#random
2016-11-21
Marcel Ramos Pérez (15:19:11): > @Marcel Ramos Pérez has joined the channel
Tim Triche (15:53:48): > @Tim Triche has joined the channel
Benjamin Haibe-Kains (16:19:29): > @Benjamin Haibe-Kains has joined the channel
Aedin Culhane (16:24:54): > @Aedin Culhane has joined the channel
Vince Carey (16:30:14): > @Vince Carey has joined the channel
Sean Davis (17:05:51): > @Sean Davis has joined the channel
Michael Lawrence (19:04:46): > @Michael Lawrence has joined the channel
Levi Waldron (19:13:06): > @Levi Waldron has joined the channel
Jack Zhu (20:14:56): > @Jack Zhu has joined the channel
Peter Hickey (22:01:35): > @Peter Hickey has joined the channel
2016-11-22
Lucas Schiffer (13:20:18): > @Lucas Schiffer has joined the channel
Kasper D. Hansen (17:27:48): > @Kasper D. Hansen has joined the channel
2016-11-23
Phil Chapman (05:12:43): > @Phil Chapman has joined the channel
2016-11-28
Martin Morgan (13:12:10): > @Martin Morgan has joined the channel
Nitesh Turaga (13:44:51): > @Nitesh Turaga has joined the channel
2016-12-12
Sean Davis (10:31:20): > Join the IBM Watson Developers slack channel if you are interested in using Watson APIs for machine learning and AI.http://bit.ly/watson_slack
2016-12-13
Levi Waldron (16:37:56): > Should we be interested?
Levi Waldron (16:45:51): > @Sean Daviswhat was the new Machine Learning package for Bioconductor that you posted somewhere?
2016-12-14
Hervé Pagès (00:59:16): > @Hervé Pagès has joined the channel
Sean Davis (10:29:52): > Is this what you were thinking of,@Levi Waldron?http://bioconductor.org/packages/MLSeq - Attachment (Bioconductor): MLSeq > This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART, to RNA-Seq data.
Sean Davis (10:32:15): > Well, probably not yet, unless you are working on text mining, image analysis, or designing intelligent chat bots (we should investigate that one with IBM at some point!). - Attachment: Attachment > Should we be interested?
2016-12-16
Sean Davis (12:10:50): > Some nice presentations here:http://nationalacademies.org/hmd/Activities/Disease/NCPF/2016-DEC-12.aspx - Attachment (nationalacademies.org): The Drug Development Paradigm in Oncology: A Workshop : Health and Medicine Division > This workshop will examine the challenges of improving the efficiency of the drug development and regulatory review process, while ensuring the safety of new therapies.
2016-12-19
Sean Davis (08:46:23): > Just a note that > > /remind me to do something tomorrow > > will have slack create a reminder for you “to do something” and will send you a private slack message tomorrow (9am is the default). It can do much more complicated reminders as well for others and for whole channels.https://get.slack.help/hc/en-us/articles/208423427-Set-a-reminder - Attachment (Slack Help Center): Set a reminder
Levi Waldron (08:46:57): > Wow that’s nice!
Sean Davis (08:47:56): > Yeah. Pretty simple but very effective.
Levi Waldron (08:48:29): > Yeah, very nice.
2016-12-22
Sean Davis (13:12:47): > Title: Big Data processing & Medicine – a use case presentation > Date: January 17, 2017, 10:00-12:00pm > Location: Porter Neuroscience Building, 35A Room 610 > Videocast:https://videocast.nih.gov/Registration: No registration is required >
> Audience: This is intended for a general scientific audience with an interest in modern computing. No programming is required. >
> Abstract: Big Data processing with Hadoop is revolutionizing medicine. Enabling Genomic Analysis on much larger scale, providing the backbone for precision medicine by unifying research & clinical silos, and enabling bedside data to be kept for retrospective analysis. This talk will cover real uses cases in Genomics and Medicine for big data and Hadoop. It will also touch on the technology used to accomplish the results. >
> Additional Details > This presentation focuses on biomedical challenges such as: > 1. Predicting clinical events in order to: > a. Reduce hospital readmissions. Hospital systems want to understand the spending and causes on hospital readmissions and reduce those readmissions. They also want to predict the probability of a discharged patient being re-admitted for the same or a similar condition. > b. Reduce preventable death from issues such as sepsis that require real time inputs as well as retrospective data through scalable machine learning. > 2. Gaining clinical insight on acute patients from data generated from multiple streaming sensors. > 3. Getting meaningful clinical value from genomic data (Whole Genome or Gene-Wide Association Studies) and speeding up analyses.
Lucas Schiffer (13:41:13): > AWESOME!
2017-01-06
Sean Davis (10:46:47): > Authorea is beginning to look like an interesting alternative to Google Docs for collaborative editing.https://www.authorea.com - Attachment (authorea.com): Authorea > Authorea is the leading platform to write, cite, collaborate, host, and publish.
Kasper D. Hansen (10:54:13): > perhaps I should have another look. Last time I considered it I ended up liking overleaf a lot more. I don’t recall exact reasons though
Sean Davis (10:56:51): > I came to the same conclusion before. I put this out there as just a suggestion. I’d definitely be interested to hear a critical evaluation from an Overleaf user. For completeness, here is the overleaf link:https://www.overleaf.com/ - Attachment (overleaf.com): Overleaf: Real-time Collaborative Writing and Publishing Tools with Integrated PDF Preview > The online platform for scientific writing. Overleaf is free: start writing now with one click. No sign-up required. Great on your iPad.
2017-01-07
Ted Habermann (11:39:53): > @Ted Habermann has joined the channel
2017-01-09
Benjamin Haibe-Kains (08:45:53): > No dep insights here, but I try several tools and ended up using overleaf for full article with LaTeX savvy users, or gdoc for main text and overleaf for suppl info for the others
Sean Davis (11:30:51): > Just added “/todo” to this slack team.https://www.zlapps.com/todo/installed - Attachment (zlapps.com): /TODO - A to-do list for your Slack team - Zlapps > Fun and useful apps for your Slack team. Manage your To-Do lists inside your Slack chat wihout leaving your application.
2017-01-13
Sean Davis (11:48:36): > @Vince Carey, here is the link to the NCBI Hackathon github organization.https://github.com/NCBI-Hackathons
2017-01-18
Azfar Basunia (10:56:28): > @Azfar Basunia has joined the channel
kristen_humphrey (12:16:39): > @kristen_humphrey has joined the channel
2017-02-09
Lori Shepherd (14:41:59): > @Lori Shepherd has joined the channel
2017-02-10
Sean Davis (19:16:57): > There are three highly active and related Containerized Tool/Workflow groups: GA4GH (Containers and Workflows Task Team), NCI (NCI Containers and Workflows Interest Group), and NIH (Commons Framework Working Group on Workflow Sharing and Docker Registry). In the NIH group, there has been a call to get concrete about demonstrating tool portability. We have proposed to organize an exercise (Phase 1) whereby a small group of interested parties download a CWL/WDL tool described on Dockstore via the GA4GH Tool Registry API, run it in their system, and then upload the results back to a central registry on Synapse along with a description of how they ran in their system of choice. Groups that complete this will be included in a forthcoming paper where we describe metadata and the GA4GH API standard for exchanging Docker-based tools and workflows in CWL/WDL. Longer term, we’d like to perform a Phase 2 challenge where we will use a more complex workflow, ideally one of the GDC pipelines and this will culminate in a presentation at ISMB/BOSC 2017. We will formalize this into an infrastructure Dream Challenge in conjunction with Sage (but that takes time and we’d like to finish Phase 1 in ~30 days and Phase 2 by April 2017). A Phase 3 will exercise the Task and Workflow execution APIs currently being developed in the GA4GH group.
Sean Davis (19:17:06): > https://www.synapse.org/#!Synapse:syn8080249
Sean Davis (19:17:47): > The note and link above are to an Dream Challenge around reproducible workflows.
Lucas Schiffer (21:19:01): > @Sean Davisthis sounds great and like a really nice push for the NCI & NIH. I will definitely try the docker tool and report back (to the central registry that is).
2017-02-20
Aedin Culhane (12:51:59): > Thanks@Sean Davis
2017-04-21
Davide Risso (11:57:31): > @Davide Risso has joined the channel
Stephanie Hicks (12:57:33): > @Stephanie Hicks has joined the channel
Davis McCarthy (13:03:31): > @Davis McCarthy has joined the channel
Aaron Lun (13:26:42): > @Aaron Lun has joined the channel
Andrew McDavid (15:05:34): > @Andrew McDavid has joined the channel
2017-04-28
Greg Finak (21:48:08): > @Greg Finak has joined the channel
hcorrada (22:18:53): > @hcorrada has joined the channel
2017-04-30
Raphael Gottardo (02:19:09): > @Raphael Gottardo has joined the channel
2017-05-03
Artem Sokolov (10:31:16): > @Artem Sokolov has joined the channel
2017-05-10
Valerie Obenchain (15:12:13): > @Valerie Obenchain has joined the channel
Vladimir Kiselev (16:34:50): > @Vladimir Kiselev has joined the channel
Mike Smith (16:52:56): > @Mike Smith has joined the channel
2017-05-11
Mike Jiang (14:48:35): > @Mike Jiang has joined the channel
2017-05-12
Wolfgang Huber (05:25:10): > @Wolfgang Huber has joined the channel
Daniel Van Twisk (13:22:14): > @Daniel Van Twisk has joined the channel
2017-05-15
Durga Addepalli (15:10:29): > @Durga Addepalli has joined the channel
2017-05-16
Steve Tsang (14:16:42): > @Steve Tsang has joined the channel
2017-05-17
Sean Davis (16:49:26): > Hi, all. Folks might be interested in the belated NIH Pi Day. Bonnie Berger will be speaking at 1pm (in Masur for those on campus) and it will be videocast.https://nihpiday.nih.gov/index.html#schedule
2017-05-18
John Readey (18:26:45): > @John Readey has joined the channel
2017-05-19
Ludwig Geistlinger (11:49:00): > @Ludwig Geistlinger has joined the channel
Tiago C. Silva (20:15:49): > @Tiago C. Silva has joined the channel
2017-06-01
Artem Sokolov (13:21:26): > I don’t know if anybody’s following the SpaceX saga, but they are going to be launching a re-used Dragon capsule tonight for the first time. The launch is scheduled for 5:55pm EST tonight, with the feed going live a little while prior.https://techcrunch.com/2017/06/01/watch-spacex-launch-its-first-reused-dragon-capsule-to-resupply-the-iss/ - Attachment (TechCrunch): Watch SpaceX launch its first reused Dragon capsule to resupply the ISS > SpaceX is going to attempt to re-use one of its Dragon capsules for the first time in an active mission to resupply the International Space Station. The..
Rafael Irizarry (14:34:11): > @Rafael Irizarry has joined the channel
Keegan Korthauer (14:38:21): > @Keegan Korthauer has joined the channel
Will Townes (17:08:26): > @Will Townes has joined the channel
Caleb Lareau (21:00:41): > @Caleb Lareau has joined the channel
2017-06-02
Leonard Goldstein (14:57:40): > @Leonard Goldstein has joined the channel
2017-06-08
Cole Trapnell (12:37:17): > @Cole Trapnell has joined the channel
Samuela Pollack (15:55:13): > @Samuela Pollack has joined the channel
2017-06-09
Fanny Perraudeau (21:03:32): > @Fanny Perraudeau has joined the channel
2017-06-10
Sean Davis (22:19:21): > https://wavebox.io/ - Attachment (Wavebox): Wavebox, the next generation web-desktop communication tools > All your web communication tools together for faster, smarter working. Gmail, Google Inbox, Outlook, Office 365, Slack, Trello & more
2017-06-23
Martin Aryee (13:28:19): > @Martin Aryee has joined the channel
2017-06-29
Steve Tsang (09:46:06): > @Steve Tsang has joined the channel
2017-07-26
Ju Yeong Kim (14:24:18): > @Ju Yeong Kim has joined the channel
2017-07-28
Leonardo Collado Torres (08:32:06): > @Leonardo Collado Torres has joined the channel
Aaron Lun (13:02:14): > @Martin AryeeAre you still around?
Aaron Lun (13:04:24): > Currently in cytof workshop, but can chat in the next break.
Martin Aryee (13:05:58): > @Aaron LunNo - I had to leave early today unfortunately. Is the problem you mentioned related to having lots of zero counts in the loops matrix, or something else? I’m leaving on a 2-week vacation now but it would be great to talk later this month.
Aaron Lun (13:06:38): > Something else - but don’t think about it on your vacation! Let me know when you get back, I’m happy to chat whenever.
Ayshwarya Subramanian (13:21:14): > @Ayshwarya Subramanian has joined the channel
2017-07-30
Kevin Rue-Albrecht (15:58:06): > @Kevin Rue-Albrecht has joined the channel
2017-07-31
Radhika Khetani (10:04:19): > @Radhika Khetani has joined the channel
John Hutchinson (10:34:49): > @John Hutchinson has joined the channel
Lorena Pantano (12:19:52): > @Lorena Pantano has joined the channel
2017-08-02
Michael Steinbaugh (12:10:54): > @Michael Steinbaugh has joined the channel
2017-08-07
Peter Hickey (13:40:44): > @Sean Davisi think it was you who mentionedhttps://github.com/rauchg/slackin- is this something bioc can setup/host to simplify sign up for the slack group? - Attachment (GitHub): rauchg/slackin > slackin - Public Slack organizations made easy
Marcel Ramos Pérez (13:47:24): > Hey@Peter Hickey, this has been implemented and it should be running athttps://bioc-community.herokuapp.com/
Peter Hickey (13:47:45): > awesome, thanks Marcel!
Sean Davis (13:49:48): > Just FYI, slackin is pretty easy (and free) to set up.
2017-08-08
Sean Davis (13:09:20): > RStudio is doing a sparklyr webinar series during the month of August. First one is tomorrow.
Sean Davis (13:09:21): > https://pages.rstudio.net/August9_Registration.html
2017-08-10
Stuart Lee (20:09:38): > @Stuart Lee has joined the channel
Di Cook (21:22:12): > @Di Cook has joined the channel
2017-08-14
Meeta Mistry (14:37:07): > @Meeta Mistry has joined the channel
2017-09-01
Thomas Girke (12:35:31): > @Thomas Girke has joined the channel
2017-09-06
Kevin Horan (19:51:47): > @Kevin Horan has joined the channel
2017-09-12
Matt Ritchie (02:57:40): > @Matt Ritchie has joined the channel
2017-10-06
Joshua Campbell (15:37:46): > @Joshua Campbell has joined the channel
David Jenkins (16:32:12): > @David Jenkins has joined the channel
2017-10-07
Evan Johnson (21:54:13): > @Evan Johnson has joined the channel
2017-10-10
Tyler Faits (10:38:57): > @Tyler Faits has joined the channel
2017-10-27
Guangchuang Yu (01:27:36): > @Guangchuang Yu has joined the channel
Guangchuang Yu (01:30:50): > @Levi Waldronthanks for inviting me.
Guangchuang Yu (01:32:16) (in thread): > I can’t find any tree or microbiome related channel
Sean Davis (06:38:08): > #microbiome_metagenome,@Guangchuang Yu
Guangchuang Yu (06:39:26): > Thanks:blush: - Attachment: Attachment > #microbiome_metagenome, @Guangchuang Yu
Nicholas Clark (11:01:54): > @Nicholas Clark has joined the channel
natedolson (11:05:58): > @natedolson has joined the channel
Laurent Gatto (11:51:14): > @Laurent Gatto has joined the channel
Stian Lågstad (13:26:15): > @Stian Lågstad has joined the channel
2017-10-30
cruiz (05:37:56): > @cruiz has joined the channel
2017-11-01
Sean Davis (21:34:32): > Genome Informatics 2017 meeting–twitter feed for those interested:https://twitter.com/search?q=%23gi2017 - Attachment (twitter.com): News about #gi2017 on Twitter > 15m ago @jim_havrilla tweeted: “Also hapLOHseq article is here: https://..” - read what others are saying and join the conversation.
2017-11-09
Parham Solaimani (11:32:01): > @Parham Solaimani has joined the channel
2017-11-10
Sean Davis (09:42:39): > @Sean Davisuploaded a file:Pasted image at 2017-11-10, 9:42 AMand commented:https://rstudio.cloud/ - File (PNG): Pasted image at 2017-11-10, 9:42 AM
2017-11-28
Simina Boca (14:19:29): > @Simina Boca has joined the channel
2017-11-29
Matthew McCall (09:28:23): > @Matthew McCall has joined the channel
2017-12-06
Kevin Wang (19:13:46): > @Kevin Wang has joined the channel
2017-12-07
Federico Marini (18:48:06): > @Federico Marini has joined the channel
Dr H (23:24:38): > @Dr H has joined the channel
2017-12-08
Charlotte Soneson (04:14:31): > @Charlotte Soneson has joined the channel
2017-12-11
Ricard Argelaguet (16:46:09): > @Ricard Argelaguet has joined the channel
2018-01-03
Stephane Ballereau (14:01:21): > @Stephane Ballereau has joined the channel
2018-01-19
Kevin Rue-Albrecht (11:46:03): > just in case some are interested: the ‘Single Cell Genomics Day Livestream’ in onhttp://satijalab.org/scgd/livestream/ - Attachment (satijalab.org): Single Cell Genomics Day Livestream > Lab Webpage —
2018-01-23
Unknown User (03:34:55): > @Levi Waldron commented on @Sean Davis’s file https://community-bioc.slack.com/files/U34P8RS3B/F7Y9YTY9G/pasted_image_at_2017_11_10_09_42_am.png: Thanks Sean, this looks handy for teaching… - File (PNG): Pasted image at 2017-11-10, 9:42 AM
2018-01-24
Derek Bazinet (rpci Dlar) (14:07:57): > @Derek Bazinet (rpci Dlar) has joined the channel
David Jenkins (22:11:04): > Here’s a sidebar theme with bioconductor colors for anyone interested:smile:[color content],[color content],[color content],[color content],[color content],[color content],[color content],[color content]
2018-01-25
Martin Morgan (10:58:42): > @David Jenkinsactual colors are athttp://bioconductor.org/about/logo/
David Jenkins (11:11:22): > Thanks@Martin Morgan! I saw those colors but on my monitor that ‘bioc blue’[color content]looks slightly different from the blue in the logo:[color content],[color content],[color content],[color content],[color content],[color content],[color content],[color content]
2018-01-26
Marcel Ramos Pérez (15:59:07): > The midnight Bioconductor theme:smile::[color content],[color content],[color content],[color content],[color content],[color content],[color content],[color content]
Nitesh Turaga (15:59:35): > I like that you get the color on the side of the hex code
Marcel Ramos Pérez (16:00:33): > And it won’t copy if you copy and paste
2018-02-01
Dror Berel (10:28:10): > @Dror Berel has joined the channel
2018-02-15
Sean Davis (03:56:32): > I had heard a talk about this and found it interesting–new from Lior Pachtor on single cell “marker genes” without transcript/gene quantification:https://www.biorxiv.org/content/early/2018/02/14/258566 - Attachment (bioRxiv): Identification of transcriptional signatures for cell types from single-cell RNA-Seq > Single-cell RNA-Seq makes it possible to characterize the transcriptomes of cell types and identify their transcriptional signatures via differential analysis. We present a fast and accurate method for discriminating cell types that takes advantage of the large numbers of cells that are assayed. When applied to transcript compatibility counts obtained via pseudoalignment, our approach provides a quantification-free analysis of 3’ single-cell RNA-Seq that can identify previously undetectable marker genes.
2018-02-23
Nancy Liu (15:16:27): > @Nancy Liu has joined the channel
2018-02-26
Dario Righelli (16:17:51): > @Dario Righelli has joined the channel
2018-02-27
Samuela Pollack (09:23:24): > @Samuela Pollack has joined the channel
2018-03-01
Peter Haverty (15:54:31): > @Peter Haverty has joined the channel
2018-03-07
Elizabeth Purdom (14:34:47): > @Elizabeth Purdom has joined the channel
2018-03-16
Cotton Seed (11:27:00): > @Cotton Seed has joined the channel
Joey McMurdie (12:29:59): > @Joey McMurdie has joined the channel
2018-03-26
Jayaram Kancherla (14:07:39): > @Jayaram Kancherla has joined the channel
2018-03-27
Han Zhang (09:05:35): > @Han Zhang has joined the channel
2018-03-28
Laurel DiBrog (13:39:57): > @Laurel DiBrog has joined the channel
Hirak (14:18:55): > @Hirak has joined the channel
Rob Patro (14:25:08): > @Rob Patro has joined the channel
2018-04-24
Mike Smith (16:46:56): > @Mike Smith pinned a message to this channel.
2018-04-30
Sean Davis (14:01:05): > I’m a big fan of python, but I had to share this XKCD:https://xkcd.com/1987/ - Attachment: Python Environment > [Title text] “The Python environmental protection agency wants to seal it in a cement chamber, with pictoral messages to future civilizations warning them about the danger of using sudo to install random Python packages.”
Federico Marini (14:15:30): > saw that too, and felt related quite immediately!
Federico Marini (14:20:11): > still he forgets that some pain can be saved with the bioconda repo
Martin Morgan (14:23:03): > I think you mean that bioconda can make the cartoon 2x more complicated!
Vince Carey (14:24:16): > I circulated this in my lab. It was not well-received. The fact that it is about “the danger of using sudo…” is perhaps worth keeping in mind.
2018-05-02
Mike Smith (11:53:15): > Does any one know a supplier for getting hex stickers printed - preferably in Europe? Maybe@Laurent Gatto
Federico Marini (11:54:11): > I recall Stickermule being proposed? But I did not try yet
Peter Hickey (12:18:23): > https://twitter.com/lincolnmullen/status/951169094367240192 - Attachment (twitter): Attachment > (1) Do any of you have recommendations for a vendor to print hex stickers? and (2) Can any of you recommend where I can get #rstats related hex stickers? Thinking about doing something for my class.
Kevin Rue-Albrecht (13:23:37): > I used StickerMule for EuroBioc2017. They send from Italy
Martin Morgan (13:57:29): > In case it’s not on the radar,https://github.com/Bioconductor/BiocStickers - Attachment (GitHub): Bioconductor/BiocStickers > BiocStickers - Stickers for some Bioconductor packages - feel free to contribute and/or modify.
Mike Smith (16:57:02): > :+1:Too many replies, so one big thumbs up to everyone. Thanks!
2018-05-03
Loyal (13:50:05): > @Loyal has joined the channel
Abbas Rizvi (16:12:24): > @Abbas Rizvi has joined the channel
Ezgi Karaesmen (16:12:32): > @Ezgi Karaesmen has joined the channel
2018-05-09
Erik Wright (11:37:30): > @Erik Wright has joined the channel
2018-05-10
Edoardo Pasolli (12:27:20): > @Edoardo Pasolli has joined the channel
Nicola Segata (15:10:31): > @Nicola Segata has joined the channel
2018-05-16
Ruth Isserlin (14:05:05): > @Ruth Isserlin has joined the channel
James W. MacDonald (15:57:59): > @James W. MacDonald has joined the channel
2018-05-19
Rhonda Bacher (12:26:38): > @Rhonda Bacher has joined the channel
2018-05-22
Lauren Fitch (11:30:15): > @Lauren Fitch has joined the channel
2018-05-24
James Hawley (10:20:25): > @James Hawley has joined the channel
2018-05-31
Surajit Bhattacharya (14:39:01): > @Surajit Bhattacharya has joined the channel
2018-06-04
Sean Davis (11:04:59): > http://zarr.readthedocs.io/en/stable/index.html
Sean Davis (11:05:14): > http://bcolz.blosc.org/en/latest/
Michael Love (13:58:39): > @Michael Love has joined the channel
2018-06-05
Yuwei Ni (10:24:30): > @Yuwei Ni has joined the channel
Diya Das (19:45:49): > @Diya Das has joined the channel
2018-06-06
Kelly Street (12:54:01): > @Kelly Street has joined the channel
2018-06-22
Jason Berndt (10:17:04): > @Jason Berndt has joined the channel
Albert Kuo (13:44:17): > @Albert Kuo has joined the channel
2018-06-25
Aaron Lun (09:47:30): > @Aaron Lunuploaded a file:My life’s aim (for this month) - File (PNG): My life’s aim (for this month)
Elana Fertig (16:03:31): > @Elana Fertig has joined the channel
Alex Hopkins (16:04:45): > @Alex Hopkins has joined the channel
2018-06-26
Kevin Rue-Albrecht (08:35:26): > @Kevin Rue-Albrechtuploaded a file:GitHub Heroand commented: And the monthly award goes to….@Aaron Lun! - File (PDF): GitHub Hero
Valentin Voillet (16:40:07): > @Valentin Voillet has joined the channel
Rob Amezquita (17:52:27): > @Rob Amezquita has joined the channel
2018-06-27
Nicholas Cooley (11:52:05): > @Nicholas Cooley has joined the channel
2018-07-01
Aaron Lun (09:38:20): > @Aaron Lunuploaded a file:BioC build system horror storiesand commented: Episode 1: Windows - File (PNG): BioC build system horror stories
Kevin Rue-Albrecht (09:40:02): > awww you missed your chance for “Episode 1: The Windows Menace”
Aaron Lun (09:45:02): > lol
Aaron Lun (09:45:30): > You can be assured that, if there’s a problem with your C(++) code, it’ll show up on Windows.
Kevin Rue-Albrecht (09:46:47): > haven’t had the pleasure to go down the C++ route yet
Kevin Rue-Albrecht (09:47:48): > I’m leaving that level of pain to the experts
2018-07-10
Petr Smirnov (08:02:44): > @Petr Smirnov has joined the channel
2018-07-15
Daniel Giguere (21:09:44): > @Daniel Giguere has joined the channel
2018-07-19
Sehyun Oh (13:58:10): > @Sehyun Oh has joined the channel
Chantal Ho (14:10:31): > @Chantal Ho has joined the channel
Brendan Innes (14:15:38): > @Brendan Innes has joined the channel
Jenny Drnevich (14:40:48): > @Jenny Drnevich has joined the channel
Nima Hejazi (15:16:57): > @Nima Hejazi has joined the channel
Qiang Hu (17:36:39): > @Qiang Hu has joined the channel
2018-07-20
Erik Drysdale (11:08:17): > @Erik Drysdale has joined the channel
2018-07-23
David Dilworth (08:58:56): > @David Dilworth has joined the channel
solomon shorser (14:00:33): > @solomon shorser has joined the channel
Robin Haw (14:02:19): > @Robin Haw has joined the channel
C. Mirzayi (please do not tag this account) (15:50:33): > @C. Mirzayi (please do not tag this account) has joined the channel
2018-07-24
Tom Belbin (09:59:16): > @Tom Belbin has joined the channel
Zhaleh Safikhani (16:01:30): > @Zhaleh Safikhani has joined the channel
Eric Milliman (17:56:45): > @Eric Milliman has joined the channel
2018-07-25
Domenick Braccia (07:00:59): > @Domenick Braccia has joined the channel
Phil Cheng (07:29:56): > @Phil Cheng has joined the channel
James MacDonald (08:35:30): > @James MacDonald has joined the channel
Jeff Johnston (08:58:45): > @Jeff Johnston has joined the channel
Shian Su (09:19:05): > @Shian Su has joined the channel
Neke Ibeh (09:28:31): > @Neke Ibeh has joined the channel
Miles (10:18:41): > @Miles has joined the channel
Derek Nedveck (10:42:21): > @Derek Nedveck has joined the channel
Sara Keeble (14:17:38): > @Sara Keeble has joined the channel
Angeline Yasodhara (14:39:31): > @Angeline Yasodhara has joined the channel
James Taylor (15:46:40): > @James Taylor has joined the channel
Ben Johnson (16:00:12): > @Ben Johnson has joined the channel
Simon Coetzee (16:06:51): > @Simon Coetzee has joined the channel
Stephen Turner (16:17:47): > @Stephen Turner has joined the channel
BJ Stubbs (16:42:01): > @BJ Stubbs has joined the channel
Michael Hoffman (21:21:57): > @Michael Hoffman has joined the channel
Anthony (23:59:44): > @Anthony has joined the channel
2018-07-26
Meng-Chun (07:26:12): > @Meng-Chun has joined the channel
oclark (09:00:33): > @oclark has joined the channel
Farnush Farhadi (09:02:04): > @Farnush Farhadi has joined the channel
Rachael Phillips (09:25:07): > @Rachael Phillips has joined the channel
Yali Zhang (10:17:20): > @Yali Zhang has joined the channel
Aake v (10:20:07): > @Aake v has joined the channel
Andrea Mcewan (10:37:51): > @Andrea Mcewan has joined the channel
Daniela Cassol (10:46:05): > @Daniela Cassol has joined the channel
Krithika Bhuvanesh (11:49:11): > @Krithika Bhuvanesh has joined the channel
Matthew Oldach (12:53:08): > @Matthew Oldach has joined the channel
Destiny McNeece-Mullens (14:54:04): > @Destiny McNeece-Mullens has joined the channel
2018-07-27
Stephen Guest (09:58:30): > @Stephen Guest has joined the channel
Lily Wang (16:46:15): > @Lily Wang has joined the channel
2018-07-28
Ludwig Geistlinger (12:51:26): > https://github.com/Torvaney/ggsoccer - Attachment (GitHub): Torvaney/ggsoccer > ggsoccer - Plot soccer event data in R/ggplot2
Ludwig Geistlinger (12:53:03): > (following up on some discussion at the Bioc2018 presenter’s dinner:wink:)
Nitesh Turaga (19:56:06): > Nothing better than combining R + soccer! Thanks@Ludwig Geistlinger
2018-07-29
Dario Righelli (10:05:51): > Where do you print your exagonal stickers? which is the “official” dimension?
Davide Risso (10:10:30): > Seehttps://github.com/Bioconductor/BiocStickers/blob/master/README.mdfor instructions/templates/examples - Attachment (GitHub): Bioconductor/BiocStickers > BiocStickers - Stickers for some Bioconductor packages - feel free to contribute and/or modify.
Davide Risso (10:12:52): > For printing, I think people use stickermule but I have no direct experience…
Kevin Rue-Albrecht (10:14:00): > I’ve gone through StickerMule, delivery was fast and nothing to complain about the quality.
Kevin Rue-Albrecht (10:14:56): > For the template, the first time, I’ve taken one of the existing one in PDF format, opened it up in Illustrator, edited it, and saved it under a different name.
Davide Risso (10:19:14): > Another option is to create it directly in R with the hexSticker package (https://github.com/GuangchuangYu/hexSticker) - Attachment (GitHub): GuangchuangYu/hexSticker > hexSticker - :sparkles:Hexagon sticker in R
Dario Righelli (10:21:59): > ok, thanks!
Dario Righelli (10:22:45): > I was looking to some vendors, and stickermule seems to be the best one…
2018-07-31
Frederick Tan (14:15:41): > @Frederick Tan has joined the channel
2018-08-01
Charity Law (18:47:14): > @Charity Law has joined the channel
2018-08-02
Chiaowen Joyce Hsiao (09:28:14): > @Chiaowen Joyce Hsiao has joined the channel
2018-08-09
Aaron Lun (11:26:35): > YEAH! 20K FTW - File (PNG): Screenshot_2018-08-09 User Aaron Lun.png
2018-08-14
Axel Klenk (10:45:11): > @Axel Klenk has joined the channel
Steve Niu (17:48:57): > @Steve Niu has joined the channel
2018-08-16
Marcus Kinsella (12:04:46): > @Marcus Kinsella has joined the channel
2018-08-17
branko (10:03:09): > @branko has joined the channel
2018-08-27
Malte Thodberg (05:53:51): > @Malte Thodberg has joined the channel
Juan R Gonzalez (14:58:41): > @Juan R Gonzalez has joined the channel
2018-08-29
rizoic (04:07:34): > @rizoic has joined the channel
Aaron Lun (10:17:54): > ARGHH forgot my Bioconductor password and my WEHI email password. Can’t log in and answer questions until I get home…
Aaron Lun (10:18:05): > Need my fix man.
Levi Waldron (13:20:36): > I can’t remember any passwords anymore:laughing:
Aaron Lun (13:23:09): > Yes, normally it would have been okay, but I haven’t turned on my mac in so long that it seems to have forgotten.
Davide Risso (13:42:22): > I guess you already tried keychain?
Kasper D. Hansen (13:58:03): > 1password. Expensive but has revolutionized my life
Stephanie Hicks (18:31:01): > big +1 for 1password
Stephanie Hicks (18:32:10): > theCommand + Backslashoperation of filling it passwords islife changing
Aaron Lun (20:33:21): > Got my fix.
Kasper D. Hansen (20:41:23): > perhaps we should add the condition that if@Aaron Lundoesn’t log into the site for 48 hours, his reputation gets reset
2018-08-30
Levi Waldron (14:22:16): > Is 1password better than Lastpass?
Levi Waldron (14:33:48): > Based on my quick google search, they seem fairly equivalent… I already I think >500 passwords on Lastpass so I’ll stick with it!
Kasper D. Hansen (14:57:56): > Lastpass is cheaper
Kasper D. Hansen (14:58:08): > It also had a security breach AFAIK some years ago
Kasper D. Hansen (14:58:27): > Apple gives out 1password for free to their employees
Kasper D. Hansen (14:58:52): > Lastpass is >>>> no manager
Levi Waldron (14:59:33): > heh, that is for sure
Kasper D. Hansen (14:59:58): > 1password has a dropbox version (not sure if it was lost in the latest update which I don’t have)
Levi Waldron (15:04:54): > I like their options for multifactor authentication which include a grid of codes that I printed on a piece of paper. Somehow relying on some data that exists only on paper as one step gives me some security peace of mind.
Levi Waldron (15:10:28): > grid multifactor authentication - cool right? - File (PNG): Pasted image at 2018-08-30, 3:10 PM
Kasper D. Hansen (21:06:33): > So you use MFA to unlock Lastpass?
Kasper D. Hansen (21:06:41): > I just have a password and/or fingerprint
Kasper D. Hansen (21:06:50): > But I also unlock it like 30 times a day
Kasper D. Hansen (21:07:19): > The fact that I can put my data on my own dropbox is a big deal for me, since that is much less attrative to hackers.
2018-09-03
Aaron Lun (15:51:20): > I see@Levi Waldrona lot on the slack loading screen. Who gets to put messages there?
Aaron Lun (15:51:35): > just curious. Well, mostly just curious.
Levi Waldron (15:51:50): > I do :)
Aaron Lun (15:52:29): > ah, I see it.
Aaron Lun (15:54:56): > oh yeah…
2018-09-04
Sean Davis (09:48:51): > Just FYI:https://twitter.com/seandavis12/status/1036974009865449473 - Attachment (twitter): Attachment > Talk today by @stevetsa1 at 11am EDT: “Containerization for Reproducible #Bioinformatics Research” available via Webex: > http://bit.ly/2NLmDpL > @NIHDataScience @IRPatNIH > #DataScience https://pbs.twimg.com/media/DmQSVhEW4AAnvV_.jpg
Sean Davis (09:49:22): > Our own@Steve Tsangis giving the talk.
Kasper D. Hansen (10:01:06): > slides?
Sean Davis (11:57:56): > @Steve Tsang?
Steve Tsang (16:18:53): > Here is the deck -https://docs.google.com/presentation/d/16f8_z6tlULBc9nXLghCp04TGyVlZzKzazUNbdprROhs/edit
Steve Tsang (16:19:47): > The presentation was delivered using the Jupyter notebook version with a docker container running in the back end. Here is the repo -https://github.com/stevetsa/nlmreproducibility - Attachment (GitHub): stevetsa/nlmreproducibility > Contribute to stevetsa/nlmreproducibility development by creating an account on GitHub.
Sean Davis (16:22:59): > Sweet!
2018-09-05
Kasper D. Hansen (10:52:22): > That was interesting, but IMO also a bit uncritical focus on containers
Sean Davis (12:05:18): > Are you using containers for anything, Kasper? Just curious.
Kasper D. Hansen (14:27:51): > Occasionally for running specific stuff. Like I use bioconda, and I have been using docker to replicate some issues wrt. compiler errors. I don’t use containers in production but I see a clear usecase here.
Kasper D. Hansen (14:28:31): > My issues are with containers as a solution to reproducibility. My understanding is that Docker changes a lot. And it is not clear to me that a workflow in a container in any way is guranteed to run the same 5 or 10 years later
Kasper D. Hansen (14:29:45): > For example the Dockerfile on p19 of the presentation does not specific specific versions of everything (although I know you can)
Sean Davis (14:29:56): > Agreed that technologies have lifespans. That said, containers make some things that are hardtodaysomewhat easier.
Kasper D. Hansen (14:30:09): > Docker and containers seem to me to solve the issue of ceploying a complicated workflow on heterogenous systems. Thats a major feat
Kasper D. Hansen (14:30:32): > My issue is specific to containers and reproducibility
Sean Davis (14:30:42): > And Steve definitely pointed out that a best practice for containers is to specify versions of everything and to version the containers themselves.
Sean Davis (14:31:11): > Full reproducibility is hard, no matter what tech is used.
Kasper D. Hansen (14:31:13): > Yeah, so do we know we can run 2 yer old docker workflows
Kasper D. Hansen (14:31:28): > Yes, I agree that full repro is hard. I also don’t think we need to strive for full reproducibility
Kasper D. Hansen (14:31:49): > And I do not have much experience with containers and no experience with containers over time.
Kasper D. Hansen (14:33:28): > Like are these repositories where you pull the software from, actually persistently, long-term maintained?
Kasper D. Hansen (14:34:13): > But I think I get that containers are massively useful for deploying code on systems
James Taylor (15:01:50): > @Kasper D. HansenDockerfiles definitely do not solve reproducibility. The actual containers need to be archived. That preserves versions. But well specified packages inside containers is better still.
James Taylor (15:02:42): > Bioconda has no Dockerfiles at all.
Steve Tsang (15:05:06): > @Kasper D. HansenPoints well taken. As an introduction, the presentation focused more on how we can leverage this technology (with other technologies) to increase reproducibility. Just FYI - I am still able to run dockerized tools I created more than 2 years ago on the Seven Bridges platform.
Steve Tsang (15:06:13): > @James TaylorYes, Docker images is the key. Wouldn’t it be better if you also have the dockerfile associated with that particular image though so you know exactly the steps/contents in the image?
