (18:51:38): > @Matthew McCall has joined the channel

2018-07-23

Aedin Culhane (10:58:53): > Hi. Who is getting into Toronto Tuesday afternoon/evening. Is there any social/dinner venue planned?

C. Mirzayi (please do not tag this account) (15:52:21): > @C. Mirzayi (please do not tag this account) has joined the channel

Matthew McCall (21:21:43): > I’m driving up tomorrow afternoon. Hoping to get in around 4pm.

2018-07-24

Matthew McCall (17:11:16) (in thread): > Made it to Toronto. Headed out to find food and beer. Want to join us?

2018-07-25

Kasper D. Hansen (09:05:58): > @Kasper D. Hansen has joined the channel

Jenny Drnevich (09:18:44): > @Jenny Drnevich has joined the channel

Daniel Giguere (09:24:37): > @Daniel Giguere has joined the channel

Shian Su (09:26:58): > @Shian Su has joined the channel

Stuart Lee (09:27:33): > @Stuart Lee has joined the channel

Neke Ibeh (09:32:03): > @Neke Ibeh has joined the channel

Wolfgang Huber (09:57:49): > @Wolfgang Huber has joined the channel

Wolfgang Huber (10:03:02): > ‘conflicted’ is not really the solution for working with the tidyverse unless we want to sprinkle our code with :: for pretty much mostbasefunctions. - File (Plain Text): conflicted

Peter Hickey (10:06:41) (in thread): > I guess thatconflictedis going to do this for everything inBiocGenerics?

Peter Hickey (10:07:14) (in thread): > and other S4 generics in BioC that mimic base functions …

Shian Su (10:12:56): > Can someone link me to the lightning talk google doc?

Stuart Lee (10:13:31) (in thread): > There’s an issue about this on their git pagehttps://github.com/r-lib/conflicted/issues/8 - Attachment (GitHub): R session terminates with conflicted and GEOquery (Bioconductor package) · Issue #8 · r-lib/conflicted > When a function in GEOquery Bioconductor package is run after loading the conflicted package, R session terminates. As I couldn't see any error messages before R terminated in Rstudio, I ran th…

Michael Steinbaugh (10:15:19): > @Michael Steinbaugh has joined the channel

Michael Steinbaugh (10:16:15): > @Wolfgang HuberAlso I’ve found that conflicted can crash my workspace with a lot of Bioconductor packages loaded up

Peter Hickey (10:16:47) (in thread): > thanks, Stuart!

Peter Hickey (10:17:34) (in thread): > it’s unclear to me that anything changled withconflicted, however

Peter Hickey (10:17:57) (in thread): > perhaps any changes aren’t on CRAN yet

Stuart Lee (10:19:52) (in thread): > One problem I’ve found with developing plyranges is the need to bind bioc generics into a quosures environment so users can make use of :: without conflicts which is clunky and makes using tidyverse approaches with bioc a bit clunky

Wolfgang Huber (10:20:44) (in thread): > https://docs.google.com/document/d/1hhd5X3_Tj2WJhtt9Ro_WjYgBJI5221tRWg_7ZyMj_AM/edit

Michael Steinbaugh (10:21:04): > Thanks

Michael Steinbaugh (11:37:39): > @Aedin CulhaneWe’ve been struggling withcolData()forSingleCellExperimentcontaining multiple samples as well. We’ve been storing the metadata in asampleDatadata frame inside themetadata()slot and then merging that data in long format to thecolData()using a cell-to-sample factor, but maybe there’s a better way

Michael Steinbaugh (11:38:38): > For bulk RNA-seq it’s easy becausecolData()describes the samples, but usually we want to perform extraction/subset operations at a sample level, not cell level

Michael Love (11:40:54): > @Michael Love has joined the channel

Michael Love (11:42:08): > there are scRNA with multiple samples now?:wink:

Michael Steinbaugh (11:42:30): > Only for labs with the big bucks, but yeah we’re dealing with replicates now

Michael Love (11:43:01): > :tada:

Michael Love (11:58:10): > more on my question about access to summarized versions of HCA - i think that of course the raw data access is critical, but probably user adoption of Bioc interface to HCA will hinge on access to summarized. there may be a benefit to starting to think about providing this, even before we decide the definitive number of cell types are in the brain

Kelly Street (12:57:22): > @Kelly Street has joined the channel

Peter Hickey (13:23:06): > James Taylor (Galaxy developer) is sharing his notes at bioc2018https://twitter.com/jxtx/status/1022169535447818240 - Attachment (twitter): Attachment > My (naïve!) notes from #bioc2018 will accumulate here https://gist.github.com/jxtx/e2c955d808bbdd3f92e8e19936887ee6

Michael Love (13:26:25): > ooh James Taylor is here

Nitesh Turaga (14:00:28): > Are there any notes anywhere for this Workshop/BOF?Impromptu: tidyverse and Bioconductor – VC 211from earlier today?

Derek Nedveck (15:09:33): > @Derek Nedveck has joined the channel

Derek Nedveck (15:11:37): > @Nitesh TuragaRE the impromptu workshop,@Martin Morganmight have notes

Nitesh Turaga (15:12:52): > Thanks@Derek Nedveck. I’ll follow up with@Martin Morgan

Kasper D. Hansen (15:39:27): > @Michael LoveI think the pragmatic answer is that we will provide access to anything exposed by the HCA data storage.