James Taylor (15:08:25): > @Steve TsangYes, if there was such a Dockerfile. Bioconda just skips that step. The code and metadata to generate the containers is all in github though and can be reconstructed. Dockerfiles are just less well specified metadata. Incomplete version info and such.
Steve Tsang (15:10:56): > I was thinking the other day, if Docker goes under and Docker Hub goes away today………[fill in the blank]
2018-09-06
Vince Carey (10:52:05): > Slide 16 is a candidate for cheat-sheet of the year. However there is a place where I generally break down owing to rarity of contact with docker: It is fine for establishing a software environment, but how do I make use of local data? I recall some concept of file system mounting and of course I can google it and cobble something together as needed. Some kind of soup-to-nuts Bioconductor package could be useful … I don’t have a compelling use case at present – some exotic open source tool that I’d rather not build locally but can get some genomics mileage with.
Kevin Rue-Albrecht (11:00:42): > Having little experience with containers in a production environment (I’ve only set up an automatic build to distribute the iSEE package and some instances of Shiny apps), I’m also curious about applications of Docker containers to process data (if that’s indeed what we’re talking about here). I seem to recall@Davis McCarthytweeting about his experience:https://twitter.com/davisjmcc/status/999059677089583104How painful would it be to put together a MWE (e.g. even a ‘not so exotic’ workflow that most people could picture easily like RNA-seq quantitation or even basic QC)? - Attachment (twitter): Attachment > I mean, I don’t want to spend my entire working life pre-processing data, but it is pretty satisfying to set hundreds of thousands of jobs running in a now completely containerised workflow :ant::ant::ant::ant:
Sean Davis (11:03:57): > @Vince Carey, using local data is pretty simple. Just “mount” the local directory into the container. > > docker run -v /data/abc:/data/abc_in_container … > > will mount the/data/abcdirectory into the container at/data/abc_in_container.
Sean Davis (11:06:53): > @Kevin Rue-AlbrechtToolkits like NextFlow, Snakemake, Toil, and Cromwell integrate nicely with docker (and some with singularity) containers. I have run 12k RNA-seq samples entirely on the google cloud using Cromwell (and wdlRunR) in about 6 hours using 24k cores (about $0.10 per sample, Salmon). The same workflow will run with other Cromwell-supported backends.
Kevin Rue-Albrecht (11:08:54): > Ow, nice. Can I naively ask what sort of learning curve a newcomer to Docker and cloud platforms would be looking at?
Sean Davis (11:44:46): > If you want to just use Docker to build a reusable image, about 1 hour should get you going.
Sean Davis (11:45:53): > If you want to adopt cloud-scale processing, the process isn’t too involved, but troubleshooting and debugging go to a whole new level.
Kasper D. Hansen (11:51:05): > One issue with Docker is that it is a no-go on local HPC resources because of the requirement for root
Kasper D. Hansen (11:51:10): > In my understanding
Kasper D. Hansen (11:51:16): > That is not an issue on AWS
Kasper D. Hansen (11:51:20): > or your laptop
James Taylor (12:28:43): > Singularity works pretty nicely for HPC needs though, and can import docker images (as unprivileged users).
Kasper D. Hansen (13:33:07): > Thats my understanding too - you’re the expert. Is there anything needed at the systems level for a user to deploy singularity (I have never tried it)?
James Taylor (13:49:55): > I believe it does need to be installed by the admin (at the very least, it needs certain modules like squashfs to be installed).
James Taylor (13:50:35): > But, lots of HPC folks are buying into it (e.g. we have it on MARCC, and you know how conservative our folks are). It’s working well for me. Changing my life honestly.
James Taylor (13:50:52): > There is also udocker for a 100% user space solution. That I have not tried.
Kevin Rue-Albrecht (13:57:26): > Joining back the conversation - thanks for the pointers! > Our Oxford-based group is currently centred around the Python-based Ruffus module (http://www.ruffus.org.uk) to build workflows, using the another Python module developed by the CGAT group (https://github.com/cgat-developers/cgat-core) to interface with HPC queue managers (e.g. writing Python functions that get turned into SLURM jobs). > It’s got good and bad sides - as everything - with version control of dependencies partially addressed by Conda environments, so I am genuinely curious about pros and cons of alternative methods. Thanks again for the pointers - Attachment (ruffus.org.uk): Ruffus — ruffus 2.6.3 documentation > Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics - Attachment (GitHub): cgat-developers/cgat-core > Core functionality of the CGAT code. Contribute to cgat-developers/cgat-core development by creating an account on GitHub.
Artem Sokolov (14:12:55) (in thread): > It’s worth mentioningdocker-compose(https://docs.docker.com/compose/overview/), which can simplify adocker runcommand if you have a large number of local directories that need to be mounted inside the container. It also resolves local paths, whereasdocker run -vrequires full paths, which can be daunting to specify. Here’s a “Hello world” example:https://github.com/datarail/concat-docker - Attachment (Docker Documentation): Overview of Docker Compose > Looking for Compose file reference? Find the latest version here. Compose is a tool for defining and running multi-container Docker applications. With Compose, you use a YAML file to configure… - Attachment (GitHub): datarail/concat-docker > An example of using Docker and Docker compose in our semi-standardised pipeline - datarail/concat-docker
Sean Davis (14:42:56): > We are heavy users of snakemake at NIH, but NextFlow is gaining popularity for HPC environments as well. I had used Ruffus for a while but moved on to Snakemake several years ago.
Sean Davis (14:47:16) (in thread): > Great point,@Artem Sokolov.
2018-09-10
Sean Davis (15:02:05): > This might be of interest to a few folks on this list:https://precision.fda.gov/challenges - Attachment (precision.fda.gov): PrecisionFDA Challenges – precisionFDA > A community for NGS assay evaluation
Sean Davis (15:02:40): > In collaboration with NIH/NCI and Nature Medicine, precisionFDA is launching yet another challenge – the NCI Mislabeling Challenge! Please note that you can read the commentary about this exciting challenge on Nature Medicine athttps://www.nature.com/articles/s41591-018-0180-x. > > So why are we doing this? In biomedical research, sample mislabeling or incorrect annotation has been a long-standing issue contributing to irreproducible results and invalid conclusions. These issues are particularly prevalent in large scale multi-omics studies, in which multiple different omics experiments are carried out at different time periods and/or in different labs and human errors can arise during sample transferring, sample tracking, large-scale data generation, and data sharing/management. On the other hand, simultaneous use of multiple types of omics platforms to characterize a large set of biological samples, as utilized in The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) projects, is becoming a powerful and popular approach to precision medicine. > > Thus, there is a pressing need to have computation programs that automatically screen for and remedy such incorrectly sample labels or annotations. This is possible because parallel data sets for the same samples actually provide better information to identify and correct mislabeled samples than what we usually have in traditional biological/medical studies. The goal of this challenge is to develop computational algorithms that can accurately detect and correct mislabeled data in large-scale multi-omics studies. - Attachment (Nature Medicine): Right data for right patient—a precisionFDA NCI–CPTAC Mult > To address a critical roadblock that can occur in translational and clinical research, the National Cancer Institute and the Food and Drug Administration, in coordination with the DREAM Challenges, are launching the first computational challenge using multi-omics datasets to detect and correct specimen mislabeling.
2018-09-13
Kayla Interdonato (11:09:10): > @Kayla Interdonato has joined the channel
2018-09-17
Federico Marini (05:20:01): > @Levi Waldronwhen I read the login messages I almost want to logout and login again:slightly_smiling_face:
Federico Marini (05:21:07): > > I don’t enjoy SummarizedExperiment everyday, but when I do,iSEEit
Federico Marini (05:21:22): > (shameless plug’s done)
Levi Waldron (14:04:05): > :joy:
2018-09-19
Stian Lågstad (10:50:52): > Might be interesting to some:https://azure.microsoft.com/en-us/blog/announcing-azure-pipelines-with-unlimited-ci-cd-minutes-for-open-source/They’re offering free builds on linux, mac, and windows for open source projects. Makes we want to move from using travis to using azure:slightly_smiling_face: - Attachment (Microsoft Azure): Announcing Azure Pipelines with unlimited CI/CD minutes for open source > With the introduction of Azure DevOps today, we’re offering developers a new CI/CD service called Azure Pipelines that enables you to continuously build, test, and deploy to any platform or cloud.
Kevin Rue-Albrecht (10:53:17): > Arf.. I didn’t take that in note properly, but someone at the Genome Informatics 2018 conference acknowledged using this platform in their presentation today. Just to say it is definitely viable in production; although I don’t have experience myself.
Federico Marini (10:54:46): > circleCI might be also a nice option
Federico Marini (10:55:02): > the conda people did the migration a while ago
Stian Lågstad (13:24:01): > Can I ignore this warning in my package build? The package doesn’t useshiftby itself, onlyIRanges::shift. > > * checking whether package 'chimeraviz' can be installed ... WARNING > Found the following significant warnings: > Warning: replacing previous import 'IRanges::shift' by 'data.table::shift' when loading 'chimeraviz' > > (Fromhttps://www.bioconductor.org/checkResults/3.7/bioc-LATEST/chimeraviz/tokay2-checksrc.html)
Stian Lågstad (13:24:30) (in thread): > (Wasn’t sure where to ask)
Aaron Lun (13:29:07) (in thread): > Do you needdata.table::shift?
Stian Lågstad (13:30:32) (in thread): > No. I only usedata.table::fread(example reference:https://github.com/stianlagstad/chimeraviz/blob/master/R/import_defuse.R#L58).data.tableis listed inDESCRIPTIONhere:https://github.com/stianlagstad/chimeraviz/blob/master/DESCRIPTION#L42
Aaron Lun (13:32:07) (in thread): > Sounds like you should have aimportFrom(data.table, fread)somewhere in your NAMESPACE, then.
Stian Lågstad (13:43:02) (in thread): > Thanks! That led me to the solution, I think:slightly_smiling_face:
2018-09-20
JiefeiWang (12:44:35): > @JiefeiWang has joined the channel
2018-09-24
Kim-Anh Lê Cao (21:43:15): > @Kim-Anh Lê Cao has joined the channel
2018-09-28
Saad Khan (12:19:49): > @Saad Khan has joined the channel
2018-10-01
Marisa Isabell Metzger (04:22:08): > @Marisa Isabell Metzger has joined the channel
2018-10-02
Nicholas Knoblauch (16:31:51): > @Nicholas Knoblauch has joined the channel
2018-10-11
Aaron Lun (06:37:36): > Just out of curiosity… is it possible to create a Rda file that performs a hostile action uponload? For example, deleting the contents of~/.
Sean Davis (07:11:13): > Definitely interested in hearing the answer to this.
Aaron Lun (09:10:06): > The very least one can do is to defineT <- FALSEandF <- TRUEto punish anyone who doesn’t follow the style guide.
Federico Marini (09:15:13): > oh, for that there was the evilR package
Federico Marini (09:15:20): > or at least I think that was the name
Aaron Lun (09:15:55): > Yeah, doing it from a package is relatively easy.
Federico Marini (09:16:45): > the T/F inversion is nothing compared to make itT <- sample(c(TRUE,FALSE),1)
Federico Marini (09:17:59): > uh, here’s the full list:
Federico Marini (09:18:00): > https://purrple.cat/blog/2017/05/28/turn-r-users-insane-with-evil/ - Attachment (purrple.cat): Turn R users insane with evil > purrple
Aaron Lun (09:23:16): > I remember seeing that. I have thought about setting up the T/F thing on my group’s R installation.
Aaron Lun (09:23:42): > … which would only trigger some of the time, leading to “it was failing just a second ago”.
Federico Marini (09:26:42): > We’d need an:evil_parrot:emoji here
Leonardo Collado Torres (10:33:33) (in thread): > hehe, if you find the gif we can add it
Federico Marini (10:34:37) (in thread): > will check:slightly_smiling_face:
Martin Morgan (14:56:39): > @Hervé Pagèsprovidesx = structure(list(), class="evil"); print.evil = function(x, ...) cat("Hello Hal\n"); save(x, print.evil, file = (fl <- tempfile()))and thenrm(x, print.evil)andload(fl); xso not quite ‘hostile on load’.
2018-10-16
Gabriele Sales (08:55:34): > @Gabriele Sales has joined the channel
2018-10-18
Sean Davis (11:11:35): > Some very cool talks here:https://events.mcs.cmu.edu/oss2018/ - Attachment (Open Science Symposium 2018): Home - Open Science Symposium 2018 > October 18-19, 2018 Follow us on Twitter #CMUOpenScience
Sean Davis (11:12:41): > My favorite so far: braindr (tindr for brain images).https://braindr.us/
Nitesh Turaga (11:22:49): > braindr is actually very interesting!
Sean Davis (11:23:20): > https://github.com/SwipesForScience - Attachment (GitHub): SwipesForScience > SwipesForScience has 3 repositories available. Follow their code on GitHub.
Sean Davis (11:23:37): > An open source toolkit for building these things.
2018-10-23
Chen Meng (11:08:16): > @Chen Meng has joined the channel
2018-10-31
Ruizhu HUANG (04:37:43): > @Ruizhu HUANG has joined the channel
2018-11-01
Aaron Lun (06:55:56): > Just got back from SCG 2018.
Aaron Lun (06:55:59): > Am absolutely busted.
Aaron Lun (06:56:21): > Haven’t slept for 24 hours. And I need to keep this up for another ~10 hours to get back on my regular sleep cycle.
Aaron Lun (06:57:10): > The take-home from the conference was that we need to really step up our#bigdata-repefforts.
Martin Morgan (08:12:09) (in thread): > Examples of what needs to be done?
Aaron Lun (08:37:10) (in thread): > Some sleep, hopefully.
Aaron Lun (08:37:28) (in thread): > Oh, you mean the big data stuff.
Aaron Lun (08:38:18) (in thread): > The immediate concern (as previously discussed with@Hervé Pagès) is to have%*%performant for DAs, ideally with sparse matrix-enabled efficiencies and parallelization.
Aaron Lun (08:47:37) (in thread): > I would also like to haveBiocSingulartested and used in as many sc-related packages as possible.
Aaron Lun (08:48:32) (in thread): > Finally, getting Rtsne to run as fast as possible - I have made some PRs but this needs more work.
Davide Risso (08:55:46) (in thread): > Do wereallyneed Rtsne?
Aaron Lun (08:56:50) (in thread): > Why? You want to UMAP?
Aaron Lun (08:57:13) (in thread): > Well, like it or not, there’s still a whole heap of people using t-SNEs (including me), so I’d like it faster rather than not.
Davide Risso (08:58:00) (in thread): > Why not? If it really is faster, and we just need a fancy way to plot cells… one method or the other seems the same to me
Davide Risso (08:58:51) (in thread): > Sure, I’m just saying that it’s esthetic and not really a cornerstone of anything we do
Aaron Lun (09:01:25) (in thread): > The whole field is about aesthetics.
Aaron Lun (09:01:42) (in thread): > And I want a t-SNE plot.
Davide Risso (09:02:21) (in thread): > Sure, not saying that we shouldn’t do it
Aaron Lun (09:02:22) (in thread): > UMAP is clearly different from t-SNE, so they aren’t swap-in replacements.
Davide Risso (09:03:15) (in thread): > I was just thinking that in terms of priorities %*% seems higher than tsne
Aaron Lun (09:04:02) (in thread): > Well, yes, that’s why I had it as number 3.
Aaron Lun (09:04:21) (in thread): > I’ve gotRtsneworking with neighbour inputs, so it’s plug and play with approximate searches inBiocNeighbors.
Aaron Lun (09:04:29) (in thread): > All that remains is to optimize the iterative steps.
Kevin Rue-Albrecht (10:16:31): > Btw, HCA stream is live (started ~1h ago) here:http://web.mit.edu/webcast/hca/
Kevin Rue-Albrecht (10:17:19) (in thread): > Not sure if that’ll help you stay awake or just bore you to sleep@Aaron Lun
Aaron Lun (10:17:44): > :sleepy:
Aaron Lun (10:18:02): > I can barely stay awake as it is.
Aaron Lun (10:18:20): > On the plus side, I did talk to a few DCP people at SCG.
Aaron Lun (10:18:32): > Some of them from John’s “secret family”.
Stephanie Hicks (10:53:37): > @Kevin Rue-Albrechtcan you post updates on here if you think there is something relevant? I will be away from my laptop most of the afternoon today and tomorrow. Really bummed to miss it the stream.
Kevin Rue-Albrecht (11:05:48): > Can do for another while. “Updates from the atlases” were a bit broad brush to my taste, they also didn’t have that much time, to be fair.
Kevin Rue-Albrecht (11:43:55): > Sten Linnarsson on the Brain Atlas: function, development and disease right now
Kevin Rue-Albrecht (12:06:51): > perhaps most relevant now: “Data Coordination Platform Demo”
Kevin Rue-Albrecht (12:09:00): > pilot data: mouse/human, 10x/smartseq/mars/indrop, immune/…/other tissues
Kevin Rue-Albrecht (12:11:03): > 82k cells (82 projects)
Kevin Rue-Albrecht (12:18:31): > “Donwstream analysis, example: Jupyter notebooks”:sob:
Kevin Rue-Albrecht (12:20:28): > At least the interface seems to be fairly convenient to batch download either data matrix, BAM files, FASTQ files (and a few other data modalities)
Kevin Rue-Albrecht (12:24:25): > https://github.com/HumanCellAtlas/data-consumer-vignettes - Attachment (GitHub): HumanCellAtlas/data-consumer-vignettes > Simple walk-throughs of interacting with the DCP as a downstream data consumer. - HumanCellAtlas/data-consumer-vignettes
Kevin Rue-Albrecht (12:32:00): > Uberon sounding as a discussion favorite for ontology-related workhttps://www.ebi.ac.uk/ols/ontologies/uberon - Attachment (ebi.ac.uk): Uber-anatomy ontology > Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
Aaron Lun (12:37:03): > I wouldn’t be too disheartened about their heavy emphasis on Python, the CZI + DCP teams are very over-represented for compsci folks who do a lot of Python work, so a Jupyter notebooks is probably just what they’re most comfortable with.
Aaron Lun (12:37:19): > That said, we should make it easy for them to use R, and currently we haven’t delivered what we promised in the 1st RFA.
Kevin Rue-Albrecht (12:37:21): > i was just teasing:slightly_smiling_face:
Martin Morgan (13:58:15) (in thread): > what do you see as the missed deliverables?
Raphael Gottardo (14:54:30): > I just talked to a few people within the DCP including Ambrose Carr at CZI. They are very supportive of R, and acknowledge that most tools are still in R. Their view is that Jupyter is cross platform, so R is supported.
Raphael Gottardo (14:55:35): > This being said, they will be providing a data API, and think we should simply plug that in in Bioconductor (Again they are really keen in us doing this).@Martin MorganI remember that this part of what you proposed to do. They suggested that we coordinate with@Marcus Kinsellato get early access to the beta, or whatever they can propose.
Raphael Gottardo (14:56:33): > They are looking for use cases, and I think we should create workflows that make use of the HCA data (ideally using the API).
Kevin Rue-Albrecht (14:58:52): > I’m personally curious about plugging an API like this intoiSEEfor immediate visualisation, like we did for ourExperimentHubdemo:grin:
Kevin Rue-Albrecht (15:03:19): > then, more ambitious workflow I imagine would be about clustering and annotating cell types/states, as mentioned among objectives of the atlases today
Marcus Kinsella (15:07:37): > can you describe what that interface would ideally look like for your tools?
Marcus Kinsella (15:11:15): > we have a fair bit of flexibility in the api design, but i’m much less familiar with how bioconductor expects to interact with remote data. several months ago, i think we had talked about some options, and i thought a lot of it came down to just putting some flavor of hdf5 file in s3
Kevin Rue-Albrecht (15:24:47): > I’m probably not the best placed to talk about big-data formats yet, but I’m just wondering about a potential package that would build queries emulating those in the DCP web interface, leading up to the download of a data matrix
Kevin Rue-Albrecht (15:25:02): > (.. accompanied with relevant metadata)
Kevin Rue-Albrecht (15:25:57): > as an R user, I’d imagine data set delivered as aSummarizedExperimentwithcolDataandrowDatafilled where possible
Kevin Rue-Albrecht (15:28:11): > I suppose the data could be cached on the client-side in hdf5 format, with theSummarizedExperimentslots pointing to the relevant matrices
Aaron Lun (15:56:10) (in thread): > The big one for me is the counts-to-clusters of the 1.3 mil data set. This could be broken up into various smaller missed targets, of which the immediate sticking point is what I discussed above.
Aaron Lun (15:57:42) (in thread): > I also haven’t heard anything related to the other aims.
Aaron Lun (16:03:47): > I suspect@Vince Careywould have the most experience playing with remote data stores, but IMO, all I would really want is an API that gives me the requested submatrix of expression values, e.g., as a JSON or binary. Then we would wrap it in a matrix class on our end and we’re away.
Aaron Lun (16:06:01): > I don’t do a lot of network stuff, but I could imagine submitting a POST request from any language (I wonder if I could even do it from C++?) and getting a JSON in return. Or any other standard data format. This could be pretty efficient if sparsity is exploited and recognised on both ends.
Sean Davis (16:25:15): > You might all take a look at restfulSE.http://bioconductor.org/packages/restfulSE/ - Attachment (Bioconductor): restfulSE > This package provides functions and classes to interface with remote data stores by operating on SummarizedExperiment-like objects.
Sean Davis (16:26:51): > For folks thinking about hosting, this is the HDF5 cloud hosting solution:https://www.hdfgroup.org/solutions/hdf-kita/hdf-kita-overview/
Vince Carey (16:28:45): > What do we know about the DCP API? We could use code in restfulSE or rhdf5client to generate DelayedArray objects that compose the RESTful queries based on subscripting operations.
Aaron Lun (16:50:24): > Would it make sense to have aRestfulMatrixinstead? This would plug in more easily with our S4 matrix framework. I can’t see anything special about the SE for data transfer - surely 1D col/rowData would be so cheap we could just grab those in one go.
Aaron Lun (16:51:04): > And I guess I started this, but we should take this conversation back to#bigdata-rep
Marcus Kinsella (16:56:55): > (happy to move this out of#randomif that would be helpful) > presently the API to expression matrices is very simple, you POST a request with a bunch of IDs that refer to “bundles” in the DCP, and it gives you a s3 bucket and prefix for a file or set of files. this satisfies the simplest “data browser” use case, where someone is looking at the website and wants to download an expression matrix based on what they see
Marcus Kinsella (16:58:34): > for scanpy, we can output the matrices in “zarr” format, which has some nice parallelism properties and i think achieves some of the things that delayedarray does in bioconductor
Sean Davis (16:59:21): > I thinkDelayedArraymight be close,@Aaron Lun?
Marcus Kinsella (17:01:37): > i guess there are two parts: the batching of operations, which scanpy does not do, though i suspect you could get it to work with dask, and efficient partial i/o of remote data, which is what they’ve made progress on
Aaron Lun (18:11:08): > What’s the granularity of these bundles? I’m not familiar with the format, but it seems natural to have bundles split by cell (i.e., each file is a collection of column vectors). They might be analogous to chunks in file-backed storage, in which case@Hervé Pagèsalready has a lot of infrasturcutre in place to handle it.
Marcus Kinsella (18:11:59): > it’s pretty much all over the place. for smartseq2 every bundle is one cell, for 10x a bundle may have many thousands of cells
Aaron Lun (18:12:16): > Oh. 1 cell! That’s… interesting.
Marcus Kinsella (18:12:28): > yes it’s very interesting
Aaron Lun (18:12:31): > Okay, but by and large, each bundle contains expression values for all genes for 1 (or many) cells.
Marcus Kinsella (18:12:55): > yeah plus a bunch of metadata
Aaron Lun (18:13:00): > Right.
Aaron Lun (18:13:51): > This might be fatigue speaking (haven’t slept for 36 hours since I woke up in Boston) but it all sounds very feasible with our existing infrastructure.
Marcus Kinsella (18:14:25): > i’m very interested in how that would work
Aaron Lun (18:14:43): > I suppose there is documentation floating around somewhere for the API? Certainly the DCP slack channel makes enough noise.
Marcus Kinsella (18:14:59): > i assume we would needsomeadaptation of the existing storage system API, but if it’s not too major that would be great
Marcus Kinsella (18:15:17): > well there are multiple APIs
Aaron Lun (18:15:43): > I was thinking of the expression matrix API you mentioned earlier, with POST requests for bundles.
Aaron Lun (18:16:27): > @Vince Carey, how much work would it be to roll outRestfulMatrixor some such thing?
Marcus Kinsella (18:16:36): > https://github.com/HumanCellAtlas/data-store/blob/master/dss-api.ymlandhttps://github.com/HumanCellAtlas/matrix-service/blob/master/config/matrix-api.yml - Attachment (GitHub): HumanCellAtlas/data-store > Design specs and prototypes for the HCA Data Storage System (“blue box”) - HumanCellAtlas/data-store - Attachment (GitHub): HumanCellAtlas/matrix-service > Contribute to HumanCellAtlas/matrix-service development by creating an account on GitHub.
Marcus Kinsella (18:17:55): > you should think of the matrix API as very much a WIP, it served its first matrices a few days ago. the data store API has had some time to settle
Aaron Lun (18:22:47): > Okay. Ah… reading these docs reminds me how long it’s been since I dealt with anything network-y.
Aaron Lun (18:26:10): > Taking this convo back to#bigdata-rep.
Raphael Gottardo (21:14:16) (in thread): > The 1-cell thing through me off. Because in that case, it’s not really a matrix@Marcus KinsellaI don’t really see why cells from a single experiment wouldn’t be in a matrix even if done on Smart-Seq2.
Marcus Kinsella (22:36:07) (in thread): > so there are a few competing concerns with how data is organized in the HCA data store: ingestion and upload, metadata structure, pipeline efficiency, enabling normalization, etc
Marcus Kinsella (22:36:39) (in thread): > so things won’t often be optimized for downstream data consumers, hence the desire to build special services and interfaces like the matrix service
Marcus Kinsella (22:37:30) (in thread): > now for SS2, tbh i feel like the competing concerns mostly argue for bundles that correspond to at least a plate, and i think that decision is going to be revisited now that this demo is done
Marcus Kinsella (22:37:36) (in thread): > but the general problem persists
2018-11-02
Raphael Gottardo (14:30:29) (in thread): > Makes sense to me, a plate would be good.
2018-11-05
Koen Van den Berge (15:57:05): > @Koen Van den Berge has joined the channel
2018-11-06
Avi Srivastava (10:36:30): > @Avi Srivastava has joined the channel
Rory Kirchner (10:47:21): > @Rory Kirchner has joined the channel
2018-11-08
Sean Davis (12:49:53): > https://twitter.com/seandavis12/status/1060546871469449216 - Attachment (twitter): Attachment > The #biodata18 software list is up at http://bit.ly/2RJmGnh > A tweet with hashtag #biodata18 and the CRAN, GitHub, BitBucket, or Bioconductor URL will get your software added. > Thanks to @strnr for helping set this up last year for the #gi2017 meeting. https://pbs.twimg.com/media/DrfQtK6X4AEcNXY.jpg
Sean Davis (12:50:17): > Halfway through day 1 and already 30 software packages mentioned.
2018-11-09
Vladimir Kiselev (06:00:49): > Thanks@Sean Davis, is there anything similar for single cell RNAseq?
Sean Davis (07:49:13): > Take a look athttps://github.com/seandavi/awesome-single-cell? - Attachment (GitHub): seandavi/awesome-single-cell > List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc. - seandavi/awesome-single-cell
Sean Davis (07:50:08): > And the slicker, but more focused:https://www.scrna-tools.org/ - Attachment (scrna-tools.org): scRNA-tools > A catalogue of single-cell RNA-sequencing analysis tools
Sean Davis (07:54:37): > Additions via pull request to awesome-single-cell are encouraged and welcome. Note that the repo is not limited to lists of software and includes speaker suggestions, data resources, web applications, and benchmark and comparison links. Material gets added based on contribution, so if you see something missing or have a few favorite go-tos, make your mark with a pull request.
2018-11-12
Pariksheet Nanda (18:56:57): > @Pariksheet Nanda has joined the channel
2018-11-15
Dane Gellerup (14:31:57): > @Dane Gellerup has joined the channel
2018-11-20
Rob Amezquita (12:18:38): > https://www.humblebundle.com/books/big-data-infographics-books - Attachment (Humble Bundle): Humble Book Bundle: Big Data & Infographics by Wiley > Pay what you want for awesome ebooks and support charity!
Rob Amezquita (12:19:57): > i can’t personally vouch for any of the individual books minus “Visualize This” and “Data Points” (basically the best parts of his blog in book format, minus interactivity), but the topic is:thumbsup:
2018-11-21
sven (10:14:19): > @sven has joined the channel
Fabiola Curion (12:47:03): > @Fabiola Curion has joined the channel
2018-11-26
Lada Koneva (08:20:42): > @Lada Koneva has joined the channel
2018-11-27
Qian Liu (14:22:20): > @Qian Liu has joined the channel
2018-11-29
Jacob Munro (17:22:42): > @Jacob Munro has joined the channel
Carmel Maher (17:27:12): > @Carmel Maher has joined the channel
Shila Ghazanfar (17:40:01): > @Shila Ghazanfar has joined the channel
Stephanie Hicks (18:15:38): > @Shian Sugreat talk! sorry if I missed it, but what’s the difference between cellbench and summarizedbenchmark?
Xueyi Dong (19:21:46): > @Xueyi Dong has joined the channel
Luyi Tian (21:38:35): > @Luyi Tian has joined the channel
2018-11-30
Kevin Rue-Albrecht (08:28:57): > bringing this from#general, apparently, Google has to stay awake tohelp ussleephttps://www.theverge.com/2018/2/5/16973646/google-home-white-noise-ambient-sounds-how-to - Attachment (The Verge): How to sleep easier with Google Home’s white noise feature > Your Google Home speaker can play sounds like a rainstorm, spinning fan, or generic white noise.
2018-12-03
Shila Ghazanfar (21:31:34): > Massive props to@Stephanie Hicksfor giving such a stellar talk over in Perth, Western Australia at BioInfoSummer:100::tada::100:https://bis.amsi.org.au/stephanie-hicks/ - Attachment (AMSI BioInfoSummer): Stephanie Hicks - AMSI BioInfoSummer
2018-12-04
Stephanie Hicks (09:38:38): > Thank you@Shila Ghazanfar!
Chance Hohensee (12:15:04): > @Chance Hohensee has joined the channel
2018-12-05
Marcel Ramos Pérez (11:07:01): > Please vote for your favoriteBioC 2019sticker here:https://github.com/Bioconductor/BiocStickers/issues/74 - Attachment (GitHub): Bioc2019 logo/sticker · Issue #74 · Bioconductor/BiocStickers > Hi @jotsetung - we will need a logo/sticker for the Bioc2019 conference in New York. Given your successful track record of conference and workshop stickers, you might be keen to give this one a go …
Rachael Parks (18:55:31): > @Rachael Parks has joined the channel
2018-12-06
Robert Ivánek (07:43:51): > @Robert Ivánek has joined the channel
Ólavur Mortensen (08:04:10): > @Ólavur Mortensen has joined the channel
Stevie Pederson (10:25:39): > @Stevie Pederson has joined the channel
2018-12-07
Mark Robinson (02:59:12): > @Mark Robinson has joined the channel
Francisco Romero (13:24:03): > @Francisco Romero has joined the channel
2018-12-10
Guy Horev (07:58:55): > @Guy Horev has joined the channel
Rob Amezquita (19:02:42): > tidy principles + S4?https://lgatto.github.io/tidies/articles/tidies.html
Aaron Lun (19:14:37): > We were talking about this athttps://github.com/sa-lee/plyexperiment - Attachment (GitHub): sa-lee/plyexperiment > A fluent interface to SummarizedExperiment. Contribute to sa-lee/plyexperiment development by creating an account on GitHub.
Martin Morgan (20:34:00): > see also#tidiness_in_bioc
Rob Amezquita (22:13:40): > thank you for the tips! i was hoping to hear about other efforts that try to harmonize between the two:slightly_smiling_face:
2018-12-12
Christian P. Larsen (16:08:14): > @Christian P. Larsen has joined the channel
2018-12-13
Michael Lawrence (12:40:40): > @Michael Lawrence has joined the channel
Rena Yang (13:51:43): > @Rena Yang has joined the channel
Wenhua Ren (17:46:22): > @Wenhua Ren has joined the channel
2018-12-14
Konstantinos Geles (Constantinos Yeles) (08:52:36): > @Konstantinos Geles (Constantinos Yeles) has joined the channel
2018-12-16
Lluís Revilla (07:51:32): > @Lluís Revilla has joined the channel
2018-12-17
Sean Davis (14:56:45): > NCI CBIIT Speaker Series > Speakers: Rob Smith, Ph.D. > Date: December 19, 2018 > Time: 11:00 a.m. ET > Topic: Informatics for Computational Mass Spectrometry > In this presentation, Dr. Rob Smith will describe the work he and his lab are doing to progress the state of Informatics for Computational Mass Spectrometry to further proteomic research. > > Dr. Rob Smith will be presenting remotely. Please join us via WebEx and register now to attend the presentation. You may also join us in person at the NCI Shady Grove Campus, Rm. 2W032-34. > About the NCI CBIIT Speaker Serieshttps://wiki.nci.nih.gov/display/CBIITSpeakers/2018/11/02/Dec+19%2C+Rob+Smith%2C+Informatics+for+Computational+Mass+Spectrometry
Nicholas Knoblauch (14:58:36): > @Nicholas Knoblauch has left the channel
2018-12-19
Leo Lahti (04:37:00): > @Leo Lahti has joined the channel
2018-12-28
Rene Welch (12:41:35): > @Rene Welch has joined the channel
2018-12-30
Evan Biederstedt (14:37:32): > @Evan Biederstedt has joined the channel
2019-01-07
Amali Thrimawithana (21:44:56): > @Amali Thrimawithana has joined the channel
2019-01-08
Valerie Obenchain (09:50:20): > @Valerie Obenchain has left the channel
Sean Davis (11:22:45): > Might be of interest to a few: Jeffrey Farrell, Ph.D. > Harvard University > Spatial and temporal reconstruction of embryogenesis using single-cell RNAseq > > on Tuesday January 15th at 10:00 a.m. in Frederick, Building 549, Auditorium > > Dr. Farrell’s research focuses on the recognition that single-cell RNA > sequencing (scRNAseq) can provide a new view of development that > uses all genes to find a global context for previous observations and to > uncover new aspects of embryogenesis. > > This seminar will also be available via WebEx. Please see below for information on the WebEx session. > > WebEx Details: > > JOIN WEBEX MEETINGhttps://cbiit.webex.com/cbiit/j.php?MTID=m1d2b194d5b22edb106fcc4c4313946caMeeting number (access code): 739 249 035 Meeting password: Stadtman011519! > > JOIN FROM A VIDEO SYSTEM OR APPLICATION > Dial sip:739249035@cbiit.webex.com > You can also dial 173.243.2.68 and enter your meeting number. > > JOIN BY PHONE > 1-650-479-3207 Call-in toll number (US/Canada) Tap here to call (mobile phones only, hosts not supported): tel:%2B1-650-479-3207,,01739249035%23%2301
Avi Srivastava (11:26:00): > sounds awesome , thanks for sharing@Sean Davis!
2019-01-09
Sean Davis (18:31:43): > “The Front Lines of Teaching Data Science”https://seankross.com/2019/01/08/The-Front-Lines-of-Teaching-Data-Science.html
2019-01-10
Sowmya S Manian (06:14:49): > @Sowmya S Manian has joined the channel
Shiwani (06:17:08): > @Shiwani has joined the channel
Tim Triche (07:50:54) (in thread): > this could have been lifted word-for-word from my experience teaching a Python for Bioinformatics course at USC
Tim Triche (07:51:41) (in thread): > we decided to switch to iPython notebooks in the second lecture, and covered Ask Uncle Google in the first
Tim Triche (07:52:29) (in thread): > at one point I used the matrix exponential as an example of checking that libraries are doing what you expect, and that floating point isn’t quietly corrupting key steps
Tim Triche (07:53:07) (in thread): > the more things change… ? Thanks for sharing that link, I feel less bad now
Sowmya S Manian (10:31:12): > Hi Everyone, > > Package to do quality control on FASTQ File?
Federico Marini (10:34:26): > FastQC - although it is not a Bioc package?
Martin Morgan (10:35:00): > https://bioconductor.org/packages/ShortReadfor the die-hards - Attachment (Bioconductor): ShortRead > This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Federico Marini (10:35:16): > or Rqc to wrap Martin’s proposal?
Federico Marini (10:35:57): > then on all the samples a one call to MultiQC and you should be served:wink:
Sowmya S Manian (11:22:37): > Thanks all of you. I am familiar with Rqc and also the FASTQC tool > I just wanted to see what all options we have from BioConductor.
Sowmya S Manian (11:22:55): > I will check ShortRead as well
Federico Marini (11:23:25): > Probably overkilling:http://bioconductor.org/packages/release/BiocViews.html#___QualityControl
Federico Marini (11:23:47): > Maybe also useful when writing up a report:http://bioconductor.org/packages/release/BiocViews.html#___ReportWriting
Sowmya S Manian (11:52:21): > @Federico MariniThanks, that helps for the overview I wanted.:+1:
Martin Morgan (12:53:26): > Also QuasRhttp://bioconductor.org/packages/release/bioc/vignettes/QuasR/inst/doc/QuasR.html#612_create_a_quality_control_report
Tim Triche (13:35:57) (in thread): > multiQC usually, since one run by itself is not often of as much interest as several
Sowmya S Manian (13:49:28): > Have usedseqTools, checkingFastqCleanerGoing to use nowBioStringsandShortReadson fastq file. > Will also checkQuasRI want to do Duplicate removal
Sowmya S Manian (13:49:47): > Adapter Trimmer
2019-01-11
Stevie Pederson (01:45:49): > Hi@Sowmya S Manian. We’re aiming to submit this to BioC in the next few weeks but this package can load pre-existing FastQC reports:https://github.com/UofABioinformaticsHub/ngsReports
Sowmya S Manian (01:50:14): > Thanks@Stevie PedersonI’ll check out this as well:+1:
2019-01-14
Rosalba Giugno (03:53:45): > @Rosalba Giugno has joined the channel
Antonino Aparo (05:06:00): > @Antonino Aparo has joined the channel
2019-01-15
Franziska Haertner (03:43:36): > @Franziska Haertner has joined the channel
Aaron Lun (22:43:46): > Wow, these spammers are getting better. This answer (https://support.bioconductor.org/p/116814/#116925) actually made me think for a minute.
Aaron Lun (22:53:44): > As did this one (https://support.bioconductor.org/p/116902/#116924), which is basically legit.
2019-01-16
Kevin Rue-Albrecht (05:56:23): > I almost got confused:laughing: - File (PNG): Pasted image at 2019-01-16, 10:56 AM
Federico Marini (06:13:11): > They clearly are no bots - this would presume some sort ofintelligencebehind it:smile:
Kevin Rue-Albrecht (06:15:11): > well, the “bot reply” Aaron’s second link actually just copied the answer from an earlier post in the same thread. I assume they’ve spammed this manually, but it’s fun to imagine them writing a parser to identify the likely good bit in earlier posts, and re-post it as themselves ^^
2019-01-17
Aaron Lun (04:07:27): > This one is a good one that probably covers a decent number of questions:https://support.bioconductor.org/p/116896/#116976
Federico Marini (04:08:06): > Indeed would solve some of the open issues
Kevin Rue-Albrecht (04:22:21): > 0 points for the key answer to a bioinformatician’s life choices? damn poor guy.:confused:
2019-01-19
Alexey Uvarovskii (06:42:03): > @Alexey Uvarovskii has joined the channel
2019-01-21
Aaron Lun (11:47:23): > huh, slack changed their identicon generator.
Aaron Lun (11:47:43): > And the ubuntu app doesn’t have a hash anymore as the slack icon
Aaron Lun (11:47:47): > brave new world, this.
2019-01-23
Eliza Duvall (10:31:09): > @Eliza Duvall has joined the channel
2019-01-24
Steve Lianoglou (13:45:22): > @Steve Lianoglou has joined the channel
Ming Tang (19:33:55): > @Ming Tang has joined the channel
F (19:35:29): > @F has joined the channel
Jingxin Fu (19:38:05): > @Jingxin Fu has joined the channel
Kylie Bemis (19:40:42): > @Kylie Bemis has joined the channel
Jiwon Lee (19:43:01): > @Jiwon Lee has joined the channel
2019-01-26
Ying Xu (07:49:54): > @Ying Xu has joined the channel
2019-01-28
Sukalyan Banga (11:20:47): > @Sukalyan Banga has joined the channel
Nathan Sheffield (11:50:36): > @Nathan Sheffield has joined the channel
2019-01-29
Leandro Roser (07:00:51): > @Leandro Roser has joined the channel
Diya Das (15:33:44): > Does anyone have experience sorting out C++ compilers for installing R packages on computing clusters? I’m specifically using PSC Bridges, and so far the help desk’s recommendation has been to downgrade R or not use BiocManager:grimacing:I’ve found the issue also persists with install.packages, but I have the vague idea that I should edit a makevars file? (it’s the -openmp flag it doesn’t like, because icpc deprecated that in favor of -qopenmp) I have no experience with C++ so I’d really appreciate some guidance.
Avi Srivastava (15:44:55): > if it’s a standard package, anaconda may be a quick work around:stuck_out_tongue_winking_eye:
Kasper D. Hansen (16:42:48): > Provided you have the right compilers, I would compile R from source
Sean Davis (17:01:04): > Or use a singularity-wrapped R.
Diya Das (17:07:09): > It turns out that a Makevars file with CXXFLAGS, CFLAGS, FFLAGS and FCFLAGS all set to -qopenmp appears to work…thanks for the suggestions though.
Diya Das (19:17:05) (in thread): > I ran this by someone who writes a lot about Rcpp and he said that you could also use the configure.args argument of install.packages, for reproducibility reasons.
2019-01-30
Jul (00:24:37): > @Jul has joined the channel
2019-01-31
Daniel Sink (18:29:04): > @Daniel Sink has joined the channel
2019-02-01
Juan Monroy-Nieto (18:27:33): > @Juan Monroy-Nieto has joined the channel
2019-02-03
Sean Davis (08:49:31): > Artificial Intelligence for Data Discovery and Reuse: > An NSF-supported conference aiming to find innovative solutions to accelerate the dissemination and reuse of scientific data in the data revolution. > Submission deadline Feb 22. > Conference May 13-15, 2019 at Carnegie Mellon University.events.library.cmu.edu/aidr2019/Supported by the NSF scientific data reuse initiative, AIDR (Artificial Intelligence for Data Discovery and Reuse) 2019 is a conference aiming to find innovative solutions to accelerate the dissemination and reuse of scientific data in the data revolution. The explosion in the volume of scientific data has made it increasingly challenging to find data scattered across various platforms. At the same time, increasing numbers of new data formats, greater data complexity, lack of consistent data standards across disciplines, metadata or links between data and publications makes it even more challenging to evaluate data quality, reproduce results, and reuse data for new discoveries. AIDR 2019 provides a platform for AI/ML researchers, data professionals, and scientists to come together and benefit from mutual expertise to address these data challenges and to facilitate the next breakthroughs in science and technology using the power of AI and scientific data.
2019-02-05
Yoon, Tae-Hyun (10:56:35): > @Yoon, Tae-Hyun has joined the channel
2019-02-06
Nigel Delaney (14:16:14): > @Nigel Delaney has joined the channel
2019-02-07
Jianhong (09:46:32): > @Jianhong has joined the channel
2019-02-08
Patrick Kimes (13:26:34): > @Patrick Kimes has joined the channel
2019-02-10
Aaron Lun (07:37:57): > Hm. Pretty quiet here today.
2019-02-11
Michael Lawrence (21:45:19): > I have to admit that the frequency of Slack activity is difficult to manage. Activity seems to come only in spurts, so actively checking for updates is not worth the time. The automatic notification settings aren’t very flexible: notify on mention/keyword or on every message. I guess on every message is the best compromise?
2019-02-12
Martin Morgan (09:12:05) (in thread): > In the slack app and for this channel I set the ‘Sidebar’ preference to show unread and starred messages, and subscribed to a relatively large number of channels. I end up with a manageable handful of easily navigate posts each time I check (a couple of times a day).
2019-02-15
Priyanka Raina (06:09:17): > @Priyanka Raina has joined the channel
2019-02-16
Huajin Wang (10:33:31): > @Huajin Wang has joined the channel
2019-02-18
Lukas Weber (05:40:25): > @Lukas Weber has joined the channel
Geet (10:24:43): > @Geet has joined the channel
Hani Kim (18:54:51): > @Hani Kim has joined the channel
Diego Diez (21:05:37): > @Diego Diez has joined the channel
2019-02-19
Daniel Huebschmann (03:31:37): > @Daniel Huebschmann has joined the channel
Catalina Vallejos (08:15:04): > @Catalina Vallejos has joined the channel
Johnson Zhang (10:18:25): > @Johnson Zhang has joined the channel
Philipp Wahle (11:38:23): > @Philipp Wahle has joined the channel
Adonis Cedeno (11:48:17): > @Adonis Cedeno has joined the channel
Luiz Antonio de Jesus Rocha (12:13:20): > @Luiz Antonio de Jesus Rocha has joined the channel
Fah Sathirapongsasuti (17:23:44): > @Fah Sathirapongsasuti has joined the channel
2019-02-20
Kellie Kravarik (11:35:24): > @Kellie Kravarik has joined the channel
Wanding Zhou (12:09:11): > @Wanding Zhou has joined the channel
2019-02-21
Aaron Lun (13:09:02): > Crap.@Michael Loveis catching up to me on the Bioc support site.
Aaron Lun (13:09:57): > The small consolation is that at least I’ve overtaken him on Google scholar’s h-index.
Aaron Lun (13:12:13): > This isn’t over Mike! Now that I’m not working 70 hour weeks, I’ll have more time for Bioc support!
Steve Tsang (13:44:59): > @Steve Tsang has joined the channel
Michael Love (13:56:28) (in thread): > join twitter, that will kill your productivity
2019-02-22
Avi Srivastava (11:46:11) (in thread): > :joy:
2019-02-24
Ning Leng (23:26:02): > @Ning Leng has joined the channel
2019-02-27
Veer Singh Marwah (11:03:11): > @Veer Singh Marwah has joined the channel
2019-02-28
Rob Amezquita (21:04:28): > https://master.bioconductor.org/help/course-materials/2015/BioC2015/csaw_lab.html->@Aaron Lun, for the bonus at the end, is the cartoon drawing foodstuffs based on dim sum?
Aaron Lun (22:04:05): > you’re on the right continent.
Aaron Lun (22:04:21): > Like my profile pic, they’re dangos.
Aaron Lun (22:04:50): > sort of like this: - File (PNG): Pasted image at 2019-03-01, 3:04 AM
2019-03-05
john (10:26:48): > @john has joined the channel
Ana Beatriz Villaseñor Altamirano (20:55:51): > @Ana Beatriz Villaseñor Altamirano has joined the channel
Alejandro Reyes (21:01:28): > @Alejandro Reyes has joined the channel
César Miguel Valdez Córdova (21:09:50): > @César Miguel Valdez Córdova has joined the channel
Joselyn Chávez (21:54:02): > @Joselyn Chávez has joined the channel
2019-03-06
Ben Story (06:44:50): > @Ben Story has joined the channel
Hyun-Hwan Jeong (15:44:53): > @Hyun-Hwan Jeong has joined the channel
2019-03-11
Johannes Rainer (01:05:19): > @Johannes Rainer has joined the channel
mirna (16:58:46): > @mirna has joined the channel
2019-03-12
Lambda Moses (01:23:47): > @Lambda Moses has joined the channel
Norman Ding (21:33:41): > @Norman Ding has joined the channel
Aaron Lun (22:49:59): > I’m coming for you@Martin Morgan! - File (PNG): Pasted image at 2019-03-12, 7:49 PM
2019-03-13
Lori Shepherd (07:41:17): > And I was so happy I finally got into the k’s:face_with_rolling_eyes:
2019-03-17
gamzeaydilek (07:12:04): > @gamzeaydilek has joined the channel
2019-03-18
Sean Davis (08:15:49): > Program for Artificial Intelligence For Data Discovery and Reuse program is online.https://events.library.cmu.edu/aidr2019/program/
2019-03-20
Aaron Lun (01:36:33): > GOT ON THE PODIUM - File (PNG): Pasted image at 2019-03-19, 10:36 PM
Aaron Lun (01:36:50): > Still can’t change my location, tho.
2019-03-22
Joan (09:20:49): > @Joan has joined the channel
2019-03-28
bioinfodirtyjobs (06:43:59): > @bioinfodirtyjobs has joined the channel
Thomas Schwarzl (11:45:58): > @Thomas Schwarzl has joined the channel
2019-03-30
Sean Davis (13:22:45): > https://pages.rstudio.net/April3rdWhatEveryDataScientistShouldKnowAboutEducation-GregWilson_Registration.html
2019-03-31
Helena L. Crowell (02:37:32): > @Helena L. Crowell has joined the channel
MuthannaWaeli (07:04:27): > @MuthannaWaeli has joined the channel
2019-04-02
saskia (02:05:54): > @saskia has joined the channel
Dario Strbenac (07:03:44): > @Dario Strbenac has joined the channel
2019-04-03
Levi Mangarin (10:45:27): > @Levi Mangarin has joined the channel
KeLiu (13:47:00): > @KeLiu has joined the channel
Tao Liu (16:51:08): > @Tao Liu has joined the channel
2019-04-04
Ruoxi Liu (21:28:49): > @Ruoxi Liu has joined the channel
2019-04-05
Dave Tang (02:46:03): > @Dave Tang has joined the channel
2019-04-06
Joan Gibert (13:25:13): > @Joan Gibert has joined the channel
FeiZhao (20:15:37): > @FeiZhao has joined the channel
2019-04-09
Craig (11:58:36): > @Craig has joined the channel
Kevin Stachelek (18:06:46): > @Kevin Stachelek has joined the channel
2019-04-10
Sridhar N (12:05:47): > @Sridhar N has joined the channel
2019-04-14
Sean Davis (09:45:21): > https://venturebeat.com/2019/04/10/google-launches-ai-platform-a-collaborative-model-making-tool-for-data-scientists/ - Attachment (VentureBeat): Google launches AI Platform, a collaborative model-making tool for data scientists > Google today debuted AI Platform, a tool for data scientists to test, build, and deploy AI models, at the Cloud Next conference in San Francisco.
2019-04-15
Tiago Lubiana (10:08:28): > @Tiago Lubiana has joined the channel
Almut (10:59:22): > @Almut has joined the channel
Jon Bråte (12:23:30): > @Jon Bråte has joined the channel
2019-04-17
Mitch (02:32:08): > @Mitch has joined the channel
Zhi Yang (18:06:28): > @Zhi Yang has joined the channel
2019-04-18
Marko Zecevic (10:29:38): > @Marko Zecevic has joined the channel
2019-04-20
Aaron Lun (21:45:33): > Gee. Really quiet around here.
Dario Strbenac (22:30:11): > Yes, even the cluster at University of Sydney is no longer queueing my jobs. They just run.
Aaron Lun (22:43:07): > I just realized it was easter
Aaron Lun (22:43:22): > apparently not a big thing over here.
Aaron Lun (22:43:44): > If it’s not a public holiday, I probably won’t know about it.
2019-04-21
Tom Gleeson (06:28:44): > @Tom Gleeson has joined the channel
2019-04-23
darlanminussi (12:47:03): > @darlanminussi has joined the channel
2019-04-25
Jake Taylor-King (06:28:06): > @Jake Taylor-King has joined the channel
2019-04-30
Anna Quaglieri (23:26:43): > @Anna Quaglieri has joined the channel
2019-05-01
dave_sevenbridges (17:04:50): > @dave_sevenbridges has joined the channel
2019-05-05
Firas (10:55:42): > @Firas has joined the channel
2019-05-06
Sean Davis (09:38:52): > Terascale PCA:https://github.com/aritra90/TeraPCA
Luka (10:55:38): > @Luka has joined the channel
Aaron Lun (12:48:11): > I read “intel’s C++ compiler” and pretty much stopped there.
Haibo Liu (15:20:51): > @Haibo Liu has joined the channel
2019-05-08
Selvi G (09:35:09): > @Selvi G has joined the channel
2019-05-13
Corina Lesseur (10:46:42): > @Corina Lesseur has joined the channel
2019-05-14
Aaron Lun (01:59:49): > so much cannabis on the support site right now.
Mamie Wang (13:51:12): > @Mamie Wang has joined the channel
2019-05-15
Krithika Venkataraman (21:53:03): > @Krithika Venkataraman has joined the channel
2019-05-16
Sean Davis (12:00:02): > https://bigdatau.ini.usc.edu/explore_erudite - Attachment (bigdatau.ini.usc.edu): Explore Erudite - BD2K Training Coordinating Center > The NIH’s Big Data to Knowledge (BD2K) Training Coordinating Center (TCC)is a multifaceted program with projects including a personalized online educational platform, science rotations, indexing of BD2K Big Data resources, community outreach, and coordinated training with BD2K partners.
2019-05-17
Astrid Deschenes (15:55:11): > @Astrid Deschenes has joined the channel
2019-05-18
Varun Ramani (06:45:04): > @Varun Ramani has joined the channel
2019-05-20
Assa (05:26:08): > @Assa has joined the channel
Sean Davis (06:38:08): > https://www.biorxiv.org/content/10.1101/642132v1
Stephanie Hicks (11:48:56): > Congratulations!
Aaron Lun (11:59:04): > is there any relation to pkgdeptools?
2019-05-21
Juan Rebollo (17:31:03): > @Juan Rebollo has joined the channel
Jeff Gentry (21:30:09): > @Jeff Gentry has joined the channel
2019-05-22
James Ban (21:32:54): > @James Ban has joined the channel
2019-05-23
Kathy Sivils (10:12:03): > @Kathy Sivils has joined the channel
lara mcgrath (14:51:31): > @lara mcgrath has joined the channel
SM (16:37:35): > @SM has joined the channel
Michael Sierant (17:24:34): > @Michael Sierant has joined the channel
2019-05-24
Pratima Chennuri (13:13:54): > @Pratima Chennuri has joined the channel
2019-05-27
Justin (15:53:45): > @Justin has joined the channel
Ni Zhao (18:30:49): > @Ni Zhao has joined the channel
2019-05-28
Kirk Reardon (02:53:17): > @Kirk Reardon has joined the channel
Michelle Miron (13:51:20): > @Michelle Miron has joined the channel
2019-05-31
Oriol Pavón (13:03:57): > @Oriol Pavón has joined the channel
2019-06-04
Erica Feick (06:53:33): > @Erica Feick has joined the channel
Simone Bell (16:37:23): > @Simone Bell has joined the channel
2019-06-05
Paddy St. David (18:11:49): > @Paddy St. David has joined the channel
Sean Davis (20:14:45): > https://seandavi.github.io/2019/06/omicidx-on-bigquery/ - Attachment (seandavi(s12)): OmicIDX on BigQuery | seandavi(s12) > OmicIDX is a project to democratize access to omics metadata. As the sizes of omics repositories have grown into the millions of available samples, thinking of the metadata themselves as Big Data seems reasonable. Additionally, by making the metadata more fit-for-use for text mining, natural language processing, ingestion into machine learning or search engines, OmicIDX aims to facilitate augmentation and analysis of these metadata. In practice, the OmicIDX mines data from the NCBI Sequence Read Archive (SRA) and NCBI Biosample databases (updated daily).
Sean Davis (20:15:22): > R version of post soon….
julen (20:30:50): > @julen has joined the channel
2019-06-06
Craig (10:00:29) (in thread): > hey@Sean Davisjust a heads up theNCBI Sequence Read Archive (SRA)link in your post is broken
Sean Davis (15:30:40) (in thread): > Thx,@Craig. Fixed.
2019-06-08
Malisa S (13:53:15): > @Malisa S has joined the channel
2019-06-10
Isaac Virshup (02:27:10): > @Isaac Virshup has joined the channel
2019-06-11
FelixErnst (07:45:05): > @FelixErnst has joined the channel
2019-06-12
Xuehan Zhang (12:46:45): > @Xuehan Zhang has joined the channel
2019-06-16
Keith Connolly (21:12:59): > @Keith Connolly has joined the channel
2019-06-17
Quy Cao (13:04:24): > @Quy Cao has joined the channel
2019-06-18
Burak Kutlu (18:38:08): > @Burak Kutlu has joined the channel
2019-06-19
ZainabAlTaie (13:43:35): > @ZainabAlTaie has joined the channel
2019-06-20
Harry Danwonno (07:24:18): > @Harry Danwonno has joined the channel
Luca Parmigiani (09:31:32): > @Luca Parmigiani has joined the channel
Nick Gomez (09:52:34): > @Nick Gomez has joined the channel
Robert Castelo (10:10:41): > @Robert Castelo has joined the channel
Rama Shankar (10:24:55): > @Rama Shankar has joined the channel
Hua Ling (10:41:15): > @Hua Ling has joined the channel
Tamas Kiss (10:57:26): > @Tamas Kiss has joined the channel
Marcello (11:39:28): > @Marcello has joined the channel
Robert Williams (11:52:02): > @Robert Williams has joined the channel
Yan Zhang (12:12:05): > @Yan Zhang has joined the channel
Sanjeev Sariya (12:24:18): > @Sanjeev Sariya has joined the channel
Sanjeev Sariya (12:29:18): > hello everyone!!
Tanya Grancharova (12:49:58): > @Tanya Grancharova has joined the channel
Thomas Sandmann (13:50:21): > @Thomas Sandmann has joined the channel
Ghada Soliman (16:59:34): > @Ghada Soliman has joined the channel
2019-06-21
Burton Karger (11:04:54): > @Burton Karger has joined the channel
Ni Zhao (11:32:00): > I almost forgot that I need to pump breast milk during next week’s meeting.:sweat_smile:. Anybody familiar with the conference building to know whether there is a nursery room within?
Martin Morgan (11:40:13): > Yes, there are facilities; the developer day room requires security access that needs to be arranged with Kelly Ruggles; details will be made available at the conference (there’s channel#bioc2019dedicated to the conference, if that helps…)
John Lawson (11:56:28): > @John Lawson has joined the channel
Ni Zhao (11:58:18): > thanks.
Komal Rathi (12:19:07): > @Komal Rathi has joined the channel
Hena Ramay (23:56:35): > @Hena Ramay has joined the channel
2019-06-23
Li Yan (09:49:03): > @Li Yan has joined the channel
Eduardo Cortes (13:13:19): > @Eduardo Cortes has joined the channel
Matt Brauer (18:07:46): > @Matt Brauer has joined the channel
Ameya Kulkarni (22:05:11): > @Ameya Kulkarni has joined the channel
Gerald McCollam (22:40:10): > @Gerald McCollam has joined the channel
Josh Kaminker (22:58:57): > @Josh Kaminker has joined the channel
Luis P Iniguez (23:04:16): > @Luis P Iniguez has joined the channel
Andrew Judell (23:48:59): > @Andrew Judell has joined the channel
2019-06-24
Anqi Zhu (08:00:45): > @Anqi Zhu has joined the channel
NN (09:03:47): > @NN has joined the channel
Doug Barrows (09:19:28): > @Doug Barrows has joined the channel
Sonali (09:40:07): > @Sonali has joined the channel
Patrick Hausmann (10:18:33): > @Patrick Hausmann has joined the channel
Svetlana (10:19:14): > @Svetlana has joined the channel
Zachary Brehm (11:55:24): > @Zachary Brehm has joined the channel
Yered Pita-Juarez (11:57:22): > @Yered Pita-Juarez has joined the channel
Aaron Wolen (13:16:43): > @Aaron Wolen has joined the channel
Seunghee Hong (13:28:47): > @Seunghee Hong has joined the channel
Martín Garrido (16:08:43): > @Martín Garrido has joined the channel
RGentleman (17:29:03): > @RGentleman has joined the channel
Joanna Dragich (23:41:34): > @Joanna Dragich has joined the channel
2019-06-25
Elisabeth (09:07:29): > @Elisabeth has joined the channel
Matt Paul (10:18:15): > @Matt Paul has joined the channel
Dongyu Liu (10:28:54): > @Dongyu Liu has joined the channel
Juanes (10:29:02): > @Juanes has joined the channel
Pascal Belleau (10:35:53): > @Pascal Belleau has joined the channel
Tiphaine Martin (11:29:54): > @Tiphaine Martin has joined the channel
Gabriel J. Odom (15:33:29): > @Gabriel J. Odom has joined the channel
2019-06-26
Eugene Joseph (08:07:08): > @Eugene Joseph has joined the channel
lievenClement (09:58:42): > @lievenClement has joined the channel
Junhao Li (13:21:06): > @Junhao Li has joined the channel
Emanuel Villafán (14:46:16): > @Emanuel Villafán has joined the channel
Seth Falcon (23:41:50): > @Seth Falcon has joined the channel
2019-06-27
Tracy McMillen (13:29:03): > @Tracy McMillen has joined the channel
2019-06-28
Fotis E. Psomopoulos (03:19:33): > @Fotis E. Psomopoulos has joined the channel
Kevin Blighe (03:23:53): > @Kevin Blighe has joined the channel
Jason Vander Heiden (13:42:14): > @Jason Vander Heiden has joined the channel
2019-07-01
Matt Brauer (15:30:23): > How to support open-source software and stay sanehttps://www.nature.com/articles/d41586-019-02046-0 > > On 10 April, astrophysicists announced that they had captured the first ever image of a black hole. This was exhilarating news, but none of the giddy headlines mentioned that the image would have been impossible without open-source software. The image was created using Matplotlib, a Python library for graphing data, as well as other components of the open-source Python ecosystem.Just five days later, the US National Science Foundation (NSF) rejected a grant proposal to support that ecosystem, saying that the software lacked sufficient impact. - Attachment (nature.com): How to support open-source software and stay sane > Releasing lab-built open-source software often involves a mountain of unforeseen work for the developers.
2019-07-02
Deepak Tanwar (10:14:58): > @Deepak Tanwar has joined the channel
Grégoire de Streel (10:15:15): > @Grégoire de Streel has joined the channel
Kevin Missault (10:16:54): > @Kevin Missault has joined the channel
Sebastian Worms (11:00:31): > @Sebastian Worms has joined the channel
TomCarroll (11:06:14): > @TomCarroll has joined the channel
2019-07-03
Martin Treppner (03:30:16): > @Martin Treppner has joined the channel
theo killian (04:12:51): > @theo killian has joined the channel
Heather Turner (22:54:16): > @Heather Turner has joined the channel
2019-07-04
A (09:02:45): > @A has joined the channel
2019-07-05
Yun Zhang (16:49:51): > @Yun Zhang has joined the channel
2019-07-10
Archana Iyer (11:37:42): > @Archana Iyer has joined the channel
2019-07-11
Pierre Gestraud (10:22:13): > @Pierre Gestraud has joined the channel
ceclaurent (10:24:32): > @ceclaurent has joined the channel
Isabel Brito (10:32:54): > @Isabel Brito has joined the channel
Jannik Buhr (15:43:43): > @Jannik Buhr has joined the channel
2019-07-15
kipper fletez-brant (14:48:58): > @kipper fletez-brant has joined the channel
Simon Dirmeier (15:08:15): > @Simon Dirmeier has joined the channel
Friederike Dündar (16:01:52): > @Friederike Dündar has joined the channel
Alexander Toenges (17:34:17): > @Alexander Toenges has joined the channel
Leonardo Collado Torres (17:39:41): > https://twitter.com/ropensci/status/1150862470581329920?s=12 - Attachment (twitter): Attachment > We’re hiring a Software Research Scientist > > Passionate about statistical methods and software? Develop standards and testing for statistical #rstats packages. > > https://ropensci.org/careers/ > > #SoftwarePeerReview
Gordon Smyth (22:17:11): > @Gordon Smyth has joined the channel
2019-07-16
Devon Ryan (05:27:38): > @Devon Ryan has joined the channel
Julie Zhu (11:00:41): > @Julie Zhu has joined the channel
Dan Bunis (13:36:24): > @Dan Bunis has joined the channel
2019-07-17
nservant (02:44:16): > @nservant has joined the channel
2019-07-18
Qiang Hu (16:53:22): > @Qiang Hu has joined the channel
2019-07-20
bogdan tanasa (00:54:13): > @bogdan tanasa has joined the channel
sc724 (20:21:08): > @sc724 has joined the channel
2019-07-22
Gabriel Hoffman (12:20:45): > @Gabriel Hoffman has joined the channel
2019-07-23
nyzhoulang (22:01:08): > @nyzhoulang has joined the channel
2019-07-24
canaanmwc (20:47:50): > @canaanmwc has joined the channel
2019-07-25
Shani Amarasinghe (01:14:35): > @Shani Amarasinghe has joined the channel
2019-07-26
Crowy (00:10:57): > @Crowy has joined the channel
Alex Bott (18:30:31): > @Alex Bott has joined the channel
2019-07-29
Shraddha Pai (15:25:40): > @Shraddha Pai has joined the channel
2019-07-30
yugao (19:50:02): > @yugao has joined the channel
2019-07-31
Julian Flesch (14:21:24): > @Julian Flesch has joined the channel
2019-08-01
Dvir Aran (01:04:50): > @Dvir Aran has joined the channel
Jared Andrews (11:59:35): > @Jared Andrews has joined the channel
Friederike Dündar (15:47:26): > What’s the best way to go from SingleCellExperiment to HDF5Ann/scanpy?
Aaron Lun (15:48:00): > Check out discussion in#singlecellexperiment.
Federico Marini (15:48:12): > uh, quite on time
2019-08-02
Kellie Kravarik (08:39:14) (in thread): > I don’t know if this is the “best” but Seurat in R interconverts between them both, I think…
Friederike Dündar (10:09:09) (in thread): > No, the HFD5Ann export does not currently work
Matt Jensen (13:45:18): > @Matt Jensen has joined the channel
Casey Greene (20:44:59): > @Casey Greene has joined the channel
2019-08-03
Erick Cuevas (11:48:31): > @Erick Cuevas has joined the channel
Mikhael Manurung (13:41:15): > @Mikhael Manurung has joined the channel
Jorge Xool-Tamayo (16:16:53): > @Jorge Xool-Tamayo has joined the channel
Alejandro Ponce (21:11:26): > @Alejandro Ponce has joined the channel
2019-08-04
Samuel David Gamboa-Tuz (09:10:11): > @Samuel David Gamboa-Tuz has joined the channel
2019-08-05
Kellie Kravarik (11:48:38) (in thread): > Yikes - interoperability is a huge issue; I wish it was better!
CARLOS ALFREDO BARRON GALLARDO (13:34:26): > @CARLOS ALFREDO BARRON GALLARDO has joined the channel
2019-08-06
Aaron Lun (02:14:18): > Noooo@Michael Love
Aaron Lun (02:14:29): > In the immortal words of Arnie… I’ll be back.
Michael Love (07:27:18): > Ooh
Michael Love (07:28:34): > I’ve had a string of Qs lately which are answerable with “that happens to be an FAQ”
Michael Love (07:28:42): > :pensive:
2019-08-09
Dario Strbenac (19:59:00): > Some sobering reading in Genome Biology for anyone doing research about variants in genomes titledIs it Time to Change the Reference Genome?https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1774-4It gives a good overview of what a reference genome is and how it is used in genomics research and what the pitfalls are. Of particular note, > > The Reference Genome is Not a Baseline > > Of the 20 donors the reference genome was meant to sample from, 70% of the sequence was obtained from a single sample, ‘RPC-11’, from an individual who had a high risk for diabetes. The remaining 30% is split 23% from 10 samples and 7% from over 50 sources. In practice, the current reference genome can be considered a well-defined and well-assembled haploid personal genome. This means, however, that the reference genome does not represent a default genome any more than any other arbitrarily chosen personal genome would.
Aaron Lun (19:59:35): > Are they taking volunteers?
Aaron Lun (20:00:12): > I’ll put my hand up to be hg39.
Dario Strbenac (20:15:23): > Hopefully, that’ll be a graph genome.
Aaron Lun (20:16:40) (in thread): > Not sure I have enough allelic heterogeneity in my body for that.
2019-08-10
Kasper D. Hansen (14:15:55): > No, hopefully it willnotbe a graph genome
Kasper D. Hansen (14:18:07): > There will not be a single graph genome which satisfies all use cases. What we need are high-quality individual genomes and then tools for making graphs out of select subsets. So that each analysis can be tailored in whatever way you want
Kasper D. Hansen (14:18:23): > The idea of a single graph genome is the idea of a single size fits all.
Kasper D. Hansen (14:19:05): > It is an ill-defined goal (what is a good graph genome, what degrees of variation should be contained in it). Whereas the constructing of high-quality individual genomes is a well defined scientific task
2019-08-14
Aedin Culhane (14:40:42): > The Vienna > Graduate School of Population Genetics is now accepting > > applications > for the course “Experimental evolution: bringing theory and > practice together” > at the University of Veterinary Medicine in Vienna, December > 2-6, 2019. > > Experimental > evolution is extensively used to address questions of > > evolutionary > biology by exposing evolving populations to different > > environmental > conditions. It offers the opportunity to replicate > > experiments > and test for convergent outcomes. With the recent drop in > > DNA sequencing > cost and the advance of sequencing technologies, the > > combination > of experimental evolution with next generation sequencing > > of pools of > individuals (Evolve & Resequence) has become a > > state-of-the-art > method to link phenotypic responses to genetic > > changes. Although > the availability of replicated time series data is > > one key advantage > of E&R, the analysis of such data sets is still in > > its infancy. > This course will introduce the participants to several > > new approaches > for the analysis of genomic time series data covering > > the latest > software tools as well as required statistical and > > computational > skills. > > The course > is targeted towards researchers interested in experimental > > evolution combined > with NGS and will cover the design of experimental > > evolution studies > as well as the analysis of Pool-Seq time series > > data. > > The course > aims to introduce participants to: > > > > State-of-the-art software packages > > > > Modeling of neutral data > > > > Identifying selected regions > > > > Comparison of n-point analysis with time series data > > > > Haplotypes reconstruction > from time-series data > > > > Inferring linkage structure of Pool-Seq data > > > > Estimating selection coefficients > > > > Calling transposable elements in time series data > > > > Inferring selection in transcriptomics data > > > > Morning lectures > by internationally renowned faculty will be followed > > by computer > practicals on the analysis of experimental evolution data > > in the afternoon. > > Faculty: > > Anthony Long > (California Irvine Univ., US) - > confirmed > > Christian Schlötterer > (Vetmeduni Vienna, A) - > confirmed > > Dmitri Petrov > (Stanford Univ., US) - > waiting for confirmation > > Henrique Teotónio > (IBENS, FR) - > confirmed > > Molly Burke > (Oregon State Univ., US) - > confirmed > > Neda Barghi > (Vetmeduni Vienna, A) - > confirmed > > Robert Kofler > (Vetmeduni Vienna, A) - > confirmed > > Susan Bailey > (Clarkson Univ., US) - > confirmed > > The course > is free > but will be restricted for the practical sessions (hands on computer lab). > > Additional > seats will be available for attending the lectures, only. > > Students and > researchers are invited to apply by submitting a single > > .pdf file containing > 1) a short CV, 2) a motivation letter and a > > statement of > computer skills topopgen.vienna@gmail.comby September 30, > 2019. > Confidence in working with Unix command line as well as in R, is strongly > recommended for the practicals. Participants are expected to > arrange their own accommodation. > > Further information > and updates available at:https://www.popgen-vienna.at/training/experimental-evolution-course/Best > regards, > > PhD students > of the Vienna Graduate School of Population Genetics - Attachment (popgen vienna - Vienna Graduate School of Population Genetics): Experimental Evolution Course - popgen vienna - Vienna Graduate School of Population Genetics
2019-08-15
Aaron Lun (00:50:58): > NOOOO!!!!!! - File (PNG): Screenshot from 2019-08-14 21-50-37.png
Aaron Lun (00:51:42): > Well, nothing to do but to lie on the floor and stare at the ceiling until I feel sleepy.
Lori Shepherd (07:34:19): > Sorry for the lack of entertainment@Aaron Lun- I’m in the process of updating now. Should hopefully be back up soon
Lori Shepherd (08:09:09): > And we are back
Federico Marini (08:35:52): > Wake up Aaron:nerd_face:
Federico Marini (08:36:34): > It’s time to put thefunin the function call
Eric Fournier (09:38:48): > @Eric Fournier has joined the channel
Constantin Ahlmann-Eltze (11:13:48): > @Constantin Ahlmann-Eltze has joined the channel
Aaron Lun (11:30:17): > Alright! Thanks@Lori Shepherd.
brejnev muhire (12:48:51): > @brejnev muhire has joined the channel
Boris Hejblum (18:44:08): > @Boris Hejblum has joined the channel
2019-08-18
Luke Zappia (19:34:26): > @Luke Zappia has joined the channel
Dario Strbenac (20:00:05): > For your bemusement, a reviewer for Nature Communications asked for short variant calling to be done in the MHC region on chromosome 6 to identify indels which would cause a frameshift mutation in HLA genes. I recommended my collaborator to quote fromhttps://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1774-4in the rebuttal, particularly the section titled The Reference Genome is Not a Baseline but they asked “can we do indel calling” anyway:face_palm:It’s estimated that there are 8 million to 9 million HLA alleles in the human populationhttps://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006862It seems that Kevin’s efforts to inform the genomics research community about how to use the reference genome meaningfully are in vain.
2019-08-19
Kin Lau (17:42:26): > @Kin Lau has joined the channel
2019-08-20
Kevin Rue-Albrecht (12:30:10): > I’m about to dig intoGenomicRangesagain but just in case someone has a smarter answer: > How do I chase down the definition ofuniqueforGRangesbeyond the following > > > showMethods("unique") > Function: unique (package BiocGenerics) > x="ANY" > x="character" > (inherited from: x="ANY") > x="CompressedList" > x="DataTable" > x="DelayedArray" > x="factor" > (inherited from: x="ANY") > x="List" > x="Rle" > x="RleList" > x="SimpleList" > x="Vector" > > showMethods("unique", classes = "ANY", includeDefs = T) > Function: unique (package BiocGenerics) > x="ANY" > function (x, incomparables = FALSE, ...) > UseMethod("unique") > > I can’t remember how to find the code for something that’s called usingUseMethod("unique")
Aaron Lun (12:31:07): > getMethod("unique", "GRanges")?
Aaron Lun (12:31:24): > Well, it would probably bounce all the way back down to theVectormethod.
Kevin Rue-Albrecht (12:34:58): > oh stupid me in fact, I ran into that one when working onunisets.uniqueis basically defined as!duplicatedfor most things out there. So it’s rarely re-implemented, as developers just need to defineduplicatedand they generally getuniquefor free
Kevin Rue-Albrecht (12:35:41): > See howduplicatedhas a definition forGenomicRanges. That’s all I was after > > > showMethods("duplicated") > Function: duplicated (package BiocGenerics) > x="ANY" > x="CompressedAtomicList" > x="CompressedList" > x="DataTable" > x="Dups" > x="GenomicRanges" > x="GRanges" > (inherited from: x="GenomicRanges") > x="List" > x="PDict" > x="PreprocessedTB" > x="RangedSummarizedExperiment" > x="Rle" > x="Vector" > x="XRawList" >
Aaron Lun (12:36:39): > Read through?pcomparefor details on what you actually need to define for your own subclass.
Kevin Rue-Albrecht (12:40:31): > Thanks. That’s probably the more elegant solution to me reading it as > > duplicatedIntegerQuads(as.factor(seqnames(x)), as.factor(strand(x)), > start(x), width(x), fromLast = fromLast, method = method) > > Also gave me the chance to spot a typo in the man page :P > > are considered equal iff they are
Aaron Lun (12:48:21): > NO, that’s right.
Aaron Lun (12:48:23): > if and only if.
Kevin Rue-Albrecht (12:53:27): > damn i’ve been out of school for too longhttps://en.wikipedia.org/wiki/If_and_only_if - Attachment: If and only if > In logic and related fields such as mathematics and philosophy, if and only if (shortened iff) is a biconditional logical connective between statements, where either both statements are true or both are false. > The connective is biconditional (a statement of material equivalence), and can be likened to the standard material conditional (“only if”, equal to “if … then”) combined with its reverse (“if”); hence the name. The result is that the truth of either one of the connected statements requires the truth of the other (i.e. either both statements are true, or both are false). It is controversial whether the connective thus defined is properly rendered by the English “if and only if”, with its pre-existing meaning. > In writing, phrases commonly used as alternatives to P “if and only if” Q include: Q is necessary and sufficient for P, P is equivalent (or materially equivalent) to Q (compare material implication), P precisely if Q, P precisely (or exactly) when Q, P exactly in case Q, and P just in case Q. Some authors regard “iff” as unsuitable in formal writing; others consider it a “borderline case” and tolerate its use.In logical formulae, logical symbols are used instead of these phrases; see the discussion of notation.