James Taylor (15:54:12): > @James Taylor has joined the channel

Charlotte Soneson (16:17:07): > Google Drive link for the suggestions from the “support site group”https://docs.google.com/document/d/1TPKn5sdBLrSuMEiXtdAyGipd7p2XNXghbHGYzmH_Xpk/edit?usp=sharing

Nitesh Turaga (16:38:26): - File (JPEG): IMG_20180725_163802.jpg

Davide Risso (16:42:24): > https://docs.google.com/presentation/d/1_SkOfeLT7j7wdQCwxfwmuChjuB7wtW-2evrbYKMWnIg/edit#slide=id.p - File (Google Slides): Biocverse

Davide Risso (16:51:08): > For those interested, join us in the new#biocversechannel!:shuffle-parrot:

Michael Love (16:52:35): > dear Bioc core folks, where should i best post the SummarizedExperiment reproducing example?

Michael Love (16:52:47): > support site, bioc-devel, github issue page?

Nitesh Turaga (16:55:28): > Someone asked in theMaintain your Bioconductor packageworkshop , “the average number of lines in a bioconductor package”. I did, across allsoftware packages > > find . -name '*.R' | xargs wc -l > blah.txt > > > > xx <- read.table("blah.txt") > sum(xx$V1)/1581 > [1] 5703.512 > > So, 5703.512 lines per package. This is a very rough estimate.

Stephen Turner (17:06:21): > @Stephen Turner has joined the channel

Nitesh Turaga (17:08:41): > genomicsclass.github.io/book

Michael Love (17:08:59): > Vince showed this:http://genomicsclass.github.io/book/

Michael Love (17:09:05): > Kasper’s class is here:https://kasperdanielhansen.github.io/genbioconductor/

Stuart Lee (17:36:44): > A bunch of us are going to the Oxley for drinks

Stuart Lee (17:37:21): > If anyone wants in

Eric Milliman (18:10:23): > @Eric Milliman has joined the channel

Martin Morgan (20:01:09) (in thread): > github issuehttps://github.com/Bioconductor/SummarizedExperiment - Attachment (GitHub): Bioconductor/SummarizedExperiment > SummarizedExperiment container

Michael Hoffman (21:23:36): > @Michael Hoffman has joined the channel

Michael Hoffman (21:27:28): > Can we live-tweet talks?

2018-07-26

Kasper D. Hansen (00:09:51): > There is a book version of my material onhttps://leanpub.com/bioconductor - Attachment (Leanpub): Bioconductor > The Bioconductor project is a widely used open source and open development platform for software for computational biology. It is a leading platform for doing data science in Genomics.  This book covers the core functionality needed to deploy Bioconductor on modern datasets, and will lay the foundation for you to learn and explore parts of the p…

Kasper D. Hansen (00:10:07): > (note that you can slide the “pay” scale so the cost is 0)

Shian Su (07:30:05): > Does anyone know where I might find the Biocviews graph that Vincent was talking about?

Michael Hoffman (08:57:32): > https://courses.bioconductor.org/takes me tohttps://courses.bioconductor.org/get_url/33

Michael Hoffman (08:57:46): > Submit gave meThe instance ID 'i-086904cf34e0be37b' does not exist

Michael Hoffman (08:58:31): > Never mind, tried it again and it worked

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Farnush Farhadi (09:11:55): > @Farnush Farhadi has joined the channel

Aedin Culhane (09:14:16): > @Michael HoffmanYes tweeting is encouraged Use#bioc2018

Aedin Culhane (09:54:41): > Please upload lightning talks tohttps://drive.google.com/open?id=12NJgqY-EVsnFnZe1NCLjsYvlnC5lqcnUThere is a folder for July 26th

Aake v (10:20:32): > @Aake v has joined the channel

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Diya Das (23:54:18): > Thanks for the dinner @ core team!

Diya Das (23:55:19): > Does anyone know if there are plans to take a group photo of all attendees at some point?

2018-07-27

Martin Morgan (05:48:42): > REMINDER: today’s sessions start with Tim Hughes’ talk at 8:30 http://bioc2018.bioconductor.org/schedule#day-2-friday-july-27 - Attachment (BioC 2018): BioC 2018: Where Software and Biology Connect > Where Software and Biology Connect. July 25 - 27, Toronto, Canada.

Michael Steinbaugh (11:02:10): > My slides are available here:https://github.com/steinbaugh/presentations/blob/master/2018-07-27/bioc2018.pdf - Attachment (GitHub): steinbaugh/presentations > Contribute to presentations development by creating an account on GitHub.

Michael Love (16:21:29): > we have a winner for best meme of BioC2018https://twitter.com/_schifferl/status/1022837614959886336 - Attachment (twitter): Attachment > Great research presentations and discussions at #Bioc2018 https://pbs.twimg.com/media/DjHY4qXWsAAfc2v.jpg

Nitesh Turaga (16:23:09): > @Lucas Schiffer

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USLACKBOT (16:24:47): > This message was deleted.

Martin Morgan (16:51:23) (in thread): > ‘they’ will miss it; he (Northrop Frye) was one of the pre-eminent literary critics of the 20th century

Michael Love (18:34:50) (in thread): > Whoa!

Aedin Culhane (21:04:05): > Thanks@Martin Morgan, soleil,@Sean Davis@Benjamin Haibe-Kainsand@Levi Waldronand everyone. Great meeting.

2018-07-30

Leonardo Collado Torres (13:45:34): > @Leonardo Collado Torres has joined the channel

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2018-11-11

Charlotte Soneson (03:40:01): > @Charlotte Soneson has left the channel

2018-11-19

Michael Love (19:36:33): > @Michael Love has left the channel

2018-11-26

Marcel Ramos Pérez (12:47:40): > archived the channel