Al J Abadi (20:28:25): > @Al J Abadi has joined the channel
2019-08-21
Dario Strbenac (02:00:15): > https://www.biorxiv.org/content/10.1101/659920v1Posted June 4 2019 “… which is freely available athttps://github.com/TaoDFang/gerrand has been submitted to Bioconductor.” It’s not in the Contributions issue tracker. I hope the referees aren’t naïve!
2019-08-23
Tim Thurman (13:13:48): > @Tim Thurman has joined the channel
2019-08-24
Madison Tyler (09:33:22): > @Madison Tyler has joined the channel
2019-08-25
Xiaotong Wang (20:21:37): > @Xiaotong Wang has joined the channel
2019-08-28
Aditya Bhagwat (10:05:14): > @Aditya Bhagwat has joined the channel
Friederike Dündar (15:15:39): > Sounds like a workshop plenty of BioC aficionados should attend:https://www.synapse.org/#!Synapse:syn20646053/wiki/594445 - Attachment (synapse.org): Synapse | Sage Bionetworks > Synapse is a platform for supporting scientific collaborations centered around shared biomedical data sets. Our goal is to make biomedical research more transparent, more reproducible, and more accessible to a broader audience of scientists. Synapse serves as the host site for a variety of scientific collaborations, individual research projects, and DREAM challenges.
2019-08-30
K Teijgeler (04:06:12): > @K Teijgeler has joined the channel
Natay Aberra (10:02:50): > @Natay Aberra has joined the channel
Istvan Albert (10:02:51): > @Istvan Albert has joined the channel
2019-09-06
Sean Davis (15:05:13): > September update of all SRA and Biosample metadata available on Google Bigquery–11M Biosample records, 208k SRA studies, 7.7M runs > Google colab notebook:rebrand.ly/omicidx_colabBigquery interface:rebrand.ly/kqd362
2019-09-11
Mark Dunning (12:49:28): > @Mark Dunning has joined the channel
venu (15:09:33): > @venu has joined the channel
2019-09-16
Axelle Loriot (09:23:08): > @Axelle Loriot has joined the channel
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
Nick Eagles (16:35:45): > @Nick Eagles has joined the channel
2019-09-19
Princy Parsana (08:47:16): > @Princy Parsana has joined the channel
mirna (18:43:38): > Hi. I have a statistical question, and I think maybe someone here can help me. I am looking for some suggestion on how to analyze transcriptomic data. The idea is to elucidate, which are the genes that participate in the morphogenesis of a holometabolous insect. For the design of this experiment, we produced RNA-seq libraries in each of the stages of development, egg, larva, pupa, and adult. In other RNA-seq experiments, I have contrasted the treatment samples against control in DESeq2. In this case, as I do not have a control condition, I am not quite sure of which contrasts could be appropriate. I could contrast each stage against all others, and thus, identify the genes that have differential expression in at least one condition. However, is this the proper way of doing it? If you have any advice or suggestions, I would greatly appreciate it. Regards.
Kasper D. Hansen (19:56:16): > You can have a factor with levels which are egg, larva etc. and then you can test if the factor is significant
Kasper D. Hansen (19:56:43): > Then you identify genes which do not have the same expression level across all developmental stages
Kasper D. Hansen (19:56:50): > However, that is bound to be a lot
Kasper D. Hansen (19:57:27): > Also, due to the developmental trajectory, it might not make sense to compare egg to adult, but only egg to larva and chain together a list of parwise comparisons
2019-09-20
Helen (18:15:19): > @Helen has joined the channel
2019-09-22
Mehul Kumar (16:47:15): > @Mehul Kumar has joined the channel
2019-09-24
Sean Davis (13:04:32): > Just FYI. For those of you interested in personal control of genomic data, we are hosting a Symposium on September 26-27, 2019. Online attendance is open and for those local to DC, feel free to come by; the meeting is open.https://events.cancer.gov/participantsharedata - Attachment (events.cancer.gov): dccp-pcgdr (Overview) | Events Registration > Symposium on Personal Control of Genomic Data for Research Overview September 26 – 27, 2019, Masur Auditorium, Building 10, NIH campus, Bethesda MD
Friederike Dündar (13:29:43): > sounds very interesting, thanks for sharing! Will definitely point my grad students to it (we have a module about ethics & sequencing data)
Leonardo Collado Torres (18:57:47): > https://twitter.com/jtleek/status/1176551367541805056?s=12 - Attachment (twitter): Attachment > Building an R package for school, work, or fun? @Shannon_E_Ellis & I have a new MOOC on building R packages on @leanpub: https://leanpub.com/universities/courses/jhu/cbds-rpackages. As always, pay what you want & a portion of every sale goes to help our training program in East Baltimore: https://clouddatascience.org/
2019-09-25
lievenClement (04:55:00): > @lievenClement has joined the channel
Steve Hargreaves (05:43:02): > @Steve Hargreaves has joined the channel
2019-10-01
Matteo Calgaro (04:29:44): > @Matteo Calgaro has joined the channel
2019-10-02
Shijie C. Zheng (14:52:00): > @Shijie C. Zheng has joined the channel
RSmith (20:37:10): > @RSmith has joined the channel
2019-10-03
Jason Travis (14:33:50): > @Jason Travis has joined the channel
2019-10-05
Aaron Lun (01:47:48): > I’m thinking of taking a leaf out of Lior’s book and starting a blog to rant about things. Does anyone have any recommendations for a hosting platform?
Avi Srivastava (08:37:51) (in thread): > lol …
Jared Andrews (11:11:41) (in thread): > Any reason not to just use github pages? With a custom domain if you so choose? Otherwise, I can recommend Bluehost as being decent, especially if you go the wordpress route. Stay away from iPage - it is probably the cheapest option out there, and it quickly becomes apparent as to why.
Rob Patro (11:45:47) (in thread): > The github pages issue might be comments, if@Aaron Lunwants support for those. Otherwise, githib pages seems like a nice platform for static pages.
Jared Andrews (11:47:53) (in thread): > Github pages supports comments via jekyll.
Jared Andrews (11:48:47) (in thread): > Disqus and staticman or whatever are easy to set up.
Rob Patro (13:11:33) (in thread): > :+1:
Rob Amezquita (20:47:04) (in thread): > yeah@Aaron Lundont you already have your single cell thoughts page? maybe retitle it to “single cell rants”
Jared Andrews (20:54:14) (in thread): > Perhaps he would like to widen the scope of his rants.
Rob Amezquita (20:54:42) (in thread): > “single cell rants…and more!”
Jared Andrews (20:55:30) (in thread): > Waiting for that poll for what Aaron should name his new rant blog.
Rob Amezquita (20:55:48) (in thread): > ooh thatll be good
2019-10-06
Aaron Lun (14:16:41) (in thread): > Thanks guys, I’ll have a look at some of the GH pages blog examples later tonight.
Mikhael Manurung (16:00:06): > For those who are working with CyTOF data, do you acquire reference samples for each measurement day? If you do, what do you actually do with the data? > > I’ve seen people using MDS plots on median marker expression to compare similarity between the reference samples. But do you actually use it to sort of ‘normalize’ your measurements?
Kevin Wang (22:55:26) (in thread): > Blogdown might be just the thing you want:https://bookdown.org/yihui/blogdown/ - Attachment (bookdown.org): blogdown: Creating Websites with R Markdown > A guide to creating websites with R Markdown and the R package blogdown.
Kevin Wang (22:56:17) (in thread): > You can use blogdown + GitHub Pages
2019-10-07
Aaron Lun (00:29:52) (in thread): > Oh, I won’t be writing R code here. It’s only tangentially work related.
Aaron Lun (00:30:10) (in thread): > But anyway, jekyll is pretty amzing.
Jared Andrews (00:31:41) (in thread): > It’s really excellent. There’s an academic theme that’s also very good. Think it’s called academic-pages.
Aaron Lun (00:33:40) (in thread): > In any case, I went with the GH pages option, which seems to be working well.
USLACKBOT (05:20:03): > This message was deleted.
Brent Biddy (18:17:22): > @Brent Biddy has joined the channel
2019-10-08
Dario Strbenac (02:00:11) (in thread): > Will it be as exciting ashttp://madhadron.com/posts/2012-03-26-a-farewell-to-bioinformatics.html?
Aaron Lun (02:04:21) (in thread): > Ah, I’ve read that one before. Good laugh there.
Mikhael Manurung (06:40:55) (in thread): > Thanks for your reply. > > If I understand correctly, you are using the reference samples as additional QC measures, right? However, you did not use it in any way to ‘adjust’ your measurements in order to remove batch effect. I’ve seen cases where a separate cluster could form due to dirty sensor that greatly reduce the machine’s sensitivity. It would be nice if there are tools to adjust for this instrument variation.
Mikhael Manurung (06:47:37) (in thread): > Nice package, by the way! Lots of utility functions that I could see myself use in the future. > > By the way, is your clusKNN function is the same in principle with Phenograph?
2019-10-10
Jacob Morrison (11:20:04): > @Jacob Morrison has joined the channel
Zhezhen Wang (13:07:19): > @Zhezhen Wang has joined the channel
zhezhen (13:08:00): > @zhezhen has joined the channel
Fred Boehm (13:18:46): > @Fred Boehm has joined the channel
venu (13:25:26): > @venu has joined the channel
Mikhail Dozmorov (13:56:28): > @Mikhail Dozmorov has joined the channel
2019-10-11
Carolyn Fish (13:12:10): > @Carolyn Fish has joined the channel
2019-10-12
SOHEILA ZAREI (00:46:37): > @SOHEILA ZAREI has joined the channel
2019-10-13
wangmcas (20:31:44): > @wangmcas has joined the channel
2019-10-14
Sean Davis (10:32:49): > For those local to NYC,https://inside.mountsinai.org/sinainnovations/is on October 15, 16. Artificial Intelligence talks at Sinai Icahn School of Medicine. - Attachment (Inside Mount Sinai): SINAInnovations 2019 | Inside Mount Sinai > SINAInnovations 2019
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
Anthony Federico (15:51:47): > @Anthony Federico has joined the channel
Oriol Senan (15:52:19): > @Oriol Senan has joined the channel
araman (15:53:04): > @araman has joined the channel
2019-10-16
Sean Davis (21:55:10): > https://datascience.cancer.gov/news-events/events/deepphe-natural-language-processing-system-extracting-cancer-phenotypes-clinical
2019-10-21
Hervé Pagès (17:22:47): > Highly recommended (on Netflix):https://www.imdb.com/title/tt11063952/ - Attachment (IMDb): Unnatural Selection (TV Series 2019– ) - IMDb > DNA, the very essence of life, can now be altered. Not only by Harvard geneticists and multi-billion dollar corporations, but also by renegade biohackers working out of their garages.
Hervé Pagès (17:29:28): > hmm, just noticing now that their helix is spiraling in the wrong direction (like the one we use in our logo on our website)
Marcel Ramos Pérez (17:33:16): > That’s better:grin: - File (JPEG): nattyflip.jpg
Hervé Pagès (17:41:21): > Can we do the same for our website?
Avi Srivastava (19:41:45): > I saw a scientist looking at the fastq file on the monitor:slightly_smiling_face: - Attachment: Attachment > Highly recommended (on Netflix): https://www.imdb.com/title/tt11063952/
2019-10-22
Matt Paul (09:56:47): > isn’t that how you do it?
Dan Bunis (15:49:23): > I started watching it recently and some of the goals of the people they showed in the first episode scare me, but seeing what these “crazy” people are doing is important. It’s a great discussion push-er for the quite urgent ethical concerns surrounding human genetic engineering & CRISPR!:100:
Tokuwa Kanno (16:36:20): > @Tokuwa Kanno has joined the channel
2019-10-23
Ritche Long (13:18:53): > @Ritche Long has joined the channel
2019-10-24
Sudeep Sahadevan (10:37:40): > @Sudeep Sahadevan has joined the channel
2019-10-29
Aaron Lun (01:29:28): > You got that right, GitHub! - File (PNG): Screenshot from 2019-10-28 22-25-52.png
2019-10-30
Ambrose Carr (22:08:18): > @Ambrose Carr has joined the channel
2019-11-04
Izaskun Mallona (07:55:15): > @Izaskun Mallona has joined the channel
2019-11-05
Diana Firkins (15:37:35): > @Diana Firkins has joined the channel
2019-11-06
Sean Davis (17:35:38): > https://osp.od.nih.gov/scientific-sharing/nih-data-management-and-sharing-activities-related-to-public-access-and-open-science/ - Attachment (Office of Science Policy): NIH Data Management and Sharing Activities Related to Public Access and Open Science > Validation and progress in biomedical research – the cornerstone of developing new prevention strategies, treatments, and cures – is dependent on access to scientific data. Sharing scientific data helps validate research results, enables researchers to combine data types to strengthen analyses, facilitates reuse of hard to generate data or data from limited sources, and accelerates
Sean Davis (17:36:02): > NIH is seeking public comment….
2019-11-08
Alan O’C (08:16:02): > @Alan O’C has joined the channel
2019-11-09
Debbie (04:09:10): > @Debbie has joined the channel
2019-11-11
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
2019-11-13
Sean Davis (08:44:15): > https://videocast.nih.gov/summary.asp?live=35197&bhcp=1 - Attachment (videocast.nih.gov): NIH VideoCast - Google Dataset Search: Facilitating data discovery in an open ecosystem. > Google Dataset Search: Facilitating data discovery in an open ecosystem.
Sean Davis (08:44:44): > Videocast open to the public on November 14, 2PM EST, on Google Dataset Search
Evgeny Vlasov (15:33:32): > @Evgeny Vlasov has joined the channel
Noor Pratap Singh (18:40:23): > @Noor Pratap Singh has joined the channel
2019-11-14
Ping Luo (08:31:59): > @Ping Luo has joined the channel
Liz Ing-Simmons (10:17:54): > @Liz Ing-Simmons has joined the channel
2019-11-15
Allison (08:42:00): > @Allison has joined the channel
Norbert Tavares (20:03:42): > @Norbert Tavares has joined the channel
2019-11-18
Sean Davis (11:03:12): > https://twitter.com/seandavis12/status/1196435524556349440 - Attachment (twitter): Attachment > The New York Genome Center is hosting an @NCBI #SingleCell in the #cloud code-a-thon from January 15-17, 2020. > Submissions for project proposals are due December 2nd. > https://support.nlm.nih.gov/Single_Cell_Codeathon_Project_Proposal/ > @DCHackathons @nygenome > #bioinformatics #RNASeq https://pbs.twimg.com/media/EJqXwlBXsAAFCJu.jpg
Siyuan Ma (11:42:26): > @Siyuan Ma has joined the channel
Mohamed Gunady (12:48:00): > @Mohamed Gunady has joined the channel
2019-11-19
Madhuri Sudharshan Gota (11:01:18): > @Madhuri Sudharshan Gota has joined the channel
Russ Bainer (16:05:51): > @Russ Bainer has joined the channel
Nolan Nichols (16:13:13): > @Nolan Nichols has joined the channel
Beryl Cummings (16:34:25): > @Beryl Cummings has joined the channel
Aaron Lun (18:31:39): > Ho ho ho. Looks like someone forgot to clear a merge conflict athttps://stat.ethz.ch/R-manual/R-devel/library/base/html/file.path.html - File (PNG): Screen Shot 2019-11-19 at 3.30.54 PM.png
Martin Morgan (20:00:34) (in thread): > I don’t see that in the svn history? And you can’t change history with svn the way you can with git?
Aaron Lun (20:01:28) (in thread): > I dunno, I’m just seeing it in the link. ¯*(ツ)*/¯
Martin Morgan (20:04:32) (in thread): > I guess the web page must be generated from a git checkout (that’s pretty ironic, I’ll admit)…
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 (11:10:20): > @Steffen Neumann has joined the channel
sonia barbieri (11:35:15): > @sonia barbieri has joined the channel
2019-11-22
Aaron Lun (02:37:40): > Very happy with the new base R colors. The old colors look like they were chosen by a 6 year old.
Mike Smith (02:40:38): > Yes, having seen the new palette it just makes me think ‘why did this not happen sooner?’ They’re so much better now.
Steffen Neumann (02:43:07) (in thread): > already fixed as of this morning
Federico Marini (03:12:29): > the old one reminded the 8-bit computer games
2019-11-27
Justin Kiggins (00:42:16): > @Justin Kiggins has joined the channel
Luka (07:40:24): > Hey! Sorry if I’m in the wrong channel, but would anyone know an efficient way to compare two large fasta files (e.g. Ychrom from hg19 and Ychrom from hs37d5)? I’m interested in exactly which positions they differ
Martin Morgan (09:12:29) (in thread): > This Biostars posthttps://www.biostars.org/p/96951/talks about creating a chain file that can be used by liftOver (including inhttps://bioconductor.org/packages/rtracklayer) to map between sequences. The approach might be dated these days? - Attachment (Bioconductor): rtracklayer > Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Luka (10:46:20) (in thread): > Thanks for your reply, appreciate it
Andrew Jaffe (16:31:43): > @Andrew Jaffe has joined the channel
Miriam Kim (16:43:57): > @Miriam Kim has joined the channel
2019-11-29
Kyle Dyson (12:04:22): > @Kyle Dyson has joined the channel
Chase Clark (12:30:25): > @Chase Clark has joined the channel
David Mas-Ponte (14:43:36): > @David Mas-Ponte has joined the channel
koki (15:40:20): > @koki has joined the channel
2019-12-02
Sean Davis (13:21:33): > Call for ISMB tutorials for Montreal 2020 open until December 16, 2019.https://www.iscb.org/ismb2020-submit/tutorials - Attachment (iscb.org): Tutorials > ISCB - International Society for Computational Biology
Jared Andrews (16:11:54): > Created a new repo to keep track of bioinformatics benchmarking studies, inspired by@Sean Davis’s awesome-single-cell repo. PRs very welcome, content being added as I have time.https://github.com/j-andrews7/Awesome-Bioinformatics-Benchmarks
Sean Davis (16:17:25): > :+1:
Aaron Lun (16:26:58): > > Papers should not be from authors showing why their tool/method is better than others. > Argh all my papers
2019-12-03
Leopoldo Valiente (13:50:47): > @Leopoldo Valiente has joined the channel
Chris Fields (15:17:24): > @Chris Fields has joined the channel
2019-12-04
Ryan SUN (02:48:36): > @Ryan SUN has joined the channel
anne (07:19:06): > @anne has joined the channel
Benjamin Reisman (09:27:15): > @Benjamin Reisman has joined the channel
Jonathan Carroll (17:36:12): > @Jonathan Carroll has joined the channel
Michael Nicholson (18:38:45): > @Michael Nicholson has joined the channel
Yamil Damian Mahmoud (19:12:08): > @Yamil Damian Mahmoud has joined the channel
Sarthak Sinha (19:35:33): > @Sarthak Sinha has joined the channel
2019-12-05
Braydon Meyer (00:31:54): > @Braydon Meyer has joined the channel
Ramon Vidal (04:31:50): > @Ramon Vidal has joined the channel
Somesh (04:53:51): > @Somesh has joined the channel
Camille BONAMY (05:43:04): > @Camille BONAMY has joined the channel
Juan Ojeda-Garcia (11:11:13): > @Juan Ojeda-Garcia has joined the channel
Mark Armstrong (17:36:25): > @Mark Armstrong has joined the channel
Avani Bhojwani (22:16:08): > @Avani Bhojwani has joined the channel
2019-12-06
Mx (12:48:05): > @Mx has joined the channel
Anahi Canedo Texon (19:45:14): > @Anahi Canedo Texon has joined the channel
BDAS (22:44:33): > @BDAS has joined the channel
2019-12-07
Goutham Atla (22:02:10): > @Goutham Atla has joined the channel
2019-12-09
Mireia Ramos-Rodríguez (04:26:44): > @Mireia Ramos-Rodríguez has joined the channel
Olly Crook (04:27:55): > @Olly Crook has joined the channel
Nathalie Pochet (05:43:57): > @Nathalie Pochet has joined the channel
Christine Choirat (07:51:38): > @Christine Choirat has joined the channel
Tobias Bønnelykke (08:13:36): > @Tobias Bønnelykke has joined the channel
Ino de Bruijn (11:23:52): > @Ino de Bruijn has joined the channel
Jovana Maksimovic (23:42:26): > @Jovana Maksimovic has joined the channel
2019-12-10
Griet Laenen (05:39:05): > @Griet Laenen has joined the channel
Jeroen Gilis (05:39:11): > @Jeroen Gilis has joined the channel
Chris Vanderaa (05:40:26): > @Chris Vanderaa has joined the channel
Sergi Sayols (08:02:36): > @Sergi Sayols has joined the channel
tpadayachee (08:14:46): > @tpadayachee has joined the channel
KfJan (10:27:18): > @KfJan has joined the channel
Chong Tang (10:58:29): > @Chong Tang has joined the channel
Katharina Hembach (11:11:59): > @Katharina Hembach has joined the channel
Elisabetta Mereu (11:18:29): > @Elisabetta Mereu has joined the channel
Sebastian Gibb (12:05:40): > @Sebastian Gibb has joined the channel
Tobias Kockmann (16:20:00): > @Tobias Kockmann has joined the channel
2019-12-11
Milan Malfait (02:23:14): > @Milan Malfait has joined the channel
Dania Machlab (05:00:30): > @Dania Machlab has joined the channel
Andrea Rau (09:10:14): > @Andrea Rau has joined the channel
2019-12-12
Emma Jablonski (04:08:12): > @Emma Jablonski has joined the channel
zx8754 (08:48:48): > @zx8754 has joined the channel
Tomas Rube (12:33:46): > @Tomas Rube has joined the channel
Leonardo Collado Torres (13:58:01): > https://twitter.com/WrightingApril/status/1205138024952188929 - Attachment (twitter): Attachment > I didn’t realize how bad Slack’s new markdown editor toolbar thingy is. Borderline unusable for code! Here’s how to disable it https://pbs.twimg.com/media/ELmCpPYXYAA9DwD.jpg
Stephanie Hicks (14:09:10): > Oh wow I’m glad that’s not just me
Stephanie Hicks (14:09:12): > Thanks!
2019-12-13
Teun van den Brand (14:18:25): > @Teun van den Brand has joined the channel
2019-12-15
yue you (18:57:20): > @yue you has joined the channel
Baofeng (22:51:29): > @Baofeng has joined the channel
2019-12-16
Pablo Rodriguez (04:03:30): > @Pablo Rodriguez has joined the channel
Federico Agostinis (09:16:21): > @Federico Agostinis has joined the channel
Alexander Pico (20:13:15): > @Alexander Pico has joined the channel
Ellis Patrick (23:17:53): > @Ellis Patrick has joined the channel
2019-12-17
Jean Yang (02:39:00): > @Jean Yang has joined the channel
Sean Davis (12:14:44): > https://nanx.me/blog/post/tidycwl-biocompute/ - Attachment (Nan Xiao | 肖楠): New Packages on CRAN: tidycwl and biocompute > An overview of the new R packages: tidycwl and biocompute
Jialin Ma (21:41:57): > @Jialin Ma has joined the channel
2019-12-18
Shubham Gupta (11:19:23): > @Shubham Gupta has joined the channel
Nick Canete (19:29:49): > @Nick Canete has joined the channel
2019-12-19
Paul Harrison (20:13:09): > @Paul Harrison has joined the channel
2019-12-20
Aaron Lun (20:49:39): > Really loving the new base colors. They’re definitely a step above.
2019-12-21
Mikhael Manurung (08:14:02): > Is there anyone who learned R in RStudio and then moved to other text-editors/IDEs such as emacs-ess? What pushed you over the edge to finally change and do you regret the move? Asking for a friend…
2019-12-22
Sara Fonseca Costa (15:57:34): > @Sara Fonseca Costa has joined the channel
Simina Boca (23:49:20): > Oh man, I confess that I moved the other way around…
Simina Boca (23:50:03): > I was using emacs-ess before RStudio, then once I got used to RStudio, emacs seemed unnecessary (I know it’s a lifestyle for some people, it wasn’t for me though)
Aaron Lun (23:53:48): > I’m just gonna say that VIM rhymes with WIN.
2019-12-23
Jared Andrews (00:01:25): > I do most R stuff in jupyter lab now. Mostly just because the ability to have multiple kernels in the same document works better out of the box than it seems to with R markdown docs. Definitely so on Windows. Still do all package dev in R Studio though, inspector is too valuable and I’ve yet to find a great one for Jupyter yet.
Hervé Pagès (01:10:34): > @Aaron LunCan’t believe people are still using vim. Feels good to know I’m not the only one and that it rhymes with WIN. LOL!
Waleed Osman (10:26:01): > @Waleed Osman has joined the channel
dylan (10:33:35): > @dylan has joined the channel
Naim Rashid (10:37:46): > @Naim Rashid has joined the channel
George Carvalho (11:16:57): > @George Carvalho has joined the channel
Kozo Nishida (16:04:26): > @Kozo Nishida has joined the channel
GuandongShang (23:59:14): > @GuandongShang has joined the channel
2019-12-24
Mikhael Manurung (04:02:47) (in thread): > Vim keybindings = magic
Wendy Wong (10:06:59): > @Wendy Wong has joined the channel
Marcel Ramos Pérez (11:50:09): > I went fromfile.edit()in the R GUI to Tmux - Vim to RStudio and now back to Tmux - Vim. RStudio has been having issues with R-devel lately:disappointed:RStudio has a lot of convenient shortcuts for package development
Sean Davis (12:19:55): > I’m equally emacs/ess and Rstudio, with a smattering of jupyter which I find particularly useful for teaching materials.
Mikhael Manurung (12:28:18) (in thread): > Any particular reason why you’re using both?
Nitesh Turaga (12:31:40): > For some reason, I find Jupyter notebooks easier to follow when thinking about the code + text mix (literate programming). It doesn’t seem like Rmarkdown allows that as seamlessly. > > But for the most part I too use emacs/ess for R.
Mikhael Manurung (12:40:44): > Any resource that you’d recommend to get started running R on emacs? I tried spacemacs, which was said to be well configured for beginners, but I still find it difficult. I really miss Ctrl+Enter in RStudio to run the current line…
Mikhael Manurung (12:43:53) (in thread): > For small tasks, emacs would be an overkill for sure!! However, I want to be, for the very least, proficient enough with emacs so that I can compare the experience in using the two platforms.
kipper fletez-brant (19:38:10) (in thread): > Vanilla emacs +better-defaults+ess?
2019-12-25
Keith Hughitt (01:31:01): > @Keith Hughitt has joined the channel
Aaron Lun (02:50:21): > https://stackoverflow.blog/2019/12/23/a-holiday-carol-for-coders/?cb=1 - Attachment (Stack Overflow Blog): A holiday carol for coders - Stack Overflow Blog > A holiday tale to warm a coder’s heart and remind ourselves what is valuable this season.
Aaron Lun (02:52:47): > the more I read it, the closer to home it got.
Aaron Lun (02:53:07): > And with that, I’m going to sleep.
Hervé Pagès (15:20:26): > > And with that, I’m going to sleep
Hervé Pagès (15:20:39): > for 3 days! Ha ha
Aaron Lun (21:16:19): > Well, I would if not for this reminder to review a MS.
Aaron Lun (21:17:00): > Some unfortunate soul is going to get a particularly grumpy review.
Aaron Lun (21:17:02): > Ho ho ho.
2019-12-30
Vahid (11:52:11): > @Vahid has joined the channel
2019-12-31
Matt Brauer (00:11:10) (in thread): > https://www.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.”
Wenhong Hou (04:46:53): > @Wenhong Hou has joined the channel
Sean Davis (09:59:43) (in thread): > Emacs is my go-to editor for other languages, so it is natural for me to use with R. In addition, git/github support is better with emacs and remote editing support in emacs is excellent. Rstudio has lots of nice R/datasci features that are harder to achieve in emacs.
Sean Davis (10:00:48) (in thread): > The emacs ein package for interacting with jupyter notebooks is really spectacular.
Sean Davis (11:44:38) (in thread): > And reference card for ess:https://ess.r-project.org/refcard.pdf
Sean Davis (11:46:11) (in thread): > I’d add polymode as well:https://github.com/polymode/polymode
Aaron Lun (22:51:32): > alright last peer review of the year is done!
Aaron Lun (22:51:39): > time to party
2020-01-01
Aaron Lun (03:10:34): > Right, back to writing unit tests.
Mikhael Manurung (23:59:34) (in thread): > Thanks! After trying out various emacs distributions, which was said to ease the pain of moving into emacs, I decided to try out vanilla emacs first! Now I understand why people says that hell is other people’s emacs setup.
2020-01-05
Steve (00:03:01): > @Steve has joined the channel
2020-01-06
Guangchuang Yu (06:31:35): > https://guangchuangyu.github.io/pkgdocs/plotbb.htmlgrammar of graphic for base plot :) - Attachment (guangchuangyu.github.io): 1 Grammar of Graphics for base plot | Documents for my packages > 1 Grammar of Graphics for base plot | Documents for my packages
2020-01-08
Erica Feick (06:44:11): > @Erica Feick has joined the channel
bransell (23:33:21): > @bransell has joined the channel
2020-01-10
Eoghann White (05:20:52): > @Eoghann White has joined the channel
MarioMessih (10:51:20): > @MarioMessih has joined the channel
Sean Davis (21:08:00): > https://www.biorxiv.org/content/10.1101/2020.01.10.897116v1.abstract
Dario Strbenac (22:00:07): > It’s an interesting topic. Comprehensive Evaluation of Transcriptome-based Cell-type Quantification Methods for Immuno-oncologyhttps://academic.oup.com/bioinformatics/article/35/14/i436/5529146is a good journal article to read before reading the pre-print.
2020-01-11
Sean Davis (07:38:48): > Thanks,@Dario Strbenac
Matthieu Miossec (17:16:49): > @Matthieu Miossec has joined the channel
2020-01-12
Talha (11:25:33): > @Talha has joined the channel
2020-01-13
Jialin Ma (15:46:27): > @Jialin Ma has joined the channel
2020-01-14
olga tsiouri (17:35:46): > @olga tsiouri has joined the channel
2020-01-15
Astrid Deschenes (13:21:12): > @Astrid Deschenes has joined the channel
2020-01-16
Nitin Sharma (07:14:52): > @Nitin Sharma has joined the channel
2020-01-17
Mohsen (12:29:23): > @Mohsen has joined the channel
Ahmet Kurdoglu (13:54:46): > @Ahmet Kurdoglu has joined the channel
Sara Stankiewicz (15:31:30): > @Sara Stankiewicz has joined the channel
Sara Ballouz (19:08:27): > @Sara Ballouz has joined the channel
2020-01-19
Aaron Lun (04:12:42): > reading the actix-web fallout, pretty crazy stuff.
David Humphreys (20:18:48): > @David Humphreys has joined the channel
2020-01-20
Kevin Rue-Albrecht (06:15:08): > Nice read:https://blog.burntsushi.net/foss/Came across this, which I imagine applies to a lot of us > * https://github.com/BurntSushi/ripgrep/blob/master/FAQ.md#release - Attachment (blog.burntsushi.net): My FOSS Story - Andrew Gallant’s Blog > I blog mostly about my own programming projects.
Aaron Lun (14:00:16): > > I spent this time gifting this user some software, but they can’t even read the README before filing a bug report? > YES.
2020-01-25
Daniel Huebschmann (14:10:56): > @Daniel Huebschmann has left the channel
2020-01-27
Marina Nikolova (13:06:32): > @Marina Nikolova has joined the channel
Barbara Hilzinger (14:24:39): > @Barbara Hilzinger has joined the channel
2020-01-28
Aaron Lun (00:23:18): > Man, I was promised a flame war about DataFrames and tibbles and data.frames, but instead I look on#generaland what do I get?
Aaron Lun (00:23:41): > Polite, civil discussion with patient explanations and consensus reached from different viewpoints.
Aaron Lun (00:23:57): > Disgusting. Not even any ad hominem attacks.
Aaron Lun (00:24:54): > We just can’t have that, so let’s get a real flame war started right here.
Aaron Lun (00:25:21): > So, what about those C programmers, right? Macros… I mean, seriously.
Aaron Lun (00:26:12): > Now, C++, that’s a real programming language.
hcorrada (06:01:08): > Have you used rust?
Hervé Pagès (13:01:53): > Yes Andrew Gallant (aka BurntSushi) implemented ripgrep in Rust and he claims that ripgrep is “faster than anything else” thanks to Rust’s regex engine (see@Kevin Rue-Albrecht’s link above). That also made me curious about Rust. According to a recent Stack Overflow survey it’s also the most loved programming language.
Aaron Lun (13:03:42): > > According to a recent Stack Overflow survey it’s also the most loved programming language. > Well, I’m sure someone also said that about Java at some point in history.
Hervé Pagès (13:04:33): > or about C++:grin:
Aaron Lun (13:10:42): > I’m not sure I would ever say I love C++.
Aaron Lun (13:10:57): > Like a long marriage, I would say that it’s more of a grudging acceptance.
Kasper D. Hansen (13:22:57): > @Aaron Lun’s acquaintances need to spend more time on the internet, if they consider that a flame war
Hervé Pagès (13:27:57): > e.g. they could start by checking this onehttp://harmful.cat-v.org/software/c++/linus
Aaron Lun (16:07:12): > I mean, with all the macros in C, you might as well be “programming” in Excel.
Hervé Pagès (16:35:41): > ha ha, nice try
Artem Sokolov (16:45:47): > Linus Torvalds must be fun at parties.
Artem Sokolov (16:46:16): > (There’s your ad hominem,@Aaron Lun)
Rob Patro (21:46:21): > Rust is pretty awesome … from the PL geek perspective. Also, the compiler is amazing and the error messages make me realize how behind-the-times modern C++ compilers are with respect to interfacing with the developer.
sangsookim (22:31:55): > @sangsookim has joined the channel
2020-01-29
Aaron Lun (00:36:23): > I dunno, that actix-web stuff got pretty crazy at the end.
Hervé Pagès (02:08:22): > but hey at least those guys know how to get into a real~shitstorm~flame war
Aaron Lun (02:19:04): > yes, that’s true.
Alan O’C (03:36:59): > > Well, I’m sure someone also said that about Java at some point in history. > I think the only people who truly love Java are middle managers. Although it’s at least less likely to end up with genuinely bad code (race conditions, memory leaks) than C++
hcorrada (06:54:39) (in thread): > It said ‘unsafe’ right there on the source!
Rob Patro (09:02:24) (in thread): > :rolling_on_the_floor_laughing:
Sean Davis (12:21:49) (in thread): > I’ve recently tried my hand at Rust as well and found it remarkably nice to work with. I only scratched the surface, of course, but the experience was enough to allay fears of perhaps using it for something useful down the road.
2020-01-30
Aaron Lun (03:10:31): > Kids these days, sheesh, don’t even have to manage their own memory.
Aaron Lun (03:10:53): > Can one even call themselves a programmer if they don’t have to debug segfaults?
Aaron Lun (03:11:54): > The sweet music of the0x00000000lines spewing out on your console
Aaron Lun (03:12:13): > The excitement of watching your code to see if it emits aSegmentation fault: core dumped
Aaron Lun (03:12:24): > They don’t know what they’re missing out on.
Aaron Lun (03:14:47): > Oh, and of course, let’s not forget the pleasure of rewriting a function to make use of CPU intrinsics, and then realizing that the cluster nodes don’t use a CPU that actually supports those intrinsics, resulting in the lovelyIllegal instructionerror.
hcorrada (06:53:28): > You can take solace in the fact that 20 years from now they will be berating their kids for not dealing withsecond mutable borrow occurs here
Kevin Rue-Albrecht (11:10:15): > https://github.com/wesbos/dad-jokes > > Unfortunately these jokes only work if you git them.
Aaron Lun (11:35:52): > oh, some of these are absolute gems
2020-01-31
Santosh Philips (14:07:32): > @Santosh Philips has joined the channel
2020-02-01
Sam Fisher (11:38:50): > @Sam Fisher has joined the channel
2020-02-03
Jen Cannon (13:02:20): > @Jen Cannon has joined the channel
2020-02-04
Matt N Tran (08:24:28): > @Matt N Tran has joined the channel
Nils Eling (08:35:13): > @Nils Eling has joined the channel
2020-02-05
Mariela (05:11:44): > @Mariela has joined the channel
Will Macnair (06:35:03): > @Will Macnair has joined the channel
Hassan DAKIK (23:26:47): > @Hassan DAKIK has joined the channel
2020-02-06
Jin Choul Chai (13:26:14): > @Jin Choul Chai has joined the channel
cakapourani (16:36:14): > @cakapourani has joined the channel
2020-02-08
Tomasz Kujawa (07:49:31): > @Tomasz Kujawa has joined the channel
Thanh Le Viet (16:36:19): > @Thanh Le Viet has joined the channel
2020-02-09
Dario Strbenac (22:35:23): > Can anyone recommend a good way to use normal/tumour RNA sequencing data to filter somatic variant calls from normal/tumour DNA sequencing data and also, I suppose, from germline calls? Or describe the frustration you had before giving up? If you don’t make use of RNA data to filter, you label every variant like Missense, Nonsense, etc. even though only a subset of genes are expressed in each tissue type (e.g. you’re analysing melanoma but you label variants in heart-specific genes as Missense). But, using RNA data, you could filter out important variants such as Nonsense, that are degraded by Nonsense Mediated Decay (I’ve seen a couple of examples in TP53 where the RNA has 0 reads containing the SNV), because the absence of reads with the SNV is support for its presence and action, which is the opposite of categories such as Missense. Then, there is the issue of whether the RNA sequencing is deep enough or undersampled, which is not so important for identifying the most differentially expressed genes, which is the main use case of the data set, but important for SNV calling.
Stuart Lee (22:52:30) (in thread): > @Anna Quaglierimight be helpful here, she has a preprint on RNA-seq variant callinghttps://www.biorxiv.org/content/10.1101/2019.12.18.881870v2.full
2020-02-10
Ariel Hippen (14:21:40): > @Ariel Hippen has joined the channel
Sofie Dam Nielsen (16:44:38): > @Sofie Dam Nielsen has joined the channel
Dario Strbenac (20:00:06) (in thread): > Thanks, but I have a slight twist in my case. The collaborators are also wanting to detect Stop Gained mutations, which have a SNP in DNA data but not in RNA data because of nonsense-mediated decay degrading those transcripts and them not being RNA sequenced. It seems weird that it would biologically exist (how can the cell tell when a transcript has a premature stop codon compared to a normal position stop codon? The cell doesn’t use ENSEMBL Variant Effect Predictor like I do!), but I have seen a couple of examples with IGV in TP53 and everyone gets mad when deleterious TP53 variants aren’t reported to them. Also, this data is total RNA-seq, which catches a broader variety of transcripts (I bet you never heard of RN7SL1 / RN7SL2 genes; one sample has 22 million reads out of 44 million total originating from it:face_with_rolling_eyes:Compositional data analysis, eh?) and a lot of intronic reads. It’s a good PhD topic for her and I hope she enjoys it and finds some good solutions for the research community!
2020-02-11
Julien Roux (03:38:43): > @Julien Roux has joined the channel
Florian Geier (03:43:36): > @Florian Geier has joined the channel
Theresa Alexander (15:29:12): > @Theresa Alexander has joined the channel
Sean Davis (15:33:09): > Text Mining and Natural Language Processing SIG presents: > > Speaker:**** Lars Juhl JensenDate: February 13, 2020, at 11am-12pmLocation:**** Building 38A Visitor Center, 1st FloorWebEx: WebEx information is provided belowMedical data and text mining: Linking diseases, drugs, and adverse reactions*****Abstract: > Clinical data describing the phenotypes and treatment of patients is an underused data source that has much greater research potential than is currently realized. Mining of electronic health records (EHRs) has the potential for revealing unknown disease correlations and for improving post-approval monitoring of drugs for adverse drug reactions. > > In my presentation I will introduce the centralized Danish health registries and show how we use them for identification of temporal disease correlations and discovery of common diagnosis trajectories of patients. I will also describe how we use text mining of the clinical narrative from Danish electronic health records and use this for identification of new adverse reactions of drugs and drug combinations from data on 1.5 million inpatients. > > The same text-mining tools are also used in the STRING protein interaction database and related databases, which will be the topic of a separate presentation at NIH on April 28th.About:Lars Juhl Jensen started his research career in Søren Brunak’s group at the Technical University of Denmark (DTU), from where he in 2002 received the Ph.D. degree in bioinformatics for his work on non-homology-based protein function prediction. During this time, he also developed methods for visualization of microbial genomes, pattern recognition in promoter regions, and microarray analysis. From 2003 to 2008, he was at the European Molecular Biology Laboratory (EMBL) where he worked on literature mining, integration of large-scale experimental datasets, and analysis of biological interaction networks. Since 2009, he has continued this line of research as a professor at the Novo Nordisk Foundation Center for Protein Research at the Panum Institute in Copenhagen and as a founder, owner and scientific advisor of Intomics A/S. He is a co-author of more than 200 scientific publications that have in total received more than 30,000 citations. He was awarded the Lundbeck Foundation Talent Prize in 2003, his work on cell-cycle research was named “Break-through of the Year” in 2006 by the magazine Ingeniøren, his work on text mining won the first prize in the “Elsevier Grand Challenge: Knowledge Enhancement in the Life Sciences” in 2009, and he was awarded the Lundbeck Foundation Prize for Young Scientists in 2010.Join WebEx meeting***Meeting Link :https://nih.webex.com/nih/j.php?MTID=m1308efb6cd07a00721c8624b49667f59Meeting Number (access code) : 621 918 729 > > Meeting Password : YQxA7sAa76Q
2020-02-14
Ines de Santiago (04:42:46): > @Ines de Santiago has joined the channel
Andrew Skelton (05:02:29): > @Andrew Skelton has joined the channel
Wenjing Ma (11:31:31): > @Wenjing Ma has joined the channel
Daniel Newhouse (12:01:51): > @Daniel Newhouse has joined the channel
Aaron Lun (13:04:00): > We should name our BioC releases.
Aaron Lun (13:12:44): > I would say after pokemon, but that could get legally problematic.
Aaron Lun (13:13:21): > I guess we could go after famous composers.
Aaron Lun (13:13:46): > Those guys are probably public domain by now.
Arshi Arora (13:13:55): > @Arshi Arora has joined the channel
FelixErnst (13:33:15): > Pokemon. Thats a healthy list of names I guess. Right’s issues aside: Silmarillion characters?
Federico Marini (14:51:33): > Tokay and malbec are… wine sorts?
Federico Marini (14:51:50): > Merida is not AFAIK, so there is another pattern
Federico Marini (14:52:07): > What about coffee pure sorts - mono-origin ones?
Federico Marini (14:52:57): > https://en.wikipedia.org/wiki/List_of_coffee_varieties - Attachment: List of coffee varieties > Coffee varieties are the diverse subspecies derived through selective breeding or natural selection of coffee plants. While there is tremendous variability encountered in both wild and cultivated coffee plants, there are a few varieties and cultivars that are commercially important due to various unique and inherent traits such as disease resistance and fruit yield. These unique traits are what producers use to select breeds when developing crops. Therefore, at a micro level, breed selection is critical to the success of a producer and is one of the key components of cup quality.At a macro level, the viability of the coffee industry as a whole is dependent upon breed selection. Already, the majority of coffee produced originates from producers using selected breeds. For this reason, breed selection is an important aspect of sustainability within coffee production.
Nicholas Cooley (14:53:14): > Could parrot R itself and go with Family Circus or Calvin and Hobbes quotes.
Federico Marini (14:54:11): > Ohyeah C&H:slightly_smiling_face:
Nicholas Cooley (14:55:33): > What happens when we can’t grow coffee anymore after climate change?
Federico Marini (15:06:44): > We would at least have nostalgic thoughts via Bioc releases
Paula Beati (15:13:34): > @Paula Beati has joined the channel
Jared Andrews (15:26:26): > People realizing coffee would be one of the first crops to go may motivate them to actually support environmental science.
Aaron Lun (15:27:16): > I’m more of a tea guy, but I guess coffee is a decent naming scheme.
Federico Marini (15:27:28): > :thumbsup:
Jared Andrews (15:30:32): > Highly support coffee.
Kasper D. Hansen (16:02:24): > I’m upvoting Calvin and Hobbes
Ines de Santiago (16:19:46): > Olá
Ines de Santiago (16:20:04): > How come I only realised there was a slack channel for bioconductor now?
Ines de Santiago (16:20:20): > :sweat_smile::zany_face::zany_face:
Aaron Lun (16:22:18): > :konata:
2020-02-15
Kevin Rue-Albrecht (04:36:33): > Coffee’s nice. Though you’d think that with all the cell types curated so far, there’d be plenty enough to make stuff like “activated monocytes”, “migrating neurons”, “apoptotic neutrophils”, …
Kevin Rue-Albrecht (04:37:31): > hell, you could throw in “empty droplets” too:stuck_out_tongue:
Dario Righelli (05:50:53): > I do really like the coffee names idea, but maybe biological/“cell types” like names are more suited. > Think about ATP and the “mithocondrion” release!:stuck_out_tongue_closed_eyes:
Christian Brueffer (07:57:58): > @Christian Brueffer has joined the channel
Aaron Lun (14:42:26): > Problem with cell type naming is that it is too close to the actual business of BioC; for example, SingleR conversations could get pretty weird if we need to distinguish between the “BioC release cell type” and “actual cell type”. Coffee is probably much more divorced from any real scientific conversations, for most of us anyway.
Aaron Lun (14:42:57): > Though I am more of a tea person.
Kevin Rue-Albrecht (15:10:18): > I have to say that it’d be a bit refreshing if release names were something not directly related to work. I was (mostly) teasing.
Kevin Rue-Albrecht (15:11:15): > That said, I doubt we’d have much of that happening in random conversations > > Oh maann, the prediction of peritoneal macrophages was sooooo off incardiac myocyte
Kevin Rue-Albrecht (15:11:26): > :stuck_out_tongue:
2020-02-16
Anna Quaglieri (00:31:52) (in thread): > Thanks@Stuart Leefor the mention! I have already had an email exchange with@Dario Strbenacabout a related problem. As I mentioned in my email, I haven’t worked with total RNA-Seq as also TCGA (which has loads of matched tumour/normal DNA/RNA had only polyA, at least for the LAML dataset that I used). Regarding your first question, is this what you mean? 1) You would like to find a better way to classify somatic mutations detected from tumour/normal DNA and 2) you would like to make use of matched RNA to inform you about nonsense mediated decay.
Dario Strbenac (01:30:06) (in thread): > That’s right; TCGA didn’t use total RNA protocol. Yes, we are considering how to use DNA and RNA to categorise variants better.
Federico Marini (09:28:14): > “Guess what a cool finding I just made it with the Kopi Luvak release”
Upasna Srivastava (19:32:28): > @Upasna Srivastava has joined the channel
2020-02-17
Henrik Bengtsson (11:56:37): > @Henrik Bengtsson has joined the channel
2020-02-18
bharati mathur (08:40:53): > @bharati mathur has joined the channel
2020-02-19
Marc RJ Carlson (14:06:28): > @Marc RJ Carlson has joined the channel
Shwetha Hara (14:09:14): > @Shwetha Hara has joined the channel
Márick Starick (22:15:08): > @Márick Starick has joined the channel
2020-02-21
Nathan Johnson (07:12:18): > @Nathan Johnson has joined the channel
2020-02-22
Sean Davis (12:44:26): > https://seandavi.github.io/post/protect-against-secrets-in-git-repositories/ - Attachment (seandavi(s12)): Protect Against Secrets in Git Repositories | seandavi(s12) > I recently got burned by inadvertently committing secrets to a github repository. This post just outlines one potential solution to avoiding repeating that experience.
Alan O’C (13:55:10) (in thread): > Thanks for sharing,git secretsseems a good solution. I tend to store secrets in~/.bash_secretswhich is sourced from my version-controlled~/.bashrcbut not stored in that repo. These are fairly low-priority secrets though, and not anything likely to cost me substantial amounts of money.
Stuart Lee (20:56:26): > has anyone tried moving away from travis to using github actions for a bioconductor package?
2020-02-23
Charlotte Soneson (02:05:39): > @Stuart Lee- yes; not a Bioconductor package in itself, but a package with some Bioconductor dependencies:https://github.com/csoneson/dreval. Also keep an eye onhttps://github.com/seandavi/BiocActionsfrom@Sean Davis,@Vince Carey,@Lorena Pantano
Sean Davis (09:58:05): > Specifically, take a look at:https://github.com/seandavi/BiocActions/blob/master/.github/workflows/main.yml
Sean Davis (09:59:23): > And some other examples (would need to be relocated in the package to run)https://github.com/seandavi/BiocActions/tree/master/inst/actions
Stuart Lee (18:16:36): > thanks@Sean Davisand@Charlotte Soneson!
2020-02-24
Leonardo Collado Torres (09:18:31) (in thread): > ohhh! nice:smiley:
Lei Yang (15:14:09): > @Lei Yang has joined the channel
Jiahao Huang (16:12:20): > @Jiahao Huang has joined the channel
2020-02-25
Andrew Erickson (11:32:35): > @Andrew Erickson has joined the channel
2020-02-26
Steffen Neumann (07:23:24): > Crap, I was too late for the programming language discussions, only saw them now.
Steffen Neumann (07:23:37): > Realprogrammers usecat >a.out
Steffen Neumann (07:27:23): > And here some docs an what bytes you really need for “Hello World”:https://www.muppetlabs.com/~breadbox/software/tiny/teensy.html
Jamie Burke (15:42:45): > @Jamie Burke has joined the channel
2020-02-27
Hervé Pagès (01:38:38) (in thread): > Size of executables… pffff!! Who cares these days. Reminds me of the 80’s when I was trying to squeeze my amazing mastermind program in <= 50 instructions to make it fit in my TI-57 (my 1st programmable toy, was love at first sight:nerd_face:). > Interesting reading BTW. Learned a few things. Also this is excellent technical writing.
Marijne (02:17:18): > @Marijne has joined the channel
Yi Wang (13:52:41): > @Yi Wang has joined the channel
Richard Straub (20:07:34): > @Richard Straub has joined the channel
2020-03-01
sibting (13:37:26): > @sibting has joined the channel
ImranF (13:39:11): > @ImranF has joined the channel
2020-03-03
Sean Davis (22:00:07): > https://www.biorxiv.org/content/10.1101/2020.02.02.930578v2
Aaron Lun (22:41:25): > Well, I guess scran doesn’t do too badly.
Aaron Lun (22:41:49): > I mean, Figure 11 would be easier to implement if Seurat just used a S(C)E object like the rest of us.
Aaron Lun (22:42:14): > Or at least just an SE object.sigh
Aaron Lun (23:02:36): > The final recommendations are interesting because I’ve been trying to go in the opposite direction w.r.t. the complexity of the analysis; just cutting out any steps that don’t provide an clear benefit. I’ve managed to boil down the essential bits to: > * QC, using the MAD approach. Could also use hard thresholds but I don’t want to have to think. > * Log-normalize with the library size. Known problems but it won’t do anything misleading. > * HVGs, and just take X genes. Just iterate until you get something you can work with. > * PCA, and just take X PCs. Again, just iterate. > * Clustering, with whatever algorithm one might like to use. Again, just iterate. > I would hack off HVGs if I could, but I need it to run the PCA in reasonable time.
Aaron Lun (23:03:42): > DEFINITELY NO IMPUTATION.
2020-03-04
Aaron Lun (00:21:02): > I will say, though, their conflict of interest statement is cute.
Aaron Lun (00:22:11): > If that’s the standard, I can’t think of a single paper that I’ve written where I wasn’t conflicted.
Hervé Pagès (00:28:46): > So all your papers are benchmarking studies where you have a horse in the race?
Aaron Lun (00:29:54): > Where all the other horses have been drugged or otherwise incapacitated.
Aaron Lun (00:31:00): > The reviewers get what the reviewers ask for!:slightly_smiling_face:
Aaron Lun (00:32:48): > > The authors should show that their method performs better than other methods. > As a reviewer, I’ve never gotten a response that says, “Actually, our method doesn’t perform as well as other methods, so we decided not to proceed with publishing. Thank you for pointing this out.” Which leads to the interesting conclusion that every method is the best method.
Aaron Lun (00:33:56): > Which is also why I don’t review papers any more, thus giving me more time to watch Halo 5 killstreak videos. About as productive, but more enjoyable.
Aaron Lun (00:49:39) (in thread): > Certainly, ever since I decided not to review papers, I’ve been feeling a lot better.
Hervé Pagès (00:54:33) (in thread): > If you change your mind and miss reviewing stuff, let us know and we’ll assign you some package submissions:wink:
Aaron Lun (00:58:16) (in thread): > Well, at least there I know that everyone’s doing it for free. What’s particularly galling about academic publishing is that someone else is making all the money while I’m doing all the work.
Aaron Lun (00:59:51) (in thread): > My aunt is a journalist and she was shocked that we wrote the content AND paid for it to be published. She said “you know, Aaron, usually it’s the other way around”. Then she made a comment about how a bunch of smart people could come up with such a stupid system. I didn’t have much I could say back.
Aaron Lun (01:00:25) (in thread): > Forgot the air quotes she put around “smart”.
Jared Andrews (10:37:38) (in thread): > Kill paper publications, force everyone to publish as Rmd/jupyter vignettes showing how all data is analyzed and figures made (outside actual experimental figures), and bam, costs are cut and you just have to pay to host a webpage. Would get some semblance of code review, increase reproducibility, and make formatting less annoying (except references). > > And no, I foresee no obvious flaws with said approach at all, it is completely foolproof.
2020-03-05
Pierre-Luc Germain (06:01:20): > @Pierre-Luc Germain has joined the channel
2020-03-06
Mariam Malik (15:37:08): > @Mariam Malik has joined the channel
2020-03-09
David J. Goldstein (09:27:50): > @David J. Goldstein has joined the channel
2020-03-10
Aaron Lun (03:12:18): > Just read the code of conduct: > > intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc.
Aaron Lun (03:12:19): > Well, I guess I’ll have to throw out all my jokes about tidyverse users.
Aaron Lun (03:12:24): > And emacs users.
Aaron Lun (03:12:26): > And Rstudio users.
Aaron Lun (03:12:29): > And C programmers.
Aaron Lun (03:16:16): > I would also say Fortran, but I’m guessing there’s no one left to offend there.
Aaron Lun (03:16:50): > People who use=instead of<-.
Aaron Lun (03:16:55): > AndTandF.
Aaron Lun (03:17:03): > And don’t put a space between theifand the(.
Aaron Lun (03:17:25): > And use two-space indenting instead of four-space indenting.
Aaron Lun (03:17:58): > And doing irritatingly fancy stuff like doing variable assignments inside function calls.
Hervé Pagès (03:30:24): > “There are only two kinds of languages: the ones people complain about and the ones nobody uses.”
Aaron Lun (03:33:43): > I was in fact reading an article on the bus predicting the death of R. But it wasn’t very believable given that it also predicted the death of C. To which I thought “yeah right”.
Aaron Lun (03:34:25): > We’ll all long be dead before the C codebase vanishes.
Hervé Pagès (04:01:07): > MacOS and the Linux kernel would need to die first. My bet is that the Linux kernel will live longer than C++:wink:
Jonathan Carroll (07:35:39): > Hey, I started with Fortran and I can write Fortran in any language now.
Lori Shepherd (09:38:06): > 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
Hervé Pagès (01:41:57): > An interesting side effect of the coronavirus: we’re only on the 10th of the month and we already have 30k downloads (distinct IPs):https://bioconductor.org/packages/stats/bioc/Which suggests we’ll probably get about 90k downloads or so at the end of the month… Crazy!
Aaron Lun (01:43:25): > Yeah, I’m the only one at work. This is great - no lines, no meetings, I can finally get some work done. I think I’ve been at my most productive over the past few days.
Aaron Lun (01:43:39): > And the funny thing is, because no one else is around, I’m probably safer than I would be if I stayed in the city.
Hervé Pagès (01:45:40): > > I can finally get some work done > yeah finally. Never too late:wink:
Aaron Lun (01:46:03): > usually I just talk a lot during meetings and try to look important
Aaron Lun (01:46:40): > like any other hot gas, I aim to expand to fill the available space
Hervé Pagès (01:48:47): > sounds like a good strategy
Aaron Lun (01:48:54): > gotta earn my bonus somehow
Hervé Pagès (01:49:11): > better than falling asleep
Aaron Lun (01:49:46): > sometimes the eyes are open and the mouth is talking but the train has left the station, so to speak.
Hervé Pagès (01:50:05): > amazing skills!
Aaron Lun (01:50:35): > well, what can I say
Aaron Lun (01:50:36): > mike didn’t hire me just for my good looks
Hervé Pagès (01:51:12): > now everything makes sense
ZedaoLiu (01:58:53): > @ZedaoLiu has joined the channel
Hervé Pagès (02:51:16): > Wow Julia is indeed very fast! > R: > > > system.time(for (i in 1:150e6) { if (i [| i ](= 5 ) 150e6 - 5) cat(i, "\n") }) > 1 > 2 > 3 > 4 > 5 > 149999996 > 149999997 > 149999998 > 149999999 > 150000000 > user system elapsed > 5.254 0.000 5.254 > > Python: > > >>> def dumbloop(niter): > ... start = time.time() > ... for i in range(0, niter): > ... if i < 5 or i >= niter - 5: > ... print(i) > ... end = time.time() > ... print("ellapsed: ", end - start) > ... > >>> dumbloop(int(150e6)) > 0 > 1 > 2 > 3 > 4 > 149999995 > 149999996 > 149999997 > 149999998 > 149999999 > ellapsed: 10.339980602264404 > > Julia: > > julia> @time for i=1:150000000 if i [| i ](= 5 ) 150000000 - 5 println(i) end end > 1 > 2 > 3 > 4 > 5 > 149999996 > 149999997 > 149999998 > 149999999 > 150000000 > 0.180177 seconds (86 allocations: 2.438 KiB) > > Another big surprise (at least to me) is that this loop is 2x faster in R than in Python!
Aaron Lun (03:03:52): > I blame the printing of zero.
Aaron Lun (03:04:27): > you have to reach all the way to the other end of the keyboard!
Jonathan Carroll (03:14:48): > Is that the first run of the R version or a JIT-compiled run? I get about 2/3 of the runtime after making it a function and running twice. > > Julia is crazy fast. Anyone know of a parallel to BioC in that world? I tried following the BioJulia stuff and it seemed… complex.
Vince Carey (10:27:53): > Jan Vitek of Northeastern U has done some R-Julia comparisons at a recent UseR.https://channel9.msdn.com/Events/useR-international-R-User-conference/useR2016/What-can-R-learn-from-Julia - Attachment (Channel 9): What can R learn from Julia > Julia, like R, is a dynamic language for scientific computing but, unlike R, it was explicitly designed to deliver performance competitive to traditional batch-compiled languages. To achieve this Juli
Hervé Pagès (10:38:23) (in thread): > BioJulia mmh… they’re reusing our biologically incorrect DNA helix:https://biojulia.net/:grin: - Attachment (biojulia.net): BioJulia > The bioinformatics infrastructure for the julia programming language.
Michael Lawrence (11:45:40): > I’m sure that R benchmark benefited from ALTREP’s lazy generation of the sequence, as well as recent scalar optimizations.
Aaron Lun (11:46:53): > python’srangehas been using iterators (I think?) for a while, ever since they dumpedxrange. So it shouldn’t be realizing the entire array either.
Michael Lawrence (12:19:54): > still, there’s a benefit
2020-03-12
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
2020-03-15
Moheb (16:25:22): > @Moheb has joined the channel
2020-03-16
Aaron Lun (01:13:25): > What happened with this rainbow vomit on theDNAString? - File (PNG): Screenshot from 2020-03-15 22-12-36.png
Aaron Lun (01:13:43): > My eyes PHYSICALLY HURT from looking at it.
Aaron Lun (01:26:44): > I’ll also note that this KEGGREST stuff is difficult to use with a limitation of 10 queries.
Aaron Lun (03:00:13): > But anyway - back to the DNAString - just… wow.
Aaron Lun (03:00:30): > I really had to clear my screen, it was just that bad.
Aaron Lun (03:13:51): > I wonder whether it would be better to color the words, rather than the a background.
Dan Bunis (04:09:54): > As a colorblind person, the ACTG would at least need to have been bolded for swapping to coloring the letters for me, but I agree that the background coloring is painful!
Nicholas Cooley (09:46:08): > As another colorblind person, if you colored the words I wouldn’t be able to use it at all.
Alan O’C (09:48:20): > What’s colour even adding? The letter shapes are distinct anyway
Nicholas Cooley (09:49:02): > you can color by patterns or things if you have the code set up correctly.
Nicholas Cooley (09:49:06): > i assume that’s what they’re going for
Nicholas Cooley (09:49:09): > ?
Nicholas Cooley (09:49:49): > how does this look in RStudio? is that where this screenshot is from
Nicholas Cooley (09:49:50): > ?
Alan O’C (09:50:20): > Pretty sure Aaron’s one of us ignorant savages who don’t use RStudio
Alan O’C (09:50:34): > So I assume that’s just a terminal
Alan O’C (09:51:47): > > you can color by patterns > You mean colour particular sub-sequences? That’d be useful. Having colour mapped to base (1-1) is about as useful as a chocolate teapot
Hervé Pagès (12:35:54): > All that matters is that it looks great on MY screen:sunglasses:
2020-03-17
Giuseppe D’Agostino (07:24:13): > @Giuseppe D’Agostino has joined the channel
Hervé Pagès (13:19:55): > Good news for the sensitive and easily grossed out people among us:https://github.com/Bioconductor/Biostrings/commit/bd0da39471bba06add05c2329d0cd5f2de2021f7
Aaron Lun (13:32:44): > oh thank god
Leonardo Collado Torres (21:05:14): > This is tomorrow in case you are interestedhttps://ropensci.org/blog/2020/03/04/commcall-mar2020/ - Attachment (ropensci.org): Community Call - Maintaining an R Package - rOpenSci - open tools for open science > For this Community Call, we’re trying something different. We’ll start with a short talk by Julia Silge, then spend most of the time on Q & A with four panelists - Elin Waring, Erin Grand, Leonardo Collado-Torres, and Scott Chamberlain - moderated by Julia. Our panelists bring a wide range of perspectives so there’s something for everyone. Collectively, they have experience developing and maintaining passion-project packages, very popular packages, too many packages on CRAN, packages on Bioconductor, and taking over maintenance (and changing things!
Aaron Lun (23:28:31): > SF shelter-in-place diary: Day 1. > > Food low. Toilet paper low. All restaurants closed. Send supplies as soon as possible. > SF shelter-in-place diary: Day 2. > > All supplies have been exhausted. No food or liquid has been consumed in the last 24 hours. Send help. > SF shelter-in-place diary: Day 3. > > Can’t get out. Can’t get out. Can’t get out. Can’t get out. Can’t get out. > SF shelter-in-place diary: Day 4. > > THE SPIDERS ARE COMING OUT OF THE WALLS! > SF shelter-in-place diary: Day 5. > > Tell my wife I lo-
2020-03-18
Mike Smith (11:02:41) (in thread): > I’m looking forward to this. I’ve advertised it to our EMBL R mailing list too.
Leonardo Collado Torres (13:21:16) (in thread): > thank you Mike!
Michael Lawrence (17:14:46): > You’re lucky you got out in time. They’re on complete lockdown up there. We’re only shelter-in-place.
Dan Bunis (17:16:55): > Mine: It’s only day two, and I’m not sure if I have enough wine:weary:
Michael Lawrence (17:17:34): > I’ve already started rationing that. Luckily Doordash delivers from Bevmo.
Dan Bunis (17:17:56): > thanks for the tip
2020-03-19
Sean Davis (10:47:17): > https://www.aacr.org/meeting/nih-aacr-immunology-2020/registration/ - Attachment (American Association for Cancer Research (AACR)): Registration | NIH-AACR Cancer, Autoimmunity, and Immunology Conference | AACR Meetings > Registration Deadline: March 16, 2020.
Sean Davis (10:47:50): > I think there may still be open registration for this online only conference.
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
2020-03-24
Jake Wagner (17:09:01): > @Jake Wagner has joined the channel
2020-03-25
brian capaldo (13:02:43): > @brian capaldo has joined the channel
2020-03-26
Tamas Kiss (05:23:49): > @Tamas Kiss has joined the channel
Paula Restrepo (09:27:43): > @Paula Restrepo has joined the channel
Vivek Das (14:09:44): > @Vivek Das has joined the channel
2020-03-27
Hervé Pagès (12:50:50): > Think of the North Sentinel Island people and what they are missing these days. They’ve missed WWI, WWII, India’s independence, The Beattles, and now the COVID-19 pandemic. They chose self-confinement a long time ago so they were ahead of everybody else.
Nicholas Cooley (13:52:54): > But they missed Frozen 2
Carmina Barberena Jonas (16:40:36): > @Carmina Barberena Jonas has joined the channel
2020-03-28
Julieta O’Flaherty (11:44:08): > @Julieta O’Flaherty has joined the channel
2020-03-29
Pavitra Roychoudhury (19:45:56): > @Pavitra Roychoudhury has joined the channel
2020-03-30
Minoo (07:32:13): > @Minoo has joined the channel
Yagoub Ali Ibrahim Adam (08:47:19): > @Yagoub Ali Ibrahim Adam has joined the channel
Susan Holmes (09:48:07): > @Susan Holmes has joined the channel
Steffen Neumann (10:11:19): > Just went waaaay back intosvn logfor R: > > ------------------------------------------------------------------------ > r8409 | pd | 2000-02-29 09:55:23 +0100 (Tue, 29 Feb 2000) | 2 lines > > preparing for release > > which subsequently was burned to CDhttps://twitter.com/joshuawlambert/status/1233897272884285441 - Attachment (twitter): Attachment > @_R_Foundation I’ve seen a copy in the wild! Pretty cool to see one in person. Wish I had my own copy. https://pbs.twimg.com/media/ER-vBmXXkAEdNVA.jpg
USLACKBOT (12:53:53): > This message was deleted.
Alan O’C (12:54:53) (in thread): > https://twitter.com/WhyDoesR/status/1237378077514240001/photo/1 - Attachment (twitter): Attachment > https://pbs.twimg.com/media/ESwMza2XQAM8yAP.png
Sean Davis (12:57:52): > A few of us are collaborating on a#covid19package for accessing, exploring, and analyzing COVID-19 datasets. There are some low-hanging contributions to be made for those interested. For folks tasked with developing educational materials around data science and data exploration, the package offers timely and up-to-date resources.
Kevin Rue-Albrecht (13:06:12): > I’ve put this together myself:https://kevinrue.github.io/COVID-19-website/A bit of educational material here:https://kevinrue.github.io/post/creating-a-dynamic-rmarkdown-website-for-covid-19-data/I update the website daily, automatically pulling the latest data from JHU (git submodule), but development of the website itself is extremely irregular and low on my priority list. - Attachment (Kevin Rue-Albrecht): Creating a dynamic Rmarkdown website for COVID-19 data | Kevin Rue-Albrecht > Overview This post refers to code available online as a GitHub repository. Create a new RStudio project Open the RStudio “New Project…” menu -> New Directory -> Simple R Markdown Website -> Type a folder name. Initialize git You may need to install.packages(“git2r”) first. git2r::init() Also, restart RStudio to apply the changes and benefit of the “Git” tab. Make a new GitHub repository Click on “New repository”.
Benilton S Carvalho (13:37:10): > @Benilton S Carvalho has joined the channel
2020-03-31
Aaron Lun (00:25:51): > Geez, it’s been quiet around here recently.
Aaron Lun (00:26:06): > Time to get another flame war going, I think.
Jared Andrews (04:29:35): > I’ve got some hot takes I can spout to rile people up. In particular about hot beverage choice, how many syllables are in the word “fire”, or whether or not golf is actually a sport. Let me know your preference.
Federico Marini (04:31:10): > Did we let down completely the crusade to have named Bioc releases? Team coffee calling dibs!
Raphaël Bonnet (07:39:47): > @Raphaël Bonnet has joined the channel
Matthew Carlucci (11:51:04): > @Matthew Carlucci has joined the channel
2020-04-02
Duy Pham (04:17:02): > @Duy Pham has joined the channel
2020-04-06
Anna Lorenc (06:40:16): > @Anna Lorenc has joined the channel
Yuzhu Duan (20:24:48): > @Yuzhu Duan has joined the channel
2020-04-09
Ian Williams (13:29:37): > @Ian Williams has joined the channel
2020-04-10
Sherlock_Fan (19:48:02): > @Sherlock_Fan has joined the channel
2020-04-12
Pierre-Luc Germain (03:09:58): > @Pierre-Luc Germain has left the channel
2020-04-13
Zinian Wang (15:12:58): > @Zinian Wang has joined the channel
Lambda Moses (20:15:46): > As I’m working on a review paper on spatial transcriptomics, I realized that MATLAB is still well and alive among biologists, and often the MATLAB repos used for image processing are not well-documented. I’ve only used MATLAB for math and electrical engineering classes, not in research, so I’m not very good at it, but I guess it’s really good for image analysis, which explains why it’s still commonly used for image analysis though there are OpenCV and scikit image. Perhaps it’s the legacy of CellProfiler and friends, which are written in MATLAB. We useRs tend to support open source and reproducible research. What are your opinions about MATLAB? Anyone does not have a MATLAB license provided by their institution or lab? Should MATLAB be replaced by open source alternatives? > > Also, I remember back in rstudio::conf this year, the keynote about RStudio becoming a public benefit corporation mentioned that an advantage of open source is that the availability of the software is not dependent on the existence or permission of a corporation. Now I sort of wonder what if MathWorks goes bankrupt. I mean I think MATLAB is awesome, except for its price tag.
Aaron Lun (20:16:13): > What’s MATLAB?
Lambda Moses (20:16:36): > https://www.mathworks.com/products/matlab.html - Attachment (mathworks.com): MATLAB - MathWorks > The official home of MATLAB software. MATLAB is the easiest and most productive software environment for engineers and scientists. Try, buy, and learn MATLAB.
Aaron Lun (20:16:55): > Yeah, I know, I’m just messing with you.
Aaron Lun (20:18:18): > Only had a brief opportunity to use it once, when fiddling with some spatial transcriptomics data back in 2017. Gave up pretty quickly trying to figure out other people’s scripts - boy, if you think R scripts written by non-computational people are bad, you should have a look at the matlab pile that gets emitted - and also because the CZI’s starfish pipeline development was in full swing, so I just thought I’d use that instead.
Lambda Moses (20:18:46): > Yeah, I’m really bothered by the poor documentation of many such repos for spatial transcriptomics
Lambda Moses (20:18:54): > Or no documentation at all
Dan Bunis (20:23:46): > I don’t have matlab from my school. Not sure how common that is, but I’d assume highly common for non-engineering biological sciences. FWIW, R and Matlab are super similar — to the point where I jumped in to R with basically no need for teaching after having learned Matlab 8 or so years prior in undergrad.
Dan Bunis (20:27:28): > Idk if that perspective helps you for your review at all:man-shrugging:. I sense that you may be considering suggesting they switch from Matlab to R, but maybe you are just contemplating leaving a note about the reduced transparency for Matlab methods?
Lambda Moses (20:29:30): > It’s not for the review; I’m just curious what useRs think of MATLAB.
Aaron Lun (20:32:11): > I think of MATLAB in much the same way that I think of the SF Giants. I know that they’re there and I know vaguely what they’re about (there’s a ball in there somewhere, right?) but I don’t really know or care what they do.
Dan Bunis (20:34:57): > Matlab was my first language, because it’s what Cornell taught (might even still) to biological engineers a decade ago. But R is great and free while Matlab is very expensive, so I don’t see a reason to go back.
2020-04-14
Alan O’C (06:20:05): > I’ve seen Matlab code supplied with a couple of papers but I find it a horrendous experience to write, and yeah it tends to have the same “software written by someone who doesn’t understand software” vibes as a lot of R code, for better or worse. I’d not use it unless there was a specific thing I needed to use, and even then I’d re-implement in another language because I don’t particularly want to have to fight to get a £1,000 pound licence for my computer(s)
Alan O’C (06:20:38): > Although a colleague uses it so I should probably not smack talk it too much:innocent:
Lukas Weber (11:29:04): > I think there are some good image processing libraries in Matlab, which are better than what is available in other languages. And it is also widely used in engineering disciplines. But yeah apart from that, I would also strongly recommend people switch from Matlab to either R or Python, mainly because Matlab is very expensive, and there is no easy way to distribute code/packages
Federico Marini (13:13:33): > Signal processing is also quite strong in there - they have those toolboxes which are in my understanding like nicely curated collection of extensions/“packages” (in the R sense)
Kasper D. Hansen (14:13:28): > The package concept in R is a clear winner for distributing methods.
Federico Marini (15:23:38): > the installation is probably ranked #2
Federico Marini (15:24:25): > Python had the beautiful oxymoron of calling one wayeasy_install:smile:
2020-04-15
Xinran Tian (12:32:31): > @Xinran Tian has joined the channel
Aaron Lun (14:22:56): > Quiet over here.
Jared Andrews (14:24:42): > Anyone read any good books lately?
FelixErnst (14:25:01): > define good
Aaron Lun (14:25:57): > I am going to go back to my cultured Slack channels and put some anime gifs to spice things up.
FelixErnst (14:26:09): > :slightly_smiling_face:
FelixErnst (14:29:16): > Good as in entertaining: I caught up on the reacher series. Good as in something to think about: Roadside Picnic, good as in my happy place: Final watch, new watch and the sixth watch
Aaron Lun (14:29:52): > big fan of iain bank’s culture series.
FelixErnst (14:32:49): > Do you recommend to start at the beginning? Or can I start anywhere?
Aaron Lun (14:34:58): > I started at player of games, and it was fine. Some of them (e.g., inversions) won’t make as much sense without the context.
Aaron Lun (14:35:29): > My favorites are player of games and use of weapons, but the other ones are a good read as well.
Aaron Lun (14:35:40): > Enough of a good read that I almost forgot to do my daily commit.
FelixErnst (14:36:48): > Thx!
Jared Andrews (14:45:42): > Reacher is good, kinda trash, but entertaining. I’ve heard of Iain Bank, will take a look.
Jared Andrews (14:46:03): > Well, not trash, but easy reads, for sure.
FelixErnst (14:49:16): > Definitely
FelixErnst (14:49:40): > Fair accessment:slightly_smiling_face:
FelixErnst (14:49:53): > The last three books I mentioned are from Sergei Lukyanenkos Night watch series. Thats basically middle ground, it starts as good vs. evil and than by the third book (you have to read the second but thats hard to stay focused on) it descends into grays. Thats when things get really good. and third to six get better by each book. Haven’t come across anything similar.
Jared Andrews (14:50:57): > Perfect, will add that to the list.
Ludwig Geistlinger (20:20:18): > Release of R-4.0.0 is scheduled for Friday 2020-04-24, ie it’s not yet released. You can however find pre-release versions here:https://cran.r-project.org/src/base-prerelease/
Stephanie Hicks (21:03:24): > Gave a talk at a local R conference in 2018 with an intro to Bioconductor and highlighted plyranges from@Stuart Lee@Di Cook@Michael Lawrence. Found out today there is a video of it! Sharing here in case it’s useful to anyone.https://m.youtube.com/watch?v=l1MQ7x8cn7Y - Attachment (YouTube): Analyzing Genomics Data in R with Bioconductor
2020-04-16
Modeline Longjohn (00:02:45): > @Modeline Longjohn has joined the channel
Dylan Harwood (09:26:26): > @Dylan Harwood has joined the channel
2020-04-17
Lori Shepherd (13:46:31): > 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 foundherePlease fill out the nomination form by June 15 :Nomination Form
2020-04-21
Pariksheet Nanda (15:59:32) (in thread): > I think it’s called Julia now?:smirk:
2020-04-22
Kelly Eckenrode (09:24:17): > @Kelly Eckenrode has joined the channel
Alex Tong (15:21:03): > @Alex Tong has joined the channel
Lucy (15:29:22): > @Lucy has joined the channel
Christopher Eeles (19:04:41): > @Christopher Eeles has joined the channel
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
Federico Marini (08:56:24) (in thread): > https://twitter.com/astrotoya/status/1253162878477238273?s=20 - Attachment (twitter): Attachment > If you could end COVID-19 by giving up one programming language, which one would it be and why Matlab?
2020-04-24
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
2020-04-28
Minoo (07:09:35): > @Minoo has joined the channel
Anamaria Elek (12:56:54): > @Anamaria Elek has joined the channel
Lori Shepherd (18:51:33): > 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/
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
2020-05-01
Kevin Rue-Albrecht (02:19:14): > … the crucial software too - File (JPEG): Image from iOS
Aaron Lun (02:20:36): > R above 1? We’re already on 4!
Aaron Lun (02:20:46): > It’s just going up and up all the time
Kevin Rue-Albrecht (02:21:42): > I only realise now that world has been all about R the last couple of months
Kevin Rue-Albrecht (02:22:33): > First time I hear people so keen to know about the daily release
michaelkleymn (09:02:05): > @michaelkleymn has joined the channel
2020-05-03
FelixErnst (05:41:09): > Most of us probably think more aboutR0thanReff… I meanReffwas just released, so we are good for 6 months…
Jack Zhao (19:59:34): > @Jack Zhao has joined the channel
2020-05-04
Nils Kurzawa (04:35:36): > @Nils Kurzawa has joined the channel
Nadine Bestard-Cuche (05:38:52): > @Nadine Bestard-Cuche has joined the channel
Zhiyuan Hu (09:06:03): > @Zhiyuan Hu has joined the channel
MarieV (12:19:30): > @MarieV has joined the channel
Sanchit Saini (15:43:52): > @Sanchit Saini has joined the channel
2020-05-05
Hervé Pagès (13:43:25): > Amazing and very promising:https://www.bbc.com/news/health-52530828 - Attachment (BBC News): Malaria ‘completely stopped’ by microbe > Scientists say the microbe - found in the wild near Lake Victoria - has enormous potential.
Jonna Heldrich (15:11:16): > @Jonna Heldrich has joined the channel
2020-05-08
Daniel Piqué (01:19:01): > @Daniel Piqué has joined the channel
Waldir Leoncio (03:28:53): > @Waldir Leoncio has joined the channel
Panagiotis Moulos (03:57:02): > @Panagiotis Moulos has joined the channel
2020-05-11
Eli Miller (11:41:31): > @Eli Miller has joined the channel
Joshua Sodicoff (12:44:53): > @Joshua Sodicoff has joined the channel
Kara Woo (14:13:56): > @Kara Woo has joined the channel
2020-05-12
Kelly (14:05:22): > @Kelly has joined the channel
2020-05-15
jhawe (05:26:26): > @jhawe has joined the channel
B P Kailash (09:33:43): > @B P Kailash has joined the channel
Leonardo Collado Torres (09:47:34): > https://twitter.com/lucystats/status/1261291451884998656?s=21 - Attachment (twitter): Attachment > Are you a woman doing statistics or data science? > > :speaking_head_in_silhouette: Tweet out your work with #WSDS and/or tag @WomenInStat so we can promote it! > > Know a woman doing statistics or data science? > > :speaking_head_in_silhouette: Tweet out their work with #WSDS and/or tag @WomenInStat so we can promote it!
Alos Diallo (21:51:06): > @Alos Diallo has joined the channel
2020-05-17
Huipeng Li (10:44:43): > @Huipeng Li has joined the channel
2020-05-18
Ayush Raman (00:17:42): > @Ayush Raman has joined the channel
Valeria Policastro (06:16:55): > @Valeria Policastro has joined the channel
Katie Hughes (09:04:55): > @Katie Hughes has joined the channel
Anna Evans (09:50:05): > @Anna Evans has joined the channel
Vasant Marur (11:36:32): > @Vasant Marur has joined the channel
2020-05-19
Tobias Hoch (11:15:12): > @Tobias Hoch has joined the channel
2020-05-20
Jesper Maag (13:24:24): > @Jesper Maag has joined the channel
2020-05-22
Riccardo L. Rossi (03:25:45): > @Riccardo L. Rossi has joined the channel
Kaveh Moeini (12:17:15): > @Kaveh Moeini has joined the channel
2020-05-25
Charlotte Soneson (04:31:16): > Don’t forget to nominate (one or several) people that you think deserve recognition for the Bioconductor Awards
- Attachment: Attachment > 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 found here > Please fill out the nomination form by June 15 : Nomination Form
Kevin Rue-Albrecht (09:14:00): > Discover new (and old) packages every day:https://kevinrue.github.io/BiocRoulette/:grin:Accompanied by a brief blog post to illustrate the use of BiocPkgTools and GitHub actions:https://kevinrue.github.io/post/biocpkgtools/ - Attachment (Kevin Rue-Albrecht): BiocPkgTools | Kevin Rue-Albrecht > Motivation There are currently 5,621, broken down as follows: Repository Packages AnnotationData 2,649 ExperimentData 809 Software 2,163 In an effort to motivate myself to keep an eye out for interesting packages - both new and old - I have used the BiocPkgTools package to develop a website updated daily and feature packages selected randomly from each repository.
Fredrik Landfors (16:45:53): > @Fredrik Landfors has joined the channel
Hanjie Shen (18:33:14): > @Hanjie Shen has joined the channel
2020-05-26
Sean Davis (10:18:41) (in thread): > Just tweeted. Great demonstration!
Kevin Rue-Albrecht (10:18:49) (in thread): > Thanks!
Kevin Rue-Albrecht (10:20:36) (in thread): > I also got some feedback about potentially generating an automated tweet every day. I haven’t toyed with that yet - I’ve only ever queriedfromTwitter, but it’s an interesting exercise too :)
chiara romualdi (11:26:06): > @chiara romualdi has joined the channel
Sean Davis (14:43:47) (in thread): > Be careful to read the Twitter terms of service!
Kevin Rue-Albrecht (18:46:05) (in thread): > Thanks. I had a tiny bit of experience about fetching tweets from Twitter to build stats (https://kevinrue.github.io/twitter-stats/Bioc2019.html), but indeed I am more nervous aboutpostingto twitter.
Kevin Rue-Albrecht (18:46:28) (in thread): > For now, I’d rather have people visit the page on my blogdown:slightly_smiling_face:
2020-05-27
Anamaria Elek (06:44:36): > Hello everyone, I would like to exploit this platform to recommend the upcoming series of webinars aimed primarily at people who are starting their journey in bioinformatics - for trainees or wet-lab-turned-computational people it might be a really good crash course in some basic computational literacy with a strong biological flavour - I know I would have liked to have something like this when I first switched pipette for keyboard:slightly_smiling_face:https://twitter.com/NGSchoolEU/status/1265584178869030916 - Attachment (twitter): Attachment > We are excited to invite you to our #programming #workshops focused on #bioinformatics. > No registration required! The streams will be accessible on YouTube :arrow_right: https://bit.ly/3grEKzx > Join our Discord server :arrow_right: https://discord.gg/MhNeqwR > #R #python #linux #snakemake #nextflow https://pbs.twimg.com/media/EZBCGcoXYAAMDML.jpg
Logan Knecht (18:46:40): > @Logan Knecht has joined the channel
Aaron Lun (22:49:31): > They’ve changed all the github Icons!
Aaron Lun (22:49:34): > I’m so confused.
Aaron Lun (22:50:02): > and also physically sick.
2020-05-28
Aaron Lun (00:06:34): > I don’t like these newfangled icons.
Aaron Lun (00:06:39): > What was wrong with the old ones?
Aaron Lun (00:06:56): > Bet they got a new UX director who wanted to change stuff around.
Aaron Lun (00:07:07): > Just as a matter of course.
Maria Doyle (00:08:18): > @Maria Doyle has joined the channel
Jared Andrews (00:10:45): > I see no difference?
Aaron Lun (00:12:49): > The star is now open rather than filled.
Aaron Lun (00:12:55): > The notification is also open rather than filled.
Aaron Lun (00:13:18): > the expand icon is also weird and different.
Aaron Lun (00:13:23): > I didn’t pay for this!
Aaron Lun (00:13:28): > Well, I didn’t pay at all.
Aaron Lun (00:25:18): > back in my day we had filled icons.
Constantin Ahlmann-Eltze (11:41:48): > Wait until they completely turn it into myspacehttps://twitter.com/pifafu/status/1265773172520914944;) - Attachment (twitter): Attachment > hey, so we heard ya & are trying out a thing where you CAN have a readme on your @github profile… > @mikekavouras built it btw! re: https://twitter.com/pifafu/status/1262830019706892288 https://pbs.twimg.com/media/EZDt1VKUMAA18r2.jpg
Alan O’C (12:04:19) (in thread): > I don’t hate it, seems a lot more useful than some of the other “social” changes they’ve introduced
Aaron Lun (22:58:11): > IT MAKES ME SICK
Stephanie Hicks (23:08:27): > yeah, i’m not sure I’m OK with this…
2020-05-29
Federico Marini (05:14:42): > next will be animated gifs as profile pics
Federico Marini (05:15:14): > I’m with Steph, I liked the fact it looked “just a little more professional” the old way
Satoshi Kume (05:22:01): > @Satoshi Kume has joined the channel
Inma Hernandez (06:48:38): > @Inma Hernandez has joined the channel
Shuyu Zheng (08:42:03): > @Shuyu Zheng has joined the channel
Aaron Lun (15:41:02): > It’s fortunate that we have a GitHub enterprise deployment so that I can enjoy the classic look for some time longer.
2020-05-30
Aaron Lun (03:22:40): > LOL - File (PNG): Screenshot from 2020-05-30 00-21-21.png
Aaron Lun (03:23:14): > Search and replace fail right there.
2020-05-31
stefano mangiola (03:47:20): > @stefano mangiola has joined the channel
Aaron Lun (19:16:42): > holy crap SF is in lockdown AND curfew
Aaron Lun (19:16:50): > how exciting
Aaron Lun (19:17:06): > they were looting around my apartment as well, apparently.
Jonathan Goeke (22:25:56): > @Jonathan Goeke has joined the channel
2020-06-01
Marcus Lindberg (03:59:41): > @Marcus Lindberg has joined the channel
Kasper D. Hansen (14:13:46): > @Aaron LunSounds like its time for you to commit 100% to your office and bring a sleeping bag:slightly_smiling_face:
Keith Curtis (14:50:01): > @Keith Curtis has joined the channel
Didac (19:14:16): > @Didac has joined the channel
Hervé Pagès (23:59:45): > A sleeping bag? That sounds like luxury to me.
2020-06-02
Aaron Lun (00:03:29): > Back in my day we just slept on the concrete outside our PI’s office.
Aaron Lun (00:03:39): > If we were lucky we got a brick to use as a pillow.
Hervé Pagès (00:04:35): > oh so you were able to sleep? you don’t know how it was back in MY day
Aaron Lun (00:05:40): > well of course I had to sleep, otherwise how could I dream about the code I was going to write the next day?
Aaron Lun (00:05:53): > Or I should say, “later in the same day”, because no one goes to sleep before midnight.
mleleu (05:38:26): > @mleleu has joined the channel
Lori Shepherd (08:34:29): > 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/
2020-06-03
Aaron Lun (02:47:36): > Github’s UI changes have gone TOO FAR - File (PNG): Screenshot from 2020-06-02 23-46-54.png
Aaron Lun (02:47:45): > Madness. Sheer madness.
Aaron Lun (02:48:01): > I better not be the bad half of the A/B test.
Aaron Lun (02:51:39): > Look at these excuses for directory icons. Makes me sick. - File (PNG): Screenshot from 2020-06-02 23-51-10.png
Alan O’C (04:54:13): > The icons are pretty terrible yeah. I’ve not been GUI-ing much since the changes but the alerts icon irritates me every time I see it
Taoyu Mei (06:12:39): > @Taoyu Mei has joined the channel
Lluís Revilla (12:21:20): > I tried to find when was the submission process of new software packages moved to Github but I can find the date:shrug:. According tohttps://github.com/Bioconductor/Contributions/issues/37it should be around october 2016:mag:. Is there any announcement with the date? > Thanks
Martin Morgan (12:58:10) (in thread): > https://support.bioconductor.org/p/83448/maybe
Martin Morgan (13:01:46) (in thread): > …alsohttps://support.bioconductor.org/p/83234/
Riyue Sunny Bao (13:14:57): > @Riyue Sunny Bao has joined the channel
Lluís Revilla (13:40:47) (in thread): > Thanks! It seems to be the that day although on a comment of a linked post you mention that it might start working as soon as May 23, 2016.
Sahra Uygun (19:04:23): > @Sahra Uygun has joined the channel
2020-06-04
Yingxin Lin (09:11:18): > @Yingxin Lin has joined the channel
Pratheepa Jeganathan (09:11:29): > @Pratheepa Jeganathan has joined the channel
Kris Sankaran (10:49:45): > @Kris Sankaran has joined the channel
2020-06-05
FelixErnst (03:55:24): > @Aaron LunI didn’t even notice until it was pointed out. Did you ever work with a Gitlab instance?
Aaron Lun (03:55:46): > On occasion.
FelixErnst (03:56:23): > and you are complaining about the new Github icons?:hushed:
FelixErnst (03:57:10): > :coffee:makes the world go round. Maybe it also helps with the icons:party_parrot:
FelixErnst (04:01:01): > Which brings me back to the Bioc release naming scheme… coffee related names didn’t stick apparently. Was there another idea?
Aaron Lun (04:02:01): > Not a fan of the bean juice.
Aaron Lun (04:02:26): > And no doubt GitHub’s UI is still the best despite the deterioration in icon quality.
Alan O’C (06:28:47): > I think Gitlab’s features are objectively better (at least they were whenever I was working with a local instance), but yeah their UI design has been a bit lacking at times
Federico Marini (11:05:31): > Does GitLab have a UI?:stuck_out_tongue:
2020-06-06
Mark Tefero Kivumbi (02:52:03): > @Mark Tefero Kivumbi has joined the channel
NABISUBI PATRICIA (13:09:19): > @NABISUBI PATRICIA has joined the channel
Aaron Lun (14:43:55): > It’s quiet here.
Olagunju Abdulrahman (19:35:38): > @Olagunju Abdulrahman has joined the channel
Freeman Wang (20:31:13): > @Freeman Wang has joined the channel
2020-06-07
Adewale Ogunleye (06:14:06): > @Adewale Ogunleye has joined the channel
Tanzeel Tagalsir (06:25:15): > @Tanzeel Tagalsir has joined the channel
SSALI IBRAHIM (08:23:10): > @SSALI IBRAHIM has joined the channel
Tasneem Awad (12:09:23): > @Tasneem Awad has joined the channel
MounikaGoruganthu (20:59:59): > @MounikaGoruganthu has joined the channel
2020-06-08
Danny Kearns (08:43:42): > @Danny Kearns has joined the channel
Shankar Shakya (09:56:34): > @Shankar Shakya has joined the channel
2020-06-09
Synnøve Yndestad (03:03:17): > @Synnøve Yndestad has joined the channel
Ye Zheng (15:58:19): > @Ye Zheng has joined the channel
Vandhana (16:23:57): > @Vandhana has joined the channel
2020-06-10
Hector Roux de Bézieux (03:16:14): > @Hector Roux de Bézieux has joined the channel
Jonathan Griffiths (05:48:25): > @Jonathan Griffiths has joined the channel
Sean Davis (09:42:25): > https://www.blue-granite.com/blog/give-your-genomics-pipeline-a-glow-up-in-azure-databricks - Attachment (blue-granite.com): Give Your Genomics Pipeline a Glow Up in Azure Databricks > Using Azure Databricks in the cloud with Glow can now allow scientists to scale up their genomic analyses using distributed computing.
Hervé Pagès (12:34:32): > Brilliant! Now I’ll be able to run my Shiny app on Azure Databricks and make it GLOW with Spark!
Sean Davis (14:57:44): > A shiny app from you,@Hervé Pagès, will blaze, glitter, flare, gleam, and glisten, not just GLOW.
Sean Davis (14:58:02): > https://www.thesaurus.com/browse/glow - Attachment (www.thesaurus.com): Synonyms of glow | Thesaurus.com > Synonyms for glow from Thesaurus.com, the world’s leading online source for synonyms, antonyms, and more.
Hervé Pagès (15:30:11): > The richness of the English language never ceases to amaze me!
Dirk Eddelbuettel (17:41:19): > @Dirk Eddelbuettel has joined the channel
Dario Strbenac (20:00:31): > Aaron’s prayers have been answered. - File (PNG): GitHub User Interface Survey
Aaron Lun (20:38:44): > how did you get to that?
2020-06-11
Roy Storey (06:12:07): > @Roy Storey has joined the channel
Dario Strbenac (08:00:05): > It appeared as an alert on the user profile menu icon.
Qian Li (10:42:19): > @Qian Li has joined the channel
2020-06-12
Stavros Papadopoulos (11:40:41): > @Stavros Papadopoulos has joined the channel
Nick Borcherding (12:35:14): > @Nick Borcherding has joined the channel
Dan Bunis (13:07:07): > cross-posting because I’m not sure how many of us are currently part of the#diversebiocchannel. - Attachment: Attachment > Although pride parades are cancelled, and social focus is largely shifted elsewhere* this year, it is still pride month. > > I’m wondering if anyone else in the group has any thoughts on this newer iteration of the general pride flag. Particularly, as a white cis gay male myself, I’d like to hear others’ thoughts on this flag iteration. > > Rather than giving my own words as to why I personally support this flag, I’d like to share its creator’s: > > > Their artist statement: > > I am so excited that my art is getting some traction. I created this in 2019 as a way to spread the message that we need to center Trans people, People of color, and specifically Trans People of Color in the queer community as a whole. There are no lines separating us as we are one big community that blends together and needs intersectional support. I am very excited about the T-shirts, Hoodies, Tanktops and now Flags that we have to spread this art and this message. As a Brown Queer Disabled Transman. This has helped me feel more supported in the community as a whole. anyways here is my art if you want to spread the word! I am a Portlander and would love the support of my local community with this message. > (full credit text in link in the thread. Please do not share without it.) > > I’m specifically considering making a square version of the flag into an emoji, and then adding it as my status icon for the rest of the June. I would love to see an open discussion on this, and it would also be wonderful to see how diverse of a community we have here, but DMs (confidentiality assured) are also welcome! > > *rightfully so. #blacklivesmatter, and the LGBT community must proclaim and actively support that because #blacktranslivesmatter, and because of so many other reasons too!
Aaron Lun (13:16:39): > I saw this and thought you were going to make a rainbow Bioconductor sticker
Aaron Lun (13:17:55): > Problem is the dots are too small to easily see the colors, but with some pastel and imagination it can be done.
Paul Hoffman (13:30:25): > @Paul Hoffman has joined the channel
Dan Bunis (13:48:23): > oh something like that would be awesome too! It would be pretty cool to have a BioC-LGBT community sticker. Perhaps just the standard flag colors (eg:pride:) with the BioC name and logo on top with a white border around each piece. I think that could work on top of most of the standard flags.
Hervé Pagès (14:04:20): > and with a biologically correct double helix:pray:
2020-06-13
Aaron Lun (00:04:39): > You’re welcome. - File (PNG): rainbow_BioC.png
Aaron Lun (00:05:09): > Yellow had to be slightly tuned, the full yellow was not visible.
Aaron Lun (00:05:55): > And now, to continue working on my anime GIF slackbot.
Aaron Lun (00:09:07): > Damn that looks good.
Sridhar N (00:59:06): > Good on ya mate!
Aaron Lun (01:07:51): > What can I say? I’m an artist. It’s just that my medium is usually code.
Sridhar N (01:12:40): > :stuck_out_tongue:
Sridhar N (01:18:54): > the only other artist i know is Artem
Sridhar N (01:18:55): > https://github.com/hackseq/hackseq18/wiki/swag
Martin Morgan (06:21:37): > Would proudly fly a rainbowized banner logohttp://bioconductor.org/about/logo/with dots colorized (and helix biologically correct, or not) if it were made available…
Stephanie Hicks (07:09:06): > That is awesome@Aaron Lun!
Martin Morgan (12:35:27): > I’d like to see the hex above added tohttps://github.com/Bioconductor/BiocStickers; and other diversity-affirming variations, too.
Federico Marini (12:54:50): > Looks damn great, well done!
Federico Marini (12:55:29): > happy to use my stickermule 10stickers-1euro special promotion for that:slightly_smiling_face:
Aaron Lun (15:14:01): > PR inbound. See how the sausage is made withhttps://github.com/LTLA/RainbowBiocSticker.
Aaron Lun (15:14:41): > To do it for the logo would require access to the underlying PDF/SVG.
Aaron Lun (15:16:05): > At any rate, I fixed the asymmetry that I couldn’t be bothered to deal with earlier, so here is the final version. - File (PNG): rainbow_BioC.png
Martin Morgan (15:38:16) (in thread): > @Aaron Lunthe only definitive files available are those on the linked page, so one would have to generate pdf / svg from those.
Martin Morgan (15:48:28): > Any takers for producing the BLM version?
Dan Bunis (15:58:34): > Can we pause on this a bit? I might be the only queer voice here right now. I’d like to thank@Aaron Lunfor making this sticker design. But I’d also like to note that after my initial affirmative response to the pride flag idea, I’ve become a bit conflicted re: performative actions versus substantive support of diversity. > > I’d like to propose that to go alongside the inclusion of stickers for the LGBT community, and perhaps one specifically for the BIPOC community (if we have members of that community that would support such a sticker), can I ask that we send out some sort of letter of support for BIPOC and LGBT individuals in the sciences? > > Bioconductor itself may not be in a place to create rules that would make it be easier to be different in science, but maybe we can still use our collective voice to support that such measures be implemented elsewhere?
Dan Bunis (16:12:13) (in thread): > My idea for each is to take the colors as they are in the original flag I posted. Blue pink white pink blue = Trans. The black -> brown skin tones part is representative of queer POC. I think such colors could be used for the wider community, but I don’t truly know.
2020-06-14
Aaron Lun (02:42:19): > I’ll be honest, I’m just in it for the stickers.
Aaron Lun (02:42:21): > But we have a community advisory board now so this would be an interesting question for them.
Aaron Lun (02:45:07): > e.g. Do we need to do more than what we usually do regarding the diversity efforts in BioC events and such? I dunno.
Aaron Lun (02:47:35): > I, for one, take my cues from boring government organizations, so for example, if the post office is willing to rainbow-ise their logo, I think that’s pretty good political cover for me. - File (PNG): Screenshot from 2020-06-13 23-45-33.png
Aaron Lun (02:48:11): > You can see they didn’t even bother to darken the yellow to make the letters more visible, what a bunch of n00bs.
phil-o (07:21:20): > @phil-o has joined the channel
Dan Bunis (11:11:39): > Quite valid points. I saw an opening to ask for more so I took it lol, but I can try to reach out directly to the community advisory board if that’s where the question should go.
Dan Bunis (12:39:21): > Looks better without the grey background slack adds - File (PNG): trans_BioC.png
Dan Bunis (13:30:51): > :man-shrugging:what do we think of this one? - File (PNG): poc_BioC.png
Laurent Gatto (13:39:07) (in thread): > @Dan BunisIf appropriate, feel free to send a pull request to add more stickers to the diversity-affirming stickers section inhttps://github.com/Bioconductor/BiocStickers/blob/master/README.md
2020-06-15
Nicolas Valentin (09:00:06): > @Nicolas Valentin has joined the channel
Aaron Lun (11:27:52): > Anyone have any recommendations for apps that call international landlines?
Robert Castelo (11:34:34): > i’ve usedhttps://internetcalls.combut from a desktop computer, i don’t know whether it works from a mobile phone. once you enter your phone number and the phone you want to call, it works by calling your phone first, and once you pick it up, then it calls the other phone. my experience is that the quality of the call was quite good. - Attachment (internetcalls.com): Internetcalls gets you the cheapest international calls of the internet > Free phone calls all around the world: Download the free Internetcalls application and save loads of money on your (inter)national calling charges right away!
Aaron Lun (11:36:06): > interesting. I was going to to buy skype credits but I’ll have a look at this.
Kasper D. Hansen (12:04:53): > I use skype for this
Aaron Lun (12:16:44): > Hm.
Lukas Weber (12:21:41): > I used to use Skype credits for this too, although it’s probably been a year or two since I’ve used it (we all switched to free calls on mobile with whatsapp and facetime)
Aaron Lun (12:22:30): > If only HMRC was so obliging.
Aaron Lun (12:22:55): > Okay, I’ll give skype a go. Hopefully they don’t put me on hold for hours and burn up all my credits.
Lukas Weber (12:23:20): > it’s really cheap, like 2c per minute to Aus
Aaron Lun (12:23:57): > Yes, I would have to be on hold for 3 hours to use of $5.
Robert Castelo (12:36:51): > If think internetcalls is 5c per call, irrespective of how long the call is, during the first 3 months after you put credit in your account.
Aaron Lun (12:54:05): > tell me about it.
Jayaram Kancherla (13:43:46): > if you have credit in google voice, you can also make international calls to landlines/mobiles
2020-06-16
Nadav Shai (00:11:02): > @Nadav Shai has joined the channel
Hervé Pagès (03:47:40) (in thread): > Finally double helices that I can use to open my bottle of wine!:wine_glass:
jessi elderkin (09:53:59): > @jessi elderkin has joined the channel
Jordan Veldboom (10:31:32): > @Jordan Veldboom has joined the channel
Leonardo Collado Torres (11:31:45) (in thread): > Hi, I just wanted to mention that the Community Advisory Board is working on such a statement lead by Aedin. Aedin is hosting a conference this week, so please be patient with us. Also, there’s#community-advisory-boardin case anyone wants to discuss more specifics about it.
Dario Strbenac (22:00:09): > Is there a website I could find the coordinates of the hg38 alternate contigs in reference to the main chromosomes? I aim to calculate average read coverage, but there don’t seem to be tools for that which support alt-aware mapping, so calculating read coverage across the chromosome segments where there are no alternate contigs beside them seems like the next best thing. Previously a similar question asked at Biostarshttps://www.biostars.org/p/442997/but unanswered.
Andre Sim (23:53:12): > @Andre Sim has joined the channel
2020-06-17
Serena Gerboni (07:57:22): > @Serena Gerboni has joined the channel
Ger (07:57:59): > @Ger has joined the channel
Josh Hope (07:58:07): > @Josh Hope has joined the channel
Marco Chiapello (07:59:04): > @Marco Chiapello has joined the channel
Mohammad Fayaz (07:59:43): > @Mohammad Fayaz has joined the channel
Claudio (08:00:21): > @Claudio has joined the channel
Olalekan Akintande (08:01:00): > @Olalekan Akintande has joined the channel
Birgitte Dige Semark (08:16:34): > @Birgitte Dige Semark has joined the channel
CGiacomelli (08:36:27): > @CGiacomelli has joined the channel
Han Tun (08:40:28): > @Han Tun has joined the channel
GiuliaPelos (08:48:36): > @GiuliaPelos has joined the channel
Robert Herczeg (09:04:09): > @Robert Herczeg has joined the channel
Ruben Dries (12:27:40): > @Ruben Dries has joined the channel
Vivek Das (12:56:51): > Hi everyone, are you all participating in BioC2020 this year? I know it might sound naive but wanted to ask.:upside_down_face:
Dan Bunis (13:09:11) (in thread): > I’m “going” and was selected for a talk (ondittoSeq)!
Vivek Das (13:11:03) (in thread): > Awesome. Super cool and congratulations:tada:
Stephanie Hicks (13:14:06) (in thread): > i’m going too
Dan Bunis (13:14:09) (in thread): > Thanks! My first talk at a conference, so quite pumped. And the fact that the conference is virtual likely means even more people might join, right?:man-shrugging::upside_down_face:
Vivek Das (13:23:22) (in thread): > You will rock:the_horns:. Best wishes,
Vivek Das (14:27:17): > I have a query#random. How many are using google Colab for EDA? Any thoughts?I have been using it for some curiosity driven gigs so far and finding it very useful. No hassles of server/HPC & so far my works are still fine both in general Bioinformatics space and also applied ML/DL. Let’s see how well I can sustain for the free usage untill I receive e-mail for the premium upgrade.
Vivek Das (14:28:10): > Specially it’s portable with Git and GPU and TPU available:smiley:
Vivek Das (15:12:36): > This seems a cool workshop in single cell.https://twitter.com/altunaakalin/status/1273164243261698056?s=21 - Attachment (twitter): Attachment > Apply for our yearly computational #genomcis course in #Berlin via https://compgen.mdc-berlin.de :computer: by July 30th > > There will be a #VR session :robot_face: > > topics: #machineLearning, bulk #RNAseq, and #scRNAseq analysis with using #Rstats.🧬:microscope: > > supported by @BIMSB_MDC @EasiGenomics @denbiOffice https://pbs.twimg.com/media/EasuBH_WsAAAFFB.jpg
Federico Marini (17:59:59): - File (PNG): image.png
Federico Marini (18:00:14): > This is the new GitHub…
Federico Marini (18:00:35): > no need to trigger@Aaron Lunon this I guess:smile:
Aaron Lun (18:00:42): > I HAVE ALREADY SEEN IT.
Aaron Lun (18:00:50): > DISCUGSUTING.
Federico Marini (18:01:06): > but it scarily looks like… gitlab
Jason (18:49:35): > @Jason has joined the channel
Aaron Lun (19:09:30): > Just looking at it again. It does sicken me.
Aaron Lun (19:09:33): > :face_vomiting:
Aaron Lun (19:09:40): > Not right. It’s just not right.
Aaron Lun (19:10:43): > And people’s faces are now circles? What, they can’t afford to transmit the extra pixels on the corners?
Aaron Lun (19:10:46): > Sick. Just sick.
Jared Andrews (19:46:12): > Agreed it looks worse. Why change for the sake of it?
Aaron Lun (20:11:14): > I shall give them my thoughts on the feedback sheet.
Aaron Lun (20:11:35): > Some strongly worded comments. “disappointed”, etc.
Kasper D. Hansen (22:04:29): > You can escalate to “severely disappointed”. That ought to catch their attention
Vivek Das (22:12:44): > Is this all happening as it’s under the Microsoft? II recently attended a Twitter steamed workshop on Git. I followed some presentations where it was all about design of the page and adding new functionality features. I do agree to the feedback feature. These things often help on software product specially if it’s from a product based company.
2020-06-18
Federico Marini (02:06:29): > in extreme cases, I would switch to “utterly …”
pamela himadewi (09:54:43): > @pamela himadewi has joined the channel
Camila Daiana Arcuschin (10:15:57): > @Camila Daiana Arcuschin has joined the channel
Simina Boca (12:19:19) (in thread): > I’m also going!
Vivek Das (13:05:33) (in thread): > @Aaron Lun, I use Skype to call India landline phones other than WhatsApp.. I put $10-20 on the Skype and it’s pretty cheap in my opinion.
Aaron Lun (13:06:04) (in thread): > Cool. I will probably try it out next month.
2020-06-19
Federico Marini (04:53:10): > Is that you,@Aaron Lun? can the utter disappointment get to this result?:smile: - File (PNG): image.png
Kevin Rue-Albrecht (04:53:46): > funny: i came here just to ask the same question ^^
Federico Marini (04:55:37): > ahahahah
Jim Hunter (14:01:53): > @Jim Hunter has joined the channel
Jelmer Poelstra (15:13:35): > @Jelmer Poelstra has joined the channel
Atul Deshpande (17:06:24): > @Atul Deshpande has joined the channel
2020-06-20
Massimiliano Manzo (02:26:55): > @Massimiliano Manzo has joined the channel
nordwave (06:13:22): > @nordwave has joined the channel
2020-06-22
Yasmine MANSOUR (17:15:08): > @Yasmine MANSOUR has joined the channel
Keren Xu (18:23:24): > @Keren Xu has joined the channel
2020-06-23
Tim Stuart (16:43:53): > @Tim Stuart has joined the channel
Dario Strbenac (20:00:02): > The new GitHub style has been released. Everything looks so big.
Federico Marini (20:21:01): > oh god there is no way back
Stuart Lee (20:26:06): > does anyone actually like it? it’s so ugly
Federico Marini (20:27:29): > not this guy:thumbsdown:
Federico Marini (20:27:52): > just looks like a mockup of gitlab, which honestly, just sucked
Alan O’C (20:39:06): > I don’t mind it:man-shrugging:But then I like gitlab a lot
Aaron Lun (21:29:55): > Well, I’ve made my thoughts on this matter quite clear, so I won’t repeat them. The only silver lining is that at least it’s not like Bitbucket.
Aaron Lun (21:36:25): > OH NO
Aaron Lun (21:36:36): > THEY CHANGED THE COLORS - File (PNG): Screen Shot 2020-06-23 at 6.36.08 PM.png
Aaron Lun (21:38:28): > There also seems to be an optical illusion where you see small grey circles between the boxes at the corners.
Peter Hickey (21:39:52) (in thread): > can’t unsee
Aaron Lun (21:40:25) (in thread): > ur welcome
Stephanie Hicks (22:02:32) (in thread): > Oh my, this is awful!
Jared Andrews (23:03:56) (in thread): > Staring at that for me then about 5 seconds is gonna give me a migraine. No more trying to catch you missing a day.
2020-06-24
Alan O’C (05:31:57) (in thread): > well spotted, down to them not being boxes I think
CristinaChe (08:18:32): > @CristinaChe has joined the channel
Abbye McEwen (11:21:08): > @Abbye McEwen has joined the channel
2020-06-25
Rob Patro (10:42:48): > @Aaron Lun: there seems to be insufficient outrage : - File (PNG): image.png
Michael Lawrence (11:05:03): > Is there an option for not even noticing that it changed?
Rob Patro (11:37:29): > lol — I guess that could be lumped in withmeh
Rob Patro (11:37:33): > it’s more like a super-meh
Mike Smith (11:43:43): > It’s one of those changes where I know something is different, but I’m not sure what. I guess they’ve rounded the corners off everything - is that mostly it?
Rob Patro (11:52:49): > There are a lot of changes
Rob Patro (11:52:53): > the color scheme changed a bit
Rob Patro (11:53:03): > they removed lines between files in the repository view (less contrast)
Rob Patro (11:53:09): > they changes a bunch of icons
Rob Patro (11:53:15): > they rounded everything
Alan O’C (14:26:15): > Repo home screen/README view is different, that’s the main change I noticed
Hervé Pagès (14:59:19): > The only thing I wished they had changed is the stupid “hidden items” feature, but they didn’t:disappointed: - File (PNG): hidden_items
2020-06-26
中村 央 (06:29:21): > @中村 央 has joined the channel
wisam (08:24:46): > @wisam has joined the channel
Jenny Smith (15:45:37): > @Jenny Smith has joined the channel
2020-06-28
Mostafa Elabd (10:21:09): > @Mostafa Elabd has joined the channel
Stefania Oliveto (17:24:27): > @Stefania Oliveto has joined the channel
2020-06-29
Federico Marini (14:48:03): > Maybe useful to the many that reacted… unenthusiastically:https://github.com/daattali/oldschool-github-extension
2020-06-30
Frank Rühle (06:10:03): > @Frank Rühle has joined the channel
000 (11:50:04): > @000 has joined the channel
2020-07-02
andrea spinelli (08:59:35): > @andrea spinelli has joined the channel
2020-07-04
Umar Ahmad (08:17:52): > @Umar Ahmad has joined the channel
Gian Marco Franceschini (09:54:44): > @Gian Marco Franceschini has joined the channel
Kasia Kedzierska (19:27:52): > @Kasia Kedzierska has joined the channel
2020-07-05
Regina Umarova (02:33:26): > @Regina Umarova has joined the channel
Aaron Lun (07:30:38): > Late night coding session!
Aaron Lun (07:30:54): > It’s 4:30 am over here. Any company?
Robert Castelo (07:50:14): > Not coding but BBQing:yum:it’s 13:45 in continental Europe - File (PNG): real_programmers.png
2020-07-06
Nguyen Thanh Dat (03:11:29): > @Nguyen Thanh Dat has joined the channel
Luca Marconato (07:31:28): > @Luca Marconato has joined the channel
Lidia Lipinska-Zubrycka (08:20:15): > @Lidia Lipinska-Zubrycka has joined the channel
Mehdi Pirooznia (08:58:01): > @Mehdi Pirooznia has joined the channel
Verena Volf (10:09:47): > @Verena Volf has joined the channel
Vivek Das (11:23:05): > https://t.co/iFXcstvrDM?amp=1
Pablo Latorre-Doménech (11:26:48): > @Pablo Latorre-Doménech has joined the channel
Kevin Rue-Albrecht (11:30:45) (in thread): > Thanks! added ->https://github.com/Bioconductor/BioC2020/issues/106#issuecomment-654308521
Vivek Das (11:32:08) (in thread): > Thanks for adding it@Kevin Rue-Albrecht
Yu-Tian Xiao (14:02:22): > @Yu-Tian Xiao has joined the channel
ZihanYang (15:38:21): > @ZihanYang has joined the channel
2020-07-07
Rajesh Shigdel (04:06:52): > @Rajesh Shigdel has joined the channel
Simone Tiberi (09:25:33): > @Simone Tiberi has joined the channel
Vivek Das (11:45:23): > #random: I wanted to make sure US faculties/PI/advisors here have seen this. It’s a pretty problematic environment currently for international students as per my understanding. Hope international students get all the needed support in US.https://twitter.com/siointerrupted/status/1280350792294076421?s=21 - Attachment (twitter): Attachment > CALL TO ACTION: I have created a small document detailing the current situation and what you can do to help. You can find it here. Your international students need you NOW! https://docs.google.com/document/d/1237MqzCVFgSjB15PKk8hCfF4ZWhrwbcWe0P4rgQkONE/edit?usp=sharing
Vivek Das (11:47:22): > Apologies to post it here but I don’t have any other means to reach out to as many faculties I can other than Twitter and this medium. Thanks and appreciate who all are taking the steps and doing the needful.
Dario Strbenac (22:00:16): > It is fortuitous that BioC Asia 2020 will be online rather than in Beijing. I can only imagine Aaron Lun arriving with a suitcase containing freshly-printed rainbow flag hex stickers. Weeks later, we would wonder what the streak of grey (rounded corners, of course) rectangles on LTLA’s GitHub activity summary meant. - File (PNG): Arbitrary Police Arrest
2020-07-08
Aaron Lun (00:08:07): > Indeed. I’ve often thought about whether I was important enough to get arrested like that. But I don’t think I’m pulling in the necessary level of megabucks yet.
Petra Palenikova (05:28:31): > @Petra Palenikova has joined the channel
David Zhang (14:34:07): > @David Zhang has joined the channel
Federico Marini (16:40:45): > OMG -> - File (PNG): image.png
Aaron Lun (17:01:40): > yes, i know.
Kevin Rue-Albrecht (17:05:02): - File (PNG): image.png
Aaron Kennington (18:11:52): > @Aaron Kennington has joined the channel
2020-07-09
Andrea Carenzo (03:52:43): > @Andrea Carenzo has joined the channel
estepi (06:31:16): > @estepi has joined the channel
shr19818 (12:18:00): > @shr19818 has joined the channel
Giuliano Netto Flores Cruz (14:23:05): > @Giuliano Netto Flores Cruz has joined the channel
2020-07-10
Hervé Pagès (00:06:45): > July 7th was the 20th anniversary of the first human genome draft:https://youtu.be/_6caCfvMIiYVenter really looks like the typical Hollywood villain in that video:laughing: - Attachment (YouTube): 20 Years of the Human Genome
Adam Chan (01:01:43): > @Adam Chan has joined the channel
Aaron Lun (03:30:44): > always good to see another Aaron here.
Shixiang Wang (04:05:18): > @Shixiang Wang has joined the channel
Luke Zappia (04:57:49): > While GitHub is updating their UI something that would actually be useful is file type icons like GitLab seems to have - File (PNG): image.png
Dario Strbenac (08:30:17): > An algorithm was just published inNature Geneticson Monday that applies a t-test to FPKM values of RNA-seq data to look for outliers! They also multiply a Binomial probability function by a Gaussian function because the distribution of their experimental data didn’t follow the null distribution and they wanted it to look more like the null distribution. Plenty more amusement in there for anyone who barely passed undergraduate statistics or did betterhttps://www.nature.com/articles/s41588-020-0659-5Aaron would be even more offended by this Methods section than the new GitHub style. Does anyone have a blog where they critique the Methods sections in Nature journals (apart from Lior)? I saw a tweet by someone a few months ago saying the statistical quality of a journal article is inversely proportional to its impact factor. Sure seems like it. - Attachment (Nature Genetics): Discovery of regulatory noncoding variants in individual cancer genome > A new computational method integrates whole-genome sequencing and transcriptomic data to identify regulatory noncoding variants in an individual cancer genome.
Alan O’C (08:43:14) (in thread): > That’s really something. I like the equation derived for the sigma of the Gaussian: (N) = 10.8(1-e^{-N/105})
Alan O’C (08:43:27) (in thread): > No magic numbers here no sirree!
Melanie Loth (13:57:27): > @Melanie Loth has joined the channel
Genevieve Stein-O’Brien (15:57:22): > @Genevieve Stein-O’Brien has joined the channel
Veronica Jimenez Jacinto (19:55:24): > @Veronica Jimenez Jacinto has joined the channel
2020-07-11
unnati97 (13:14:00): > @unnati97 has joined the channel
2020-07-13
Dario Strbenac (00:00:17) (in thread): > I sent Lior the link. He couldn’t resist looking at it. - File (PNG): Lior Reaction
yuting (00:19:40): > @yuting has joined the channel
Ashu Sethi (03:30:15): > @Ashu Sethi has joined the channel
Dana Silverbush (10:18:10): > @Dana Silverbush has joined the channel
Meena Choi (10:35:15): > @Meena Choi has joined the channel
Patrick K Taylor (12:52:06): > @Patrick K Taylor has joined the channel
Denis Kariakin (15:21:20): > @Denis Kariakin has joined the channel
Haibo Liu (17:50:10): > @Haibo Liu has joined the channel
Celso Milne (20:01:17): > @Celso Milne has joined the channel
2020-07-14
Qirong Lin (01:36:35): > @Qirong Lin has joined the channel
Nur-Taz Rahman (11:21:58): > @Nur-Taz Rahman has joined the channel
Jessica (17:17:36): > @Jessica has joined the channel
Ken Wang (19:40:03): > @Ken Wang has joined the channel
Aaron Lun (23:22:05): > it’s times like these that the residual weed coming through my apartment’s vents really help.
2020-07-15
CJ (05:01:02): > @CJ has joined the channel
Pedro Baldoni (07:23:47): > @Pedro Baldoni has joined the channel
Spencer Nystrom (08:15:45): > @Spencer Nystrom has joined the channel
wmuehlhaeuser (08:37:52): > @wmuehlhaeuser has joined the channel
Kai Hu (09:08:06): > @Kai Hu has joined the channel
Izabela Mamede (19:14:10): > @Izabela Mamede has joined the channel
Chitrasen (21:53:19): > @Chitrasen has joined the channel
2020-07-16
Ruth Schmidt (09:44:18): > @Ruth Schmidt has joined the channel
Arvind Mer (09:47:30): > @Arvind Mer has joined the channel
Denis O’Meally (12:07:41): > @Denis O’Meally has joined the channel
2020-07-17
Cyril Anyetei-Anum (00:57:40): > @Cyril Anyetei-Anum has joined the channel
lala motlhabi (02:17:20): > @lala motlhabi has joined the channel
Julia Hlavka-Zhang (09:34:47): > @Julia Hlavka-Zhang has joined the channel
Ming-Ru Wu (19:29:35): > @Ming-Ru Wu has joined the channel
Roy Gulla (20:57:25): > @Roy Gulla has joined the channel
2020-07-18
Jennifer Doering (00:18:54): > @Jennifer Doering has joined the channel
randy williams (06:13:06): > @randy williams has joined the channel
Markus Riester (11:16:57): > @Markus Riester has joined the channel
Ting Sun (13:58:28): > @Ting Sun has joined the channel
2020-07-19
Kirill Tsyganov (18:54:53): > @Kirill Tsyganov has joined the channel
David Dilworth (20:44:49): > @David Dilworth has joined the channel
Kurt Showmaker (20:45:26): > @Kurt Showmaker has joined the channel
2020-07-20
Anabella (00:00:09): > @Anabella has joined the channel
Dr Awala Fortune O. (01:52:51): > @Dr Awala Fortune O. has joined the channel
Alexandra Garnham (02:06:38): > @Alexandra Garnham has joined the channel
Bishoy Wadie (03:57:22): > @Bishoy Wadie has joined the channel
Mirko Brüggemann (05:41:45): > @Mirko Brüggemann has joined the channel
Manoj Teltumbade (09:56:25): > @Manoj Teltumbade has joined the channel
junwon (12:20:41): > @junwon has joined the channel
Carl McIntosh (12:36:47): > @Carl McIntosh has joined the channel
Monika Krzak (12:37:50): > @Monika Krzak has joined the channel
Niklas Michel (12:43:43): > @Niklas Michel has joined the channel
Rydham Goyal (13:13:56): > @Rydham Goyal has joined the channel
Shashi Ravishankar (14:42:43): > @Shashi Ravishankar has joined the channel
Will Arnold (14:50:54): > @Will Arnold has joined the channel
Brianna Barry (18:27:16): > @Brianna Barry has joined the channel
Jimmy Breen (22:03:35): > @Jimmy Breen has joined the channel
2020-07-21
Anke Busch (05:57:20): > @Anke Busch has joined the channel
Charlie George (07:06:23): > @Charlie George has joined the channel
Helen Horkan (07:25:33): > @Helen Horkan has joined the channel
Dr Isha Goel (08:37:16): > @Dr Isha Goel has joined the channel
Krutika (10:38:35): > @Krutika has joined the channel
Philippe Boileau (17:31:45): > @Philippe Boileau has joined the channel
2020-07-22
Haoyu Yang (01:12:14): > @Haoyu Yang has joined the channel
Biljana Stankovic (08:01:44): > @Biljana Stankovic has joined the channel
Nitesh Turaga (08:20:27): > We have no Bioconductor software packages starting withJorj. If Any new developers are looking to take that letter! > > > print(to_install_tbl %>% group_by(start) %>% count() %>% arrange(desc(n)), n = 25) > # A tibble: 25 x 2 > # Groups: start [25] > start n > <chr> <int> > 1 s 201 > 2 m 192 > 3 c 188 > 4 r 150 > 5 g 147 > 6 p 121 > 7 b 103 > 8 a 95 > 9 d 95 > 10 t 78 > 11 i 65 > 12 f 63 > 13 e 61 > 14 o 42 > 15 h 41 > 16 n 39 > 17 l 30 > 18 q 19 > 19 v 17 > 20 k 11 > 21 w 10 > 22 u 7 > 23 x 7 > 24 y 4 > 25 z 2 > > > letters[!letters %in% to_install_tbl$start] > [1] "j" >
Cornelia Rueckle (08:23:29): > @Cornelia Rueckle has joined the channel
Dilara Ayyildiz (10:16:07): > @Dilara Ayyildiz has joined the channel
Jeff Gentry (11:50:07) (in thread): > Rename genefilter to jenefilter
Sisira Nair (11:52:59): > @Sisira Nair has joined the channel
Sean Davis (11:59:33) (in thread): > I’m sure that won’t break ANYTHING….
Jeff Gentry (15:21:53) (in thread): > @Sean DavisYOLO
Katia Silvera (15:45:02): > @Katia Silvera has joined the channel
Subhajit Dutta (15:46:17): > @Subhajit Dutta has joined the channel
Mindy (15:48:20): > @Mindy has joined the channel
Claire Campbell (15:56:54): > @Claire Campbell has joined the channel
2020-07-23
Elsa Quezada (11:35:46): > @Elsa Quezada has joined the channel
jgearing (19:00:43): > @jgearing has joined the channel
Tania Guerrero (22:26:27): > @Tania Guerrero has joined the channel
2020-07-24
Isha Goel (07:43:47): > @Isha Goel has joined the channel
Rajiv Kumar Tripathi (14:52:03): > @Rajiv Kumar Tripathi has joined the channel
dnusskern (14:59:20): > @dnusskern has joined the channel
2020-07-26
Hans-Richard Brattbakk (05:45:02): > @Hans-Richard Brattbakk has joined the channel
Reza Rezaei (09:50:56): > @Reza Rezaei has joined the channel
Aaron Lun (21:39:45): > now, the hardest task of the day
Aaron Lun (21:40:06): > finding an appropriately SFW zoom background.
2020-07-27
Aaron Lun (03:14:14): > Ugh. Was going to go to bed early for tomorrow but held up by bluster’s check failure.
Aaron Lun (03:14:17): > On windows 32.
Dario Strbenac (03:15:32): > Is your local time setting wrong?
Aaron Lun (03:18:22): > what do you mean?
Dario Strbenac (03:20:10): > Your profile states your local time is 8:20 a.m. Were you going to go to bed at 8:20 a.m.?
Aaron Lun (03:21:01): > pretty sure that’s because I never bothered to change it from cambridge time.
Triin (03:24:59): > @Triin has joined the channel
Aaron Lun (03:37:40): > Fixed. But at this point, i might as well just stay awake until the conference starts.
Aaron Lun (03:38:12): > I didn’t get any sleep before the 2015 conference either.
Aditi Verma (05:18:10): > @Aditi Verma has joined the channel
Lora Kasselman (06:23:38): > @Lora Kasselman has joined the channel
Ameek Bhalla (08:35:44): > @Ameek Bhalla has joined the channel
Riyue Sunny Bao (08:43:22): > @Riyue Sunny Bao has joined the channel
James Ashmore (08:43:25): > @James Ashmore has joined the channel
Gavin Rhys Lloyd (08:43:54): > @Gavin Rhys Lloyd has joined the channel
jackgisby (08:44:30): > @jackgisby has joined the channel
Dharani Kamalachandran (08:54:24): > @Dharani Kamalachandran has joined the channel
You ZHOU (08:55:35): > @You ZHOU has joined the channel
Rowling (10:20:14): > @Rowling has joined the channel
Richard Friedman (10:58:07): > @Richard Friedman has joined the channel
Arun Chavan (12:06:56): > @Arun Chavan has joined the channel
Ray Su (12:07:03): > @Ray Su has joined the channel
Mark Long (12:59:58): > @Mark Long has joined the channel
Mai Nishiguchi (13:21:24): > @Mai Nishiguchi has joined the channel
Marco Tello (15:07:31): > @Marco Tello has joined the channel
Cem Kuscu (15:38:21): > @Cem Kuscu has joined the channel
joost groot (17:26:58): > @joost groot has joined the channel
2020-07-28
Mikie Phan (05:04:17): > @Mikie Phan has joined the channel
Markus Schroeder (08:25:43): > @Markus Schroeder has joined the channel
rohitsatyam102 (08:27:11): > @rohitsatyam102 has joined the channel
Ayush Aggarwal (08:28:53): > @Ayush Aggarwal has joined the channel
Randall Johnson (08:48:22): > @Randall Johnson has joined the channel
jj.chrzanowski1 (09:07:33): > @jj.chrzanowski1 has joined the channel
Marcin Kaszkowiak (09:47:36): > @Marcin Kaszkowiak has joined the channel
Zuzanna Nowicka (09:48:01): > @Zuzanna Nowicka has joined the channel
syliu (09:58:29): > @syliu has joined the channel
Mirko Signorelli (10:02:14): > @Mirko Signorelli has joined the channel
Mario Keller (10:03:03): > @Mario Keller has joined the channel
Dan (10:07:02): > @Dan has joined the channel
Yuri Kotliarov (10:09:28): > @Yuri Kotliarov has joined the channel
Prat (10:56:49): > @Prat has joined the channel
Selvi Guharaj (12:41:41): > @Selvi Guharaj has joined the channel
Hedia Tnani (12:54:30): > @Hedia Tnani has joined the channel
Sachendra Kumar (12:57:32): > @Sachendra Kumar has joined the channel
Wennan Chang (13:02:58): > @Wennan Chang has joined the channel
Nur M Shahir (13:05:30): > @Nur M Shahir has joined the channel
Christian Mertes (16:14:52): > @Christian Mertes has joined the channel
Tinashe Prince Maviza (17:01:08): > @Tinashe Prince Maviza has joined the channel
Hendrick Gao-Min Lim (17:31:50): > @Hendrick Gao-Min Lim has joined the channel
beyondpie (22:48:43): > @beyondpie has joined the channel
2020-07-29
Peng Yue (00:28:42): > @Peng Yue has joined the channel
David Burton (07:52:48): > @David Burton has joined the channel
Peng Ding (08:22:09): > @Peng Ding has joined the channel
Nastasja (09:08:45): > @Nastasja has joined the channel
Susan Holmes (10:54:29) (in thread): > I used Matlab in the early 2000s for doing image analysis but it is expensive for people overseas and the free version (Octave) doesn’t have anything like the R community. I switched all of my image analyses to EBImage and with Wolfgang Huber we have a chapter on image analyses and spatial analyses with Bioc/R and there is a much smoother transition to the stats part with R, so I don’t recommend Matlab for any applications nowadays.
Nick Owen (12:54:28): > @Nick Owen has joined the channel
Najeeb (13:10:19): > @Najeeb has joined the channel
Iara Souza (14:08:34): > @Iara Souza has joined the channel
Tim Howes (14:11:38): > @Tim Howes has joined the channel
lu wang (17:42:35): > @lu wang has joined the channel
Yoichiro Ohne (18:14:30): > @Yoichiro Ohne has joined the channel
sumankhanal (19:53:38): > @sumankhanal has joined the channel
Muhammad Ilyas (20:32:53): > @Muhammad Ilyas has joined the channel
Antonio Colaprico (21:32:00): > @Antonio Colaprico has joined the channel
2020-07-30
sani (09:41:00): > @sani has joined the channel
Adrija Kalvisa (09:46:08): > @Adrija Kalvisa has joined the channel
Jonelle Villar (11:15:48): > @Jonelle Villar has joined the channel
Bharati Mehani (11:33:32): > @Bharati Mehani has joined the channel
Andreas Gschwind (12:53:36): > @Andreas Gschwind has joined the channel
Brice Sarver (12:57:43): > @Brice Sarver has joined the channel
Saulius Lukauskas (12:59:30): > @Saulius Lukauskas has joined the channel
Sidharth Sen (13:07:19): > @Sidharth Sen has joined the channel
Aditi Singh (13:07:54): > @Aditi Singh has joined the channel
Sunil Nahata (16:11:02): > @Sunil Nahata has joined the channel
Connie Li Wai Suen (20:24:01): > @Connie Li Wai Suen has joined the channel
2020-07-31
Madara Hetti-Arachchilage (00:42:16): > @Madara Hetti-Arachchilage has joined the channel
Francesca Finotello (03:59:07): > @Francesca Finotello has joined the channel
Pedro Madrigal (10:06:38): > @Pedro Madrigal has joined the channel
Shivani Sharma (10:57:40): > @Shivani Sharma has joined the channel
philip terry (11:19:48): > @philip terry has joined the channel
Hector Climente (13:11:52): > @Hector Climente has joined the channel
Kirk Reardon (14:03:21): > @Kirk Reardon has joined the channel
Lara Ianov (16:08:08): > @Lara Ianov has joined the channel
Kristyna Kupkova (16:20:09): > @Kristyna Kupkova has joined the channel
Rona Vitancol (20:50:55): > @Rona Vitancol has joined the channel
2020-08-01
vedha (18:18:12): > @vedha has joined the channel
2020-08-02
Spiro Stilianoudakis (20:17:06): > @Spiro Stilianoudakis has joined the channel
2020-08-03
Steve Brooks (11:59:38): > @Steve Brooks has joined the channel
Junyan Xu (12:52:24): > @Junyan Xu has joined the channel
xtmgah (15:15:31): > @xtmgah has joined the channel
Jordan L. (17:36:57): > @Jordan L. has joined the channel
2020-08-04
Liz Hare (11:45:49): > @Liz Hare has joined the channel
2020-08-05
Alex Dinh (02:07:09): > @Alex Dinh has joined the channel
Hans-Rudolf Hotz (03:16:34): > @Hans-Rudolf Hotz has joined the channel
Nitesh Mani (10:02:58): > @Nitesh Mani has joined the channel
2020-08-06
Jaspreet (Jass) Bagga (17:35:05): > @Jaspreet (Jass) Bagga has joined the channel
2020-08-07
Aaron Lun (00:32:24): > Apparently, I’m finally earning enough money to have to start repaying my student loans.
Aaron Lun (00:38:38): > … almost 10 years after graduation.
Aaron Lun (00:38:58): > Should have been a lawyer.
Peter Hickey (01:23:20) (in thread): > it sucks when you’re overseas and suddently get that as a lump sum bill at tax time as opposed to it being taken out each pay when working in Oz
Aaron Lun (01:28:33) (in thread): > 20k
Peter Hickey (01:31:58) (in thread): > bugger
James MacDonald (10:33:42) (in thread): > So if you are working overseas they just say ‘pay up sucker’?
James MacDonald (10:43:02) (in thread): > Are there any restrictions in Ireland? Like proof that you have the ability to understand the coursework? Or can anybody go to University for any subject they choose?
Jędrzej Chrzanowski (13:12:35): > @Jędrzej Chrzanowski has joined the channel
2020-08-10
Sean Davis (08:38:20): > Sound familiar? - File (PNG): image.png
Wenxuan Fan (10:28:22): > @Wenxuan Fan has joined the channel
Jo Lynne Rokita (13:06:43): > @Jo Lynne Rokita has joined the channel
Le Zhang (13:54:19): > @Le Zhang has joined the channel
Casey Greene (17:11:34): > Where’s the Twitter DM?
Aaron Lun (17:12:25): > + slack
Aaron Lun (17:12:36): > + github issue
Sean Davis (17:21:52): > Those are for folks who get REAL WORK done….
Aaron Lun (17:22:22): > i’ll take that as a compliment
Aaron Lun (17:22:33): > given that those are the two things closest to “social media” that I have
2020-08-11
Aaron Lun (04:08:38): > I will say, I went to town on my GitHub profile.
Aaron Lun (04:08:50): > Can’t believe I only have a rating of A++ with a 2-year commit streak.
Aaron Lun (04:10:48): > ah bum. I guess it got broken because I deleted some private repos. Oh well.
Leonardo Collado Torres (09:54:08) (in thread): > you deleted git history? bold move hahaha
2020-08-12
Leonardo Collado Torres (14:40:01): > Has anyone used Calendly and do you have any recommendations about it?https://calendly.com/pages/pricing - Attachment (calendly.com): Pricing - Calendly > Calendly is free for 14 days. No card required. Explore our basic, premium, and pro plans an learn how each plan can make your day-to-day scheduling simpler than ever before.
Sean Davis (15:18:27): > I have tried it and I think@Levi Waldronuses it. I have to admit that I don’t keep my calendar updated well enough to allow a service like this to work. The free version is pretty limited, but it works.
Levi Waldron (15:23:15): > I use the free version and like it a lot. I make half hour blocks and just tell people to request an hour of the need it, then extend the time in Google calendar. I don’t know of anything else equivalent.
Levi Waldron (15:24:42): > But I keep my calendar fastidiously, at least for anything I’m going to remember to attend:smile:
2020-08-13
Leonardo Collado Torres (15:09:42): > Thanks Sean and Levi! I Had to look up the definition of fastidiously hehe. I learned a new word ^^ I also keep my calendar fastidiously hehe. Though I have a complicated scenario with 2 calendars: an Outlook-powered one for LIBD (their own server with non-default config) & Google calendar. Maybe I’ll use the free version with my Google calendar then
2020-08-14
Roye Rozov (01:56:48): > @Roye Rozov has joined the channel
Laurent Gatto (02:21:19) (in thread): > Hi Leo - I have (been imposed) a similar setup. It is possible to export the Outlook calendar and view it in the google calendar. I doesn’t seem to sync properly though.
Laurent Gatto (02:21:37) (in thread): > (In case that helps)
Vadim Nazarov (15:08:27): > @Vadim Nazarov has joined the channel
Aaron Lun (16:47:23): > partying hard
Aaron Lun (16:47:54): > https://i.chzbgr.com/full/8551220736/h38976F8A/party-real-hard - Attachment: Attachment
Simina Boca (18:15:48): > Did you all see this?:rolling_on_the_floor_laughing:https://vimeo.com/447645552 - Attachment (Vimeo): Making Your Zoom Look More Professorial > A recent article aimed at college instructors said that students “need to see someone professorial” when they log in to their online classes this fall. I’m doing my best to help. > > Other videos I’ve made that should be helpful for college students and instructors:
2020-08-16
Candice she.them (00:07:37): > @Candice she.them has joined the channel
Nitesh Turaga (11:30:47): > https://www.youtube.com/watch?time_continue=171&v=esILqJRuvN4&feature=emb_logo - Attachment (YouTube): git magic — predicting a git commit before it happens
Dirk Eddelbuettel (13:25:54): > Does anybody have a js hack to turn that animated emoji off?
Marcel Ramos Pérez (14:20:23): > There’s an option somewhere on Slack to turn animated emoji off. I don’t remember where though ..
Dirk Eddelbuettel (14:32:23): > Thank youso much@Marcel Ramos Pérez– that was what I needed. Finding it (in the web-based rather than desktop app) version was easy: - File (PNG): image.png
Dirk Eddelbuettel (14:32:44): > That toggle was on, is no longer, and serenity is restored. Yay team!
2020-08-17
Ying Xu (04:58:31): > @Ying Xu has joined the channel
Daniel Baker (12:17:20): > @Daniel Baker has joined the channel
2020-08-18
Evgeniy Rumynskiy (14:55:05): > @Evgeniy Rumynskiy has joined the channel
2020-08-19
Aaron Lun (04:04:46): > youtube just tried to sell me an ion chromatography system.
Aaron Lun (04:06:16): > Looks like that ad targeting system needs a bit of work.
Jonathan Griffiths (04:13:49) (in thread): > Look on the bright side - they think you’ve got a lot of money to throw around!
Aaron Lun (04:15:11) (in thread): > google should know I’m more of a mass spec kind of guy
Aaron Lun (04:15:58) (in thread): > chromatography? ok boomer
Leonardo Collado Torres (10:08:20): > maybe Google knows that there’s nothing that you are interested in buying… beyond paper copies of the OSCA book:sweat_smile:
2020-08-21
Dario Strbenac (20:00:12): > Anyone know where to find the proportion of A, C, G, T in a reference genome (e.g. hg38)?
Hervé Pagès (21:43:42): > Don’t know where to find this but it’s easy to compute if a BSgenome package is available: > > library(BSgenome) > genome <- getBSgenome("hg38") > afq <- sapply(seqnames(genome), > function(seqname) alphabetFrequency(genome[[seqname]], > baseOnly=TRUE)) > rowSums(afq) > # A C G T other > # 911537909 633799113 636431323 914210243 161368694 > > BSgenome packages include scaffolds (unlocalized & unplaced) in addition to the “assembled molecules” (a.k.a chromosomes). Replaceseqnames(genome)withgetChromInfoFromUCSC("hg38", assembled.molecules.only=TRUE)$chromin the call tosapply()above to include only the chromosomes.
2020-08-23
Sean Davis (12:50:09): > Please join us for a data science seminar on Friday, 09/04/2020, at 12 p.m. ET. > Title: Galaxy for Immunological and Infectious Disease ResearchSpeakers:Dave Clements, Galaxy Community Manager, Johns Hopkins University > > Steven Weaver, Senior Programmer Analyst, Temple UniversityAbstract:Galaxy is an open web-based platform for data integration and analysis in the life sciences. Galaxy makes sophisticated bioinformatics analysis accessible to bench researchers without requiring them to learn Linux system administration or command line interfaces. Every tool and tool setting is automatically recorded by Galaxy, making analyses reproducible by default. Analyses can also be shared with colleagues and with the public, enabling others to re-use and reproduce analyses pipelines. > In the first part of this webinar, we will introduce Galaxy and its supporting ecosystem and community. This will include the many ways Galaxy is available to researchers, and a brief overview of the Galaxy user interface. > In the second part, we will walk through an application of Galaxy to SARS CoV-2 research. We developed and published public reproducible Galaxy workflows for processing raw deep sequencing read data and calling intra-host genomic variants, as well as processing GISAID full-genome data in a comparative evolutionary framework (covid19.datamonkey.org). The goal of our analysis is to make use of all readily available sources of information to create a frequently updated list of sites in the SARS-CoV-2 genome that may be subject to positive or negative selection. High ranking sites on the list, especially those that are consistently detected over time or accumulate additional evidence in their favor with more data, could be taken as a set of candidates for functional impact or other downstream analyses. We search for evidence of selection at three different evolutionary levels: intra-host (next generation sequencing (NGS) data), between SARS-CoV-2 isolates (assembled genome data), and among beta-coronavirus isolates that are closely related to SARS-CoV-2 (assembled genome data). In this webinar, we will review the comparative analysis dashboard that can be used to which sites may have a functional impact or could be used for further downstream analysis, as well as how Galaxy can be used to implement the pipeline on researchers’ datasets. > Participants will learn how Galaxy is available, the basics of using Galaxy for data analysis, and how it can be applied in immunology in an example domain. > Join ZoomGov Meetinghttps://nih.zoomgov.com/j/1617561452?pwd=bE5YOVgrL2tHbFZidUJQOWZzdGlpZz09Meeting ID:161 756 1452Passcode: 586729 > One tap mobile+16692545252,,1617561452#,,,,,,0#,,586729#US (San Jose)+16468287666,,1617561452#,,,,,,0#,,586729#US (New York) > > Dial by your location > +1 669 254 5252 US (San Jose) > +1 646 828 7666 US (New York) > Meeting ID:161 756 1452Passcode: 586729 > Find your local number:https://nih.zoomgov.com/u/ayFfvRtd4 - Attachment (Zoom Video): Join our Cloud HD Video Meeting > Zoom is the leader in modern enterprise video communications, with an easy, reliable cloud platform for video and audio conferencing, chat, and webinars across mobile, desktop, and room systems. Zoom Rooms is the original software-based conference room solution used around the world in board, conference, huddle, and training rooms, as well as executive offices and classrooms. Founded in 2011, Zoom helps businesses and organizations bring their teams together in a frictionless environment to get more done. Zoom is a publicly traded company headquartered in San Jose, CA. - Attachment (Zoom Video): Video Conferencing, Web Conferencing, Webinars, Screen Sharing > Zoom is the leader in modern enterprise video communications, with an easy, reliable cloud platform for video and audio conferencing, chat, and webinars across mobile, desktop, and room systems. Zoom Rooms is the original software-based conference room solution used around the world in board, conference, huddle, and training rooms, as well as executive offices and classrooms. Founded in 2011, Zoom helps businesses and organizations bring their teams together in a frictionless environment to get more done. Zoom is a publicly traded company headquartered in San Jose, CA.
2020-08-24
Aaron Lun (00:52:36): > I’ve been staring at this manuscript for two hours, trying to write a review.
Aaron Lun (00:53:32): > So far my review file contains: > > 1. > > - >
Aaron Lun (00:53:37): > And that’s it.
Simina Boca (01:16:38): > Did you already read it?
Simina Boca (01:17:32): > I usually start with a short summary of the paper, as per Jeff Leek’s advicehttps://github.com/jtleek/reviews
Aaron Lun (01:28:29): > Of course I read it
Aaron Lun (01:29:02): > I read it last week, in fact, but I was so bored by it that I couldn’t bring myself to write the review at the same time.
Aaron Lun (01:29:34): > My current opening line is: > > The best thing that can be said about this manuscript is that it is short.
Aaron Lun (02:06:02): > Bioinformatics lists the status of every MS I’ve reviewed for them, and my god, it’s a bloodbath
Aaron Lun (02:06:20): > don’t think there was a single accept
Jose Alquicira (07:46:56): > @Jose Alquicira has joined the channel
Jonathan Griffiths (07:54:15) (in thread): > does this really say more about you, the journal overall, or the editor’s opinion of you as a reviewer?
Jared Andrews (09:16:19): > Bioinformatics gets about a billion submissions and probably has a higher reject rate than most. Can definitely afford to be picky.
Sean Davis (09:27:27): > Special CCR Grand Rounds2020 AAAS Martin and Rose Wachtel Cancer Research Award and Lecture**** ********“Mapping Cancer Genetics at Single Cell Resolution”******** ******** *******Luke Gilbert, Ph.D.Assistant Professor, Department of Urology > University of California, San Francisco ******* *******Friday, August 28, 2020******12:00–1:00 p.m.******* *******WebEx Event InformationWhen it’s time,join the meeting ******Join by phone1-650-479-3207Call-in toll number (US/Canada)Can’t join the meeting? ******To register for the lecture, please visit ***https://american-association-for-the-advancement-of-science.ticketbud.com/aaas-wachtel-award-lectureLuke Gilbert is an Assistant Professor in the Department of Urology, the Helen Diller Family Comprehensive Cancer Center and the Innovative Genomics Institute at the University of California, San Francisco. > > Dr. Gilbert was an early pioneer in repurposed CRISPR systems that are used to turn genes on (CRISPRa) and off (CRISPRi) by editing the epigenome. The Gilbert lab continues to develop new epigenetic editing approaches as well as new CRISPR functional genomics platforms. Recently, the Gilbert lab developed two next-generation CRISPR functional genomics platforms to systematically and quantitatively map genetic interactions. > > The Gilbert lab is focusing on utilizing our expertise to tackle big problems in cancer such as metastasis and drug resistance in cancer. They use genome-scale screens, genetic interaction mapping and genome engineering to identify genetic and epigenetic causes underlying why some patients are cured and others are not by cancer therapy. - Attachment (Cisco Webex Site): Meet virtually with Cisco Webex. Anytime, anywhere, on any device. > Simple, modern video meetings for everyone on the world’s most popular and trusted collaboration platform. - Attachment (help.webex.com): Video Conferencing - Troubleshooting Meetings > Troubleshooting Meetings - Attachment (american-association-for-the-advancement-of-science.ticketbud.com): AAAS Martin and Rose Wachtel Award Lecture 2020 | Buy Tickets | Ticketbud > AAAS Martin and Rose Wachtel Award Lecture 2020 - August 28, 2020 at Webex link will be emailed to registered attendees the week of the event. Find event and ticket information on Ticketbud.
Sean Davis (11:04:41): > Explore the intersection of data visualization and cancerData are only as useful as the insights we can glean from them. How might recent advances in interactive media and data visualization help illuminate and solve pertinent challenges in cancer research?Join us in a series of virtual eventsto explore these questions and spark new collaborations between experts in cancer research, data visualization, user-experience, virtual/augmented reality, and game design/development. > > > > There will be a series of four Micro Labs followed by a virtual poster session and 2-day Expo. Each Micro Lab starts with an inspiring conversation between thought leaders from the Cancer Moonshot and creative visualization experts followed by an opportunity to engage new colleagues from other fields in a fascinating discussion on the frontiers of cancer data visualizationMICROLAB 1: August 31, 1:30PM ETTracy FullertonDirector of USC Game Innovation Lab, pursuing experimental design of games in cultural realms including art, science, politics, and learning.Corrie PainterPatient advocate and research scientist at the Broad Institute; directs Count Me In, partnering researchers with patients to spread cancer discoveries.MICROLAB 2: September 1, 2:30PM ETJoe GrayDirector, OHSU Spatial Systems Biomedicine, creating a multi-scale tumor atlas and using systems analysis of extrinsic and intrinsic factors affecting cancer.Sabrina CulybaAn independent designer with experience spanning animatronics to theme park rides, virtual/augmented reality, and transformational games.MICROLAB 3: September 2, 1:00PM ETNils GehlenborgHarvard professor integrating visual and computational approaches to support sense-making of biology and reproducible collaborative research across epigenomics and genomics.Kunle OdunsiPhysician scientist and co-leader of Roswell Park Cancer Center’s Tumor Immunology and Immunotherapy Program, advancing diagnostics and treatments for gynecological cancer patients.MICROLAB 4: September 4, 11:30AM ETLindsay GraceKnight Chair of interactive media at the University of Miami School of Communication, exploring social impact through design.Karen EmmonsNational Academy member and Director of Harvard’s Community Engagement Program employing interdisciplinary approaches to reducing cancer risk and health disparities.POSTER SESSION: September 21-23 (Asynchronous)What are exciting visualization techniques? What are the data challenges in cancer? Submit your poster with a companion video and enjoy submissions from your peers across data visualization & cancer.2-DAY EXPO: September 24 & 25, 10AM - 6PM ETCollaborate with your peers on how to apply data viz to cancer challenges. Join us for an interactive symposium where we’ll explore the insights and get a chance to meet and connect with experts from both industries. > > > > Visit themeeting website to registerand learn more. > > Please forward this email to anyone you think may be interested in attending.
2020-08-25
Yilin Chen (01:23:05): > @Yilin Chen has joined the channel
Iwona Belczacka (05:43:13): > @Iwona Belczacka has joined the channel
Modupeh Betts (21:30:46): > @Modupeh Betts has joined the channel
2020-08-27
Vikki (21:02:48): > @Vikki has joined the channel
2020-08-30
Yagya Sharma (01:50:25): > @Yagya Sharma has joined the channel
Bob Policastro (10:59:47): > @Bob Policastro has joined the channel
2020-08-31
Mark Chen (12:11:03): > @Mark Chen has joined the channel
2020-09-01
Aaron Lun (16:43:40): > TOO QUIET!
Dirk Eddelbuettel (16:47:12): > Posted in another slack’s#randomearlier: - File (PNG): image.png
Jared Andrews (16:48:02): > Eh, I’d at least consider it for a minute.
Aaron Lun (16:48:26): > I used to watch all the med students in my cohort go in for the haggle
Wei Wang (17:49:39): > @Wei Wang has joined the channel
Aaron Lun (17:50:39): > Anyway, time to spice things up a bit by using->in random places in my code.
Aaron Lun (17:51:03): > Especially insideifstatements.
Aaron Lun (17:51:40): > Like > > if (1 +2 > 3 -> x) { > print(x) > } >
Aaron Lun (17:52:40): > I can only imagine the grateful face of my maintenance programmer as they admire this expression
Hervé Pagès (20:37:15): > I’ve seen systematic use of the right arrow in a package I was looking at recently. They were using the tidyverse pipe for almost every expression. So with the data flowing from left to right it seemed kind of natural to place the assignment to the right of the expression. I said “no way”, of course.
Hervé Pagès (20:38:31): > I think we need a right-to-left version of the pipe:%<%:grin:
2020-09-02
Sebastian Worms (04:50:49): > I’m fairly certain you’re the reason they keep the ICJ open in the Hague:stuck_out_tongue:
Martin Morgan (07:25:06): > Pipe-wise, magrittr hasmtcars %<>% select(cyl)which sends mtcars to the right, and reassigns the result to mtcars…
James MacDonald (10:21:01): > I would prefer something likemtcars %<?>% select(cyl), providing a dealer’s choice of what would happen.
Marcel Ramos Pérez (10:24:07): > if (rbinom(1, 1, .5)) ...:stuck_out_tongue:
Federico Marini (10:30:20): > reminds me ofhttps://github.com/romainfrancois/evil.R/blob/master/R/evil.R
Federico Marini (10:30:46): > > # T and F are wrong 5% of the time > makeActiveBinding( "T", function() runif(1) < .95, as.environment("evil_shims") ) > makeActiveBinding( "F", function() runif(1) < .05, as.environment("evil_shims") ) >
Hervé Pagès (12:23:14) (in thread): > nobody has sued me so far:crossed_fingers:
Jan Linke (12:42:18): > @Jan Linke has joined the channel
2020-09-03
Rachel Winfield (06:54:31): > @Rachel Winfield has joined the channel
Monika Krzak (07:08:57): > Hi all , I have question about methods / ideas which would help to detect important covariates (biological or technical) that should be potentially included in the model formula when doing sc de analysis. At the moment I am using variance decomposition (cc here@Davis McCarthyand@Aaron Lun) to identify most contributing factors. As in MAST paper (cc here@Greg Finak) most contribution also in my data comes from CDR. Ideally one would need to perform analysis of deviance on nested models to identify other important covariates, but I have too many combinations to be tested. Are there any methods out there with similar spirit to variance decomposition or more focused on testing various models to help selecting the most optimal one ? To follow the question I created<#C01A0UWNVNW>slack channel, any ideas are very welcome here or there:slightly_smiling_face:
Dario Strbenac (20:00:13): > Even Microsoft Outlook thinks that global assignment is dangerous and that you should be prevented from reading about it. - File (PNG): Alert
Aaron Lun (20:00:41): > indeed
2020-09-04
Dario Strbenac (03:15:30): > But aren’t some genes only expressed in normal tissue and other in both normal and cancer cells? This would only apply to those genes which are cancer-specific. - File (PNG): RNA-seq Purity Adjustment
Alan O’C (06:09:26): > Tumour purity can influence genes expressed only in normal cells for example through compositional effects (ie, given a fixed library size, if more “cancer genes” are sequenced. then there’s less reads available for “non-cancer genes”). Even if not, adjusting for a non-informative covariate in limma/DESeq2 etc shouldn’t be a problem right?
Dario Strbenac (06:30:18): > I think it will be a problem. Say you have gene A which is only expressed in normal cells and only 20% of the cells are cancer cells. It wouldn’t be right to multiply the read count of gene A by 1/0.2 = 5 to rescale it based on the tumour purity. Gene A’s expression in tumour is zero and all of its reads come from normal cells. I think this highlights the difficulty of accounting for different cell types and is probably a key reason why CIBERSORTx, which estimates cell type specific count matrices using scRNA-seq for deconvolution, made it intoNature Biotechnology.https://www.nature.com/articles/s41587-019-0114-2In bulk RNA-seq, you can’t tell which genes are specific to which kinds of cells, so a one-size-fits-all scaling factor seems optimistic. - File (PNG): Composition
Dario Strbenac (08:10:04): > Indeed. Even with the simple situation of one biopsy at one site and simultaneous DNA and RNA library preparation on it, the adjustment of different genes for the purity differences between biopsies of different patients is tricky.
Alan O’C (08:20:40) (in thread): > A similar work was published on biorxiv in 2018/nature comms 2019 (not cited); I’d suggest perhaps CIBERSORTx getting into Nat Biotech has more to do with the popularity of CIBERSORT:wink:
Alan O’C (08:21:24) (in thread): > With the caveat that I will always remain bitter about how they choose to distribute their program. Anyway good point
Dario Strbenac (08:30:10) (in thread): > Oh, certainly. It seems like one of those saturated single-cell research topics. It would be nice to have the source code and be able to understand better what calculations it’s doing behind the scenes.
Aaron Lun (11:17:48): > Don’t see the point of reconstructing cell-type-specific count matrices after deconvolution. Seems like you’re effectively just doing DE analyses on your reference profiles.
Dario Strbenac (21:00:06) (in thread): > Couldn’t you then take the Cancer matrix and then split the patients into groups such as responder and treatment-resitant and then do differential expression between those groups to ask the question “what cancer cell genes are associated with treatment resistance, ignoring those immune cells everyone fawns over for a moment?” I think the scenario is you might have done scRNA-seq on half a dozen patients but you already historically have a couple of hundred bulk RNA-seq samples and you want to do a more detailed analysis of them. I like how they gave their method the nickname Digital Cytometry. That’s good marketing.
Aaron Lun (21:02:02) (in thread): > Sounds hairy to make inferences on “stuff that didn’t match any of our references so we’ll just call it the cancer profile”.
Aaron Lun (21:02:50) (in thread): > god knows how much quantitative discrepancies there are between bulk and single-cell data
2020-09-05
Bob Policastro (20:25:42) (in thread): > Haha, python just added assignment expressions in 3.8 too, so enjoy the fun in both languages. I don’t think it would work backwards like this though.
Aaron Lun (20:30:21) (in thread): > Come to think of it, I brought this up after reading some of the rubyconf highlights, where they were talking about something similar (=>I think it was, can’t remember exactly).
Bob Policastro (20:32:42) (in thread): > I’m just happy I get to plausibly use the walrus operator in python and R now
2020-09-06
rohitsatyam102 (09:47:23): > Do we have R packages that can be used for human genome Assembly and evaluation?
rohitsatyam102 (09:49:26): > Also for annotation post assembly
Alan O’C (09:53:05) (in thread): > Seems like that would be two levels of arbitrary categorisation (responder/non-responder and cancer/non-cancer expression). > > Also it seems really tenuous to me to use deconvolution methods in a scenario where you are specifically expecting differences in expression profiles for the cells being deconvoluted
Aaron Lun (21:01:34): > my god, everyone’s photos on the BiocAsia website look unusually professional
Aaron Lun (21:02:34): > whereas I’m like - File (PNG): image.png
Tyrone Chen (22:30:10): > @Tyrone Chen has joined the channel
2020-09-07
Jonathan Griffiths (03:25:40) (in thread): > ah man
Jonathan Griffiths (03:25:49) (in thread): > walking in to see your new ’do that day was something else
Jonathan Griffiths (03:30:08) (in thread): > However you have been outdone by a colleague who came in with a handlebar mousache, reflective ’shades, and a Springsteen-inspired ’80s getup. Serious committment
Aaron Lun (03:40:30) (in thread): > hold on, that just seems like John every day.
Kevin Rue-Albrecht (05:18:50) (in thread): > professional is so…. normal - File (PNG): thats-all-aaron.png
Kevin Rue-Albrecht (05:20:02) (in thread): > I’d upvote this one any time for the back cover of OSCA:innocent:
Kasper D. Hansen (05:44:04) (in thread): > That is an awesome picture
Kasper D. Hansen (05:44:19) (in thread): > and great work in an image editor
2020-09-08
James MacDonald (09:56:47) (in thread): > I am disappointed in the lack of verticality though. A floppy mohawk?
2020-09-09
rohitsatyam102 (07:43:50): > can we use Pkgdown to make websites for teaching purpose? If not, are there other alternatives to it apart from blogdown
Federico Marini (07:46:10): > If you see how the workshops at Bioc2020 were done, I think the answer is yes
Federico Marini (07:46:52): > Workshop pacakges had vignettes in them -> you can use that to get them rendered via rmarkdown and then have the landing page
Federico Marini (07:47:41): > if you set up cleverly the GH actions, it can even autodeploy upon push- for this I’d leave you to the GHA-master@Kevin Rue-Albrecht:wink:
Lluís Revilla (08:29:57): > There is always the option to use Distill to make websites
Constantin Ahlmann-Eltze (09:01:26): > There is also a webinar by Alison Hill and Desirée De Leon on how to share rmarkdown documents with netlify for teaching materialshttps://rstudio.com/resources/webinars/sharing-on-short-notice-how-to-get-your-materials-online-with-r-markdown/ - Attachment (rstudio.com): Sharing on Short Notice: How to Get Your Materials Online With R Markdown > Educators create a lot of files for teaching- slides, exercises, solutions, assignments, data, figures - that all ultimately need to be shared with other people.
Dirk Eddelbuettel (09:10:19): > > can we use Pkgdown to make websites for teaching purpose? If not, are there other alternatives to it apart from blogdown > Of course there are! Don’t just fall for the loudest pied piper but find what suits you. You can (for the simplest case of static pages) > * simply edit in either Markdown or if you wish in RMarkdown > * use any applicable converter function to turn (R)md into html, just as one does for pdf creation; at the end of the day they pretty much all callpandocso you could also do that yourself. > * post them on any website and to me the simplest remain GitHub pages > None of thisrequiresany package that may change and break subtly in the future (as apparently happened to blogdown users), or disappear, or add additonal complexity (distill is really nice, but do youreallyneed it all?). One can also look into other frameworks. What the Python folks have inmkdocsisn’t bad either (and calls one of their markdown parsers rathern than pandoc). For what it is worth I keep updating the website for a course I teach for the 3rd time now (athttps://stat430.com) and I use “just” thehugobinary and tooling there (and host via GitHub Pages) though I did look into two of the*downpackages at the beginning. My (very personal) preference is to havesomeunderstanding of the different processing steps so that I can disentangle and adapt them as needed. Hugo is already pretty complicated so I prefer not to layer too many other steps on top. That method seems to have found other fans ashugodownis also an apparent simplification (NB have not used it or looked in any detail at it). > > But I don’t mean to discourage any efforts here: ifpkgdownorblogdownorbookdownorhugodownor … work for you by all means enjoy them. There is ample documentation and there are some helpers. Some of us may have some concerns about long-term viability of those approaches but on the marging those are our concerns, not yours so make your choice and enjoy. At the end of the day the most important part is alwaysyour content.
Sean Davis (10:55:21) (in thread): > Our requirements for Bioc2020 were: > 1. Structure each “workshop” as a self-contained, installable, testable package. > 2. Provide workshop authors with a simple (from lines-of-code perspective) approach to serve documentation and course materials. > 3. Build a reproducible, completely self-contained environment for running workshops in a portable way. > Number 1 was pretty easy to accomplish. Number 2 has many possible solutions, but we promoted pkgdown because it is relatively easy to use and produces a very standard set of resources that authors and many users have come to know. Number 3 is a bit specific to how Bioc runs workshops, but containers are really one of the few ways to memorialize a workshop for the ages. If you don’t need number 3, then Docker images aren’t important. If you don’t need number 1, then pkgdown doesn’t really apply. > I tend to agree with@Dirk Eddelbuettelbelow that pkgdown, blogdown, and friends are cool tools, but with some technical skill, it is easy to be creative with static website generators and documentation frameworks without a real need to go beyond rmarkdown or even simple markdown. > Finally, consider using jupyter notebooks as well. For some, they provide a nice alternative to Rstudio/Rmarkdown.
Sean Davis (10:56:48) (in thread): > If you want to reproduce the Bioc2020 model, just usehttps://github.com/seandavi/BuildABiocWorkshop2020repo as a template. Documentation there describes the process to modify with your own content.
rohitsatyam102 (10:59:03) (in thread): > Thanks@Sean Davisfor this detailed thread.
rohitsatyam102 (11:01:45): > Thanks @Drik@Constantin Ahlmann-Eltze@Lluís Revilla@Federico Marini@Sean Davis. Will surely try all these suggestions. I got a lot of time this month. It will be fun learning website development this way
Dirk Eddelbuettel (11:10:51) (in thread): > Glad to have been of help. These explorations can be fun. I am currently (slowly) noodling on a possible alternative topkgdownwhich has some design decisions that do not match my package structure (I use a GNU-style ChangeLog I want to render, my NEWS is in Rd format as for base R and I want that too, my vignettes tend to be pdf and on and on. ) Can be fun to explore these things, and it isreally nicewhen you have something that “remains functional”. My personal blog is a non-R static html compiler I used for 17+ years now, CRANberries uses the same etc….
Dirk Eddelbuettel (11:11:08) (in thread): > Oh, and typo: Dirk != Drik
frederick boehm (12:29:39): > @frederick boehm has joined the channel
Ornit Nahman (12:46:13): > @Ornit Nahman has joined the channel
Matt Stone (14:03:29): > @Matt Stone has joined the channel
Mian Li (21:46:59): > @Mian Li has joined the channel
2020-09-10
Sean Davis (14:39:32): > Applications for the 2021 Research Parasite Awards must be received by September 15, 2020 at 5PM HST (Hawaii Standard Time) atparasite.award@gmail.com****. ****https://researchparasite.com/
rohitsatyam102 (15:44:02) (in thread): > My sincere apologies for the misspelling.
Dirk Eddelbuettel (15:44:49) (in thread): > Oh, no worries. Being a really poor typist I have done the same one countless times.
Casey Greene (17:52:33): > Yeeeees!
Casey Greene (17:52:43): > Don’t miss your chance to apply!
Aaron Lun (17:53:40): > ah, was hoping for some cool tapeworm picture on the start page
Aaron Lun (17:55:26): > though the wasp larvae parasitism is also pretty spectacular
2020-09-11
wangchao (05:43:35): > @wangchao has joined the channel
Jenny Drnevich (11:06:14): > This is my University
- Attachment: Attachment
Dirk Eddelbuettel (11:23:51) (in thread): > Isn’t the public mocking about Urbana rather than Chicago?
Jenny Drnevich (11:29:50) (in thread): > Yes, it is about the main Illinois campus in Urbana, where I am. I actually am happy about having to spit twice a week, although Faculty/staff just got reduced to one required test per week.
Dirk Eddelbuettel (11:30:48) (in thread): > I’m part time there but fully remote. I was confused because your online presence still pointed to UIC where my wife is faculty. Anway,:wave:
Jenny Drnevich (11:46:25) (in thread): > Weird - I’ve never been affiliated with UIC but I do have some collaborators there so maybe that’s where that came from? I’m mostly remote but go in one day a week just to get out of the house and away from the kids!
Dirk Eddelbuettel (11:47:54) (in thread): > I guess I read by ‘source url’ rather than by the actual listed affiliation. So I once again get zero for reading comprehension. For reference the page I landed on washttps://www.psych.uic.edu/profile/jenny-drnevich-zadeh
Jenny Drnevich (11:53:31) (in thread): > Yes, I just noticed that after googling myself! I guess their page gets more traffic and that’s why it is at the top. I see you’re in the Stats department. Any chance I could bug you off-slack for help with correctly specifying 2nd and 3rd order interaction contrasts using limma’s modeling approach? I just can’t figure out what I am doing wrong…
Dirk Eddelbuettel (11:54:18) (in thread): > Would love to help but I only know limma by name and haven’t used it. Sorry!
Jenny Drnevich (11:57:58) (in thread): > Thanks anyway!
Ilir Sheraj (19:54:18): > @Ilir Sheraj has joined the channel
2020-09-12
Aaron Lun (22:24:57): > https://www.youtube.com/watch?v=MAlSjtxy5ak - Attachment (YouTube): Every programming tutorial
Dirk Eddelbuettel (22:58:25): > Variation: - File (PNG): image.png
Dirk Eddelbuettel (22:58:58): > Or of course the classic:
Dirk Eddelbuettel (22:59:00): - File (PNG): image.png
Aaron Lun (23:43:23): > I shall use that as a template to make some memes to annoy my colleagues.
Aaron Lun (23:43:27): > the next time they ask me “how to do X”.
2020-09-14
Dario Strbenac (03:00:11): > > While TPM and RPKM/FPKM normalization methods both account for sequencing depth and gene length, RPKM/FPKM are not recommended.The reason is that the normalized count values output by the RPKM/FPKM method are not comparable between samples. > Harvard bioinformatics core training workshophttps://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.htmlWhat do you think about the assertion the TPM is comparable between samples but FPKM is not?
Aaron Lun (03:11:12): > wut
Nilay Yönet (03:14:14): > @Nilay Yönet has joined the channel
Kasper D. Hansen (05:57:29): > I don’t get that page really, but perhaps there is something I just don’t understand
Kasper D. Hansen (05:58:21): > I don’t get the RPKM / FPKM example
Belinda Phipson (06:08:18): > @Belinda Phipson has joined the channel
rohitsatyam102 (06:51:06) (in thread): > Hope this could help:https://rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/ - Attachment (rna-seqblog.com): RPKM, FPKM and TPM, clearly explained > from StatQuest It used to be when you did RNA-seq, you reported your results in RPKM (Reads Per Kilobase Million) or FPKM (Fragments Per Kilobase Million). However, TPM (Transcripts Per Kilobase Million) is now becoming quite popular. Since there seems to be a lot of confusion about these ter
Ludwig Geistlinger (09:46:39): > I believe this discussion originates from: Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci 2012;131(4):281–5.
sanne.maas (09:50:22): > @sanne.maas has joined the channel
Selvi G (10:16:34): > Dear All, > > Good Morning! > > I am a bioinformatics scientist at DFCI - DS. > > We download a lot of data to maintain our centralized databases. We are in the process of improving our network bandwidth and are trying to gauge the biotech industry standard. > > Would anyone be willing to share what their network bandwidths and inbound/outbound speeds are at their organization? > > Thanks, > SelviG
Lluís Revilla (10:36:14) (in thread): > At work (not on industry) withspeedtest.net; ping: 2 Download Mbps: 734.71, Upload Mbps: 469.83
Sean Davis (13:44:34) (in thread): > NIH has two independent 100Gb connections to the outside and a 200Gb (100 x 2) in a “ring” configuration that extends between three “hub buildings”. Other buildings have 10 or 40 Gb connections from the ring. Buildings themselves typically have one or more 10Gb trunks that serve 1Gb connections to individual machines except in special cases where high bandwidth is necessary (10Gb can be employed for special equipment or use cases). So, in practice, everyone has at least a 1Gb connection to the desktop. One special case is our HPC cluster which has 8 independent data transfer nodes, each with 10Gb connection, so we can theoretically sustain 80Gb from the HPC to the outside world (typically requiring something like Globus/UDP to even approximately reach). In practice, a border firewall limits transfer speeds somewhat.
Sean Davis (13:48:26) (in thread): > A highly simplified overview of NIH network features is here:https://www.cit.nih.gov/service-area/network-services-ns
Selvi G (14:20:33) (in thread): > @Lluís RevillaThanks!
Selvi G (14:22:18) (in thread): > @Sean DavisThanks for the detailed info, Sean! This is very helpful. I will pass it on to our IT Director.
2020-09-15
Mostafa el-Tager (06:38:30): > @Mostafa el-Tager has joined the channel
Thomas Gade Koefoed (10:27:45): > @Thomas Gade Koefoed has joined the channel
2020-09-16
Mike Morgan (10:58:15): > @Mike Morgan has joined the channel
Hervé Pagès (14:30:00): > after being around for 15 years. wow!
Hervé Pagès (14:30:52): > so maybe it’s not too late for Biostrings:grin:
Aaron Lun (14:33:01): > think the extra colors will push you over the line
Hervé Pagès (14:33:37): > you won’t be my reviewer, hopefully:grin:
Aaron Lun (14:37:23): > don’t worry, I’m too small fry for CNS
Hervé Pagès (14:42:14): > Don’t worry, I’m not going to publish a Biostrings paper anytime soon. It would need a serious revamp first.
Aaron Lun (15:18:24): > ah. My academic coupon for GitHub expired.
Aaron Lun (15:18:55): > End of an era.
Nitesh Turaga (15:19:16): > What github features did you use that were tied with that coupon?
Aaron Lun (15:19:38): > Nothing, I think. Just the joy of having the little “pro” badge next to my name.
Nitesh Turaga (15:19:54): > Lol.
Aaron Lun (15:20:03): > Do we still get private repos with the public account?
Nitesh Turaga (15:20:07): > We all think you are aProif that is any consolation.
Nitesh Turaga (15:20:14): > Yes we do.
Aaron Lun (15:20:27): > oh, good. Don’t have to go through and delete my embarrassing repos then.
2020-09-17
FelixErnst (02:02:19): > My guess is that if you ask nicely, they will extend it. If you really want to …:grin:They did last year for me
Alan O’C (05:39:54): > The reason I used it back in the day was to have private repos - since they introduced those for free I don’t see the point
2020-09-18
Chris Cheshire (05:41:02): > @Chris Cheshire has joined the channel
2020-09-23
Dominik Böhler (15:34:33): > @Dominik Böhler has joined the channel
Soroor (22:25:23): > @Soroor has joined the channel
2020-09-24
Aaron Lun (00:44:28): > just changed my slack theme to chocomint
Aaron Lun (00:44:34): > tried banana but it waaay too intense.
Luke Zappia (02:35:40): > Can’t remember if I made this or got it from someone else but here is a theme based on the:bioc:logo:[color content],[color content],[color content],[color content],[color content],[color content],[color content],[color content],[color content],[color content]
Aaron Lun (02:36:27): > yes, that’s what I was using before, but I got bored of it.
Alan O’C (04:00:00): > Looks nice but it’s too bright for my taste
Alan O’C (04:00:36) (in thread): > Actually in dark mode it’s okay
Asya Khleborodova (13:16:08): > @Asya Khleborodova has joined the channel
2020-09-25
Anna Liza Kretzschmar (22:53:23): > @Anna Liza Kretzschmar has joined the channel
2020-09-27
Aaron Lun (20:08:25): > my god, I’m finally back online.
Aaron Lun (20:08:53): > internet is still technically down but I’m using my phone as a modem
Aaron Lun (20:09:02): > at last I can push my changes
Marcel Ramos Pérez (20:13:21): > Resourceful!
Aaron Lun (20:28:05): > struggling to download some single-cell data right now.
Aaron Lun (21:41:09): > oh thank the gods, it’s back for real.
Aaron Lun (21:41:21): > incidentally, the same power outage also cut my running water.
Aaron Lun (21:42:02): > I’ve not drank anything for almost 10 hours
Aaron Lun (21:50:36): > I bought a gallon of ice tea to get me through
Aaron Lun (21:51:23): > and lots and lots of chlorox.
2020-09-28
FelixErnst (09:45:31): > Has anybody every tried plotting a heatmap of a 70k*2k matrix? Any tips on aggregating the data?
Alan O’C (09:48:29): > Zuguang Gu had some posts on big heatmaps recently, more about rasterisation thoughhttps://jokergoo.github.io/2020/06/30/rasterization-in-complexheatmap/
Jared Andrews (09:55:52): > Yeah, rasterization is also the way to go if you want any shot of opening heatmaps saved to PDF in an editing program (Illustrator) afterwards.
Spencer Nystrom (13:10:10): > Depending on the data type you can take a random sample. For genomic signal heatmaps, for example there are many instances where the full matrix or a subset matrix look the same as long as the subset is large enough. But not always the ideal solution.
Aaron Lun (13:12:03): > Back in the day I had to make a large t-SNE that was too large for PDF, but the journal wouldn’t accept bitmaps. So I saved the t-SNE as a bitmap and thenloaded it back into Ras a raster image in a plot to save the axes and title as a PDF.
Jared Andrews (13:21:31): > Yes, we just added rasterization to dittoSeq to help take care of that for scatter/dim plot figures with tons of cells.
Alan O’C (13:27:55): > ggrastr provides raster geoms too
Jared Andrews (13:32:52): > That’s what we use internally for dittoSeq.
Jared Andrews (13:33:44): > Really need to swap pheatmap out for complexHeatmap in dittoSeq so that we can use rasterization for that as well.
Nathan Dyjack (23:36:25): > @Nathan Dyjack has joined the channel
José Sánchez (23:48:02): > @José Sánchez has joined the channel
2020-09-29
Aaron Lun (15:09:18): > just changed my slack notification sound to a lady saying “hummus”
Aaron Lun (15:09:22): > it’s pretty terrifying
Jared Andrews (15:19:02): > Hesitate to ask, but why?
Jared Andrews (15:20:00): > You can also have someone saying “complete” when your R code finishes running if you use beepr:https://cran.r-project.org/web/packages/beepr/index.html
Jared Andrews (15:20:31): > Or the Wilhelm scream.
Dirk Eddelbuettel (15:21:22) (in thread): > That one gets all the fame, but RPushbullet was earlier and can do more. Karl Broman featured it in a short comment years ago too…
Dirk Eddelbuettel (15:21:54) (in thread): > https://cran.r-project.org/package=RPushbullet - Attachment (cran.r-project.org): RPushbullet: R Interface to the Pushbullet Messaging Service > An R interface to the Pushbullet messaging service which provides fast and efficient notifications (and file transfer) between computers, phones and tablets. An account has to be registered at the site http://www.pushbullet.com](http://www.pushbullet.com)) site to obtain a (free) API key.
Dirk Eddelbuettel (15:22:48) (in thread): > Blimey. He even published adone()function. I missed that.https://rdrr.io/cran/broman/man/done.html - Attachment (rdrr.io): done: Send a short message via RPushbullet. in broman: Karl Broman’s R Code > Send a short message via RPushbullet, to be used to indicate that some R job is complete.
Jared Andrews (15:23:04) (in thread): > That’s nifty, though it requires a bit more effort.
Dirk Eddelbuettel (15:23:18) (in thread): > Here is the post:https://kbroman.wordpress.com/2014/09/04/error-notifications-from-r/ - Attachment (The stupidest thing…): Error notifications from R > I’m enthusiastic about having R notify me when my script is done. > But among my early uses of this, my script threw an error, and I never got a text or pushbullet about that. And really, I’m even more interested in being notified about such errors than anything else. > It’s relatively easy to get notified of errors. At the top of your script, include code like options(error = function() { } ) > Fill in the function with your notification code. If there’s an error, the error message will be printed and then that function will be called. (And then the script will halt.) > You can use geterrmessage() to grab the error message to include in your notification. > For example, if you want to use RPushbullet for the notification, you could put, at the top of your script, something like this: > > options(error = function() { > library(RPushbullet) > pbPost(“note”, “Error”, geterrmessage()) > }) > > Then if the script gives an error, you’ll get a note with title “Error” and with the error message as the body of the note. > Update: I knew I’d heard about this sort of thing somewhere, but I couldn’t remember where. Duh; Rasmus mentioned it on twitter just a couple of days ago! Fortunately, he reminded me of that in the comments below. > Another update: Ian Kyle pointed out in the comments that the above function, if used in a script run with R CMD BATCH, won’t actually halt the script. The simplest solution is to add stop(geterrmessage()), like this: > > options(error = function() { > library(RPushbullet) > pbPost(“note”, “Error”, geterrmessage()) > if(!interactive()) stop(geterrmessage()) > })
Jared Andrews (15:23:30) (in thread): > Phone notifications are quiiiiite nice though.
Dirk Eddelbuettel (15:23:58) (in thread): > Yes, but then your phone puzzes miles or meters away where you don’t herebeepscream. Or get notified from a cloud service. And on and on…
Jared Andrews (15:24:17) (in thread): > True enough.
Dirk Eddelbuettel (15:27:18) (in thread): > Setup is easy but one has to sit down once and create the (still free) token.
Hervé Pagès (17:00:16): > if “hummus” is terrifying then try “baba ghanoush”
2020-09-30
Robin Zhou (16:37:20): > @Robin Zhou has joined the channel
2020-10-01
Friederike Dündar (15:13:31): > Looking for someone who’s used open Edx to set up an online class and would be willing to share some thoughts on it.@Stephanie Hicksperhaps?@Michael Love?
Stephanie Hicks (15:49:41): > hi@Friederike Dündar— I made minor contributions to Rafa and@Michael Love’s course. Definitely recommend pinging@Michael Lovefor this topic.
Federico Marini (15:51:08): > I have nothing against having it in#randombut it is a good fit for#education-and-training? There you might have a more targeted readership:wink:
Friederike Dündar (16:21:57): > Sure thing. Wasn’t aware of that channel, will ping Mike there again.
Federico Marini (16:22:48) (in thread): > guess that was created during your maternal leave:wink:BTW: welcome back!
Friederike Dündar (16:25:22) (in thread): > Maternal leave was technically over almost a year ago:sweat_smile:But 2020 has been a kicker of a year in general
Friederike Dündar (16:25:35) (in thread): > btw, Mike wasn’t in that channel either
Federico Marini (16:29:26) (in thread): > > 2020 has been a kicker of a year in general > Stillis:disappointed:
Friederike Dündar (16:30:00) (in thread): > yeah, would not have minded the European fashion of a full year of leave instead of 6 weeks
Federico Marini (16:31:24) (in thread): > Oh, can imagine. Germany’s a paradise for that. And parental leave for fathers is not even that crazy idea
Friederike Dündar (16:32:11) (in thread): > yeah, who would have thought
Federico Marini (16:34:51) (in thread): > Patriarchal-structured societies are still quite widespread, thinking it is 2020:disappointed:
Friederike Dündar (16:36:32) (in thread): > Tbf, Germany is not that much more progressive; they just manage to create a financial incentive for fathers to take a minimum amount of leave
Friederike Dündar (16:36:45) (in thread): > it’s telling that they usually call it “Urlaub”
Federico Marini (16:37:26) (in thread): > :nauseated_face:
Friederike Dündar (16:37:41) (in thread): > on the other hand it is almost impossible to find full-day child care in Germany as in so many hours that parents can actually work 8hrs/day
Federico Marini (16:39:14) (in thread): > Especially in Rhineland-Palatinate, that I can confirm on my skin in triplicates (well, one round of technical replicates:slightly_smiling_face:)
Friederike Dündar (16:39:50) (in thread): > not just there, I believe:slightly_smiling_face:
Friederike Dündar (16:41:04) (in thread): > the annoying thing is that success in child care aren’t necessarily the most reproducible outocmes ;)
Federico Marini (16:49:20) (in thread): > I can sadly say that the usual Vitamin B helps - and we were not fully packed of that
Friederike Dündar (16:50:49) (in thread): > How did you survive the lockdown?
Federico Marini (16:55:39) (in thread): > lucky enough to live close to open fields & enough cyclable roads
Federico Marini (16:56:04) (in thread): > patience, lots thereof.
Friederike Dündar (16:56:07) (in thread): > and you worked on those fields and bikes?
Federico Marini (16:56:26) (in thread): > no, but that was the steam-off valve
Federico Marini (16:57:08) (in thread): > Homeschooling of the kids was on me in the morning, and then I could start my workday when gf came back from the school - being herself a teacher
Friederike Dündar (16:57:11) (in thread): > I felt like the steaming off was required constantly though:expressionless:
Federico Marini (16:57:51) (in thread): > yup, nerves and stress levels were at DEFCON 5 anyway
Friederike Dündar (16:58:33) (in thread): > notlooking forward to the winter, I have to say
Federico Marini (17:01:21) (in thread): > only thing is, now we can see that coming- doesn’t make it any lighter, or shorter, though
Friederike Dündar (17:02:13) (in thread): > well, at least we’ve traded a 1BR for 3BR, that will hopefully make a difference:fearful:
Federico Marini (17:02:26) (in thread): > If you now @EffinBirds on twitter:https://twitter.com/LeeenyL/status/1311690037042515975?s=20 - Attachment (twitter): Attachment > How in Twitterhell did I never see @EffinBirds until now? https://pbs.twimg.com/media/EjQOqUCWAAAzhAU.jpg
Friederike Dündar (17:02:36) (in thread): > not for the amount of work I’ll get done but for the overall levels of sanity
Federico Marini (17:03:11) (in thread): > Been with twins for enough time in 60m2, so I can easily relate
2020-10-02
MD MEHADI HASAN (19:07:46): > @MD MEHADI HASAN has joined the channel
2020-10-03
Aaron Lun (02:49:04): > I accidentally pressed “logout” on the BioC support site… spent half an hour digging through files to figure out my credentials, I haven’t had to log in explicitly for years. Oops.
Aaron Lun (14:19:44): > More amusing CHECK warnings: > > Warning: 'FUN' is deprecated. >
Aaron Lun (14:20:05): > Well, at least it’s not defunct.
2020-10-04
Curtis (04:28:15): > @Curtis has joined the channel
2020-10-05
David Sims (06:46:43): > @David Sims has joined the channel
Kevin Rue-Albrecht (11:10:39): > Excel jokes never get old:https://www.theguardian.com/politics/2020/oct/05/how-excel-may-have-caused-loss-of-16000-covid-tests-in-england - Attachment (the Guardian): How Excel may have caused loss of 16,000 Covid tests in England > Public Health England data error blamed on limitations of Microsoft spreadsheet
Jenny Drnevich (11:45:17) (in thread): > Ha! Although I learned something new - HGNC finally changed those symbols that Excel had treated as dates: SEPT1 has become SEPTIN1. I’ll still export as .txt rather than .csv and then manually tell Excel to read it in as character.
Friederike Dündar (11:56:40) (in thread): > I guess no one ever claimed that Excel was virus-proof…
2020-10-06
Batuhan Cakir (09:16:15): > @Batuhan Cakir has joined the channel
Anjali Silva (16:16:09): > @Anjali Silva has joined the channel
2020-10-07
ravindra raut (02:34:57): > @ravindra raut has joined the channel
Nathan (23:20:33): > @Nathan has joined the channel
2020-10-08
Davide Corso (05:23:51): > @Davide Corso has joined the channel
Flavia E (07:52:26): > @Flavia E has joined the channel
Rongting Huang (09:44:56): > @Rongting Huang has joined the channel
rohitsatyam102 (18:27:40) (in thread): > I have had a tough time correcting them for one of my paper, opening them first in notepad++ and then pasting them as text in excel
2020-10-09
Ellora (02:32:46): > @Ellora has joined the channel
Ellora Chua (02:34:07): > @Ellora Chua has joined the channel
Anna Danese (05:35:22): > @Anna Danese has joined the channel
Pio d’Adamo (07:22:29): > @Pio d’Adamo has joined the channel
Yuyao Song (13:28:20): > @Yuyao Song has joined the channel
Maria Colome-Tatche (16:51:23): > @Maria Colome-Tatche has joined the channel
2020-10-10
Aaron Lun (16:42:03): > O M G
Aaron Lun (16:42:08): > my curved monitor finally arrived
Aaron Lun (16:45:37): > It’s so big, some websites don’t even render naturally anymore
Aaron Lun (16:46:48): > my line width has now been expanded to around 800 characters per line
Alan O’C (16:50:37): > Just think of the Perl one liners you can write now
Casey Greene (17:09:53): > Too bad it doesn’t help you read perl one liners
Alan O’C (17:10:44): > If you figure out some way to tile GUI windows nicely on a wide screen without going full tiling window manager let me know
Dirk Eddelbuettel (17:15:39): > So … inquiring minds want to know. Asking the Borg about “Largest curved monitors” leads to 49” Dell. Is that the ball park? 49” ?
Aaron Lun (17:17:36): > no, just a mere 34 inch
Aaron Lun (17:18:23): > I always get my cm and in mixed up so it didn’t seem so big in my mind when I chose it
Alan O’C (17:20:14): > 34cm monitor would be quite a throwback! I think my old CRTs were bigger than that
Aaron Lun (17:21:43): > I figured I misunderstood the dimensions when it came in a box that went up to my gut
Casey Greene (19:14:03): > We use the 38” dells in our lab and they are a lot of space:laughing:
Aaron Lun (19:15:11): > yeah, the latest problem now is that all my anime needs to be upscaled or I have to sit back 2 meters to watch it without noticing the pixellation
2020-10-11
Hervé Pagès (18:24:55): > Just ordered my 27” monitor 2 days ago. Will be a huge upgrade for me (I’ve been looking at my 15” laptop screen for years). Should arrive in about a week. Can’t imagine being on a 34” monitor! I don’t even have room for that (would need to order a bigger desk).
rohitsatyam102 (18:35:26): > I myself never used more than 27” monitor
Taiyun Kim (21:48:46): > @Taiyun Kim has joined the channel
2020-10-12
Michael Lawrence (11:28:33): > 27” 1440p hits the sweet spot.
brian capaldo (11:42:20): > I barely know what to do with my 15inch MacBook screen
Kevin Rue-Albrecht (11:47:48): > happy to be spammed with suggestions (direct messages), given that Amazon Days 2020 are the next couple of days:grimacing:
Federico Marini (12:29:40) (in thread): > I recently kept an eye on this:https://www.amazon.com/Samsung-LC43J890DKNXZA-CHG90-Curved-Monitor/dp/B07CT1T7HH
Kevin Rue-Albrecht (12:44:03) (in thread): > What the fpkm:flushed:that looks so cool indeed!
James MacDonald (15:37:40): > What’s this single monitor claptrap? I have dual 22” monitors, which pale in comparison to my wife’s triple 22” monitors, one of which is mounted vertically. I obviously need two more…
Aaron Lun (15:58:26): > I don’t understand. How do you approximate the curve with only two monitors?
Kasper D. Hansen (16:05:45): > dual 27”
Robert Castelo (17:00:18): > I work with a 32” Dell monitor since 2007 and still functions well.
James MacDonald (17:23:41) (in thread): > Exactly! Which is why I need four. I mean, that’s a pretty janky curve approximation with just three, no?
Aaron Lun (17:23:57) (in thread): > yeah, damn straight
Amarinder Singh Thind (21:54:51): > @Amarinder Singh Thind has joined the channel
2020-10-13
Aaron Lun (00:11:58): > Another problem is that iSEE looks so sluggish now
Aaron Lun (00:12:19): > not entirely sure why, but you really notice the millisecond delays when the screen is so big.
Friederike Dündar (03:16:25): > because light takes its sweet time to travel from one edge of the curve to the other side?
Aaron Lun (03:18:41): > indeed
Aaron Lun (03:18:46): > general relativity in action
Aaron Lun (03:19:34): > none of that special relativity nonsense that the flat screeners have to settle for
Friederike Dündar (03:36:19): > do you also have to deal with the sun setting on one side and rising on the other?
Aaron Lun (03:38:46): > if I move my terminal to the far side of the screen, I can see time dilation taking effect
Friederike Dündar (03:51:19): > a new metric for measuring screen size: how many days you can have the terminal at a different spot in the screen
Aaron Lun (03:52:35): > of course, I should mention thatallsides of my screen are the far sides
Friederike Dündar (03:53:14): > not to mention the dark side
FelixErnst (07:34:09): > and the resolution is 1440p?
FelixErnst (07:34:31): > vertically I mean
Federico Marini (08:00:12): > looks like so, yes
Federico Marini (08:00:38): > the 43 inches is 1080
Noah Pieta (21:30:20): > @Noah Pieta has joined the channel
Zhiwei Bao (21:43:00): > @Zhiwei Bao has joined the channel
Andrew Liu (22:39:30): > @Andrew Liu has joined the channel
2020-10-14
Aaron Lun (01:10:19): > aww man the monitor has SPEAKERS
Aaron Lun (01:10:30): > it’s worth every penny I didn’t pay for it.
Aaron Lun (01:15:18): > bass is a bit overwhelming though
FelixErnst (01:53:59): > aka. it bounces itself of the table?
최호재 (01:59:56): > @최호재 has joined the channel
AishwaryaS (02:20:02): > @AishwaryaS has joined the channel
Emi Tanaka (02:37:27): > @Emi Tanaka has joined the channel
Pol Castellano (06:36:44): > @Pol Castellano has joined the channel
宋世璇 (08:23:08): > @宋世璇 has joined the channel
Vicky Hellon (09:02:44): > @Vicky Hellon has joined the channel
Debbie Li (19:36:00): > @Debbie Li has joined the channel
Fish Little (19:44:06): > @Fish Little has joined the channel
Nitika Kandhari (19:56:44): > @Nitika Kandhari has joined the channel
Zepeng QU (20:06:10): > @Zepeng QU has joined the channel
蔡漢龍 (20:19:32): > @蔡漢龍 has joined the channel
Jacob Westaway (21:12:35): > @Jacob Westaway has joined the channel
2020-10-15
rohitsatyam102 (03:19:24): > Hi everyone. Any idea where BioCAsia 2020 is being recorded. I missed the workshop session today?
Peter Hickey (03:21:48): > yes, it is being recorded. btw there’s a#biocasia2020channel:slightly_smiling_face:
rohitsatyam102 (03:33:43): > Thanks@Peter Hickey
Gwen (08:16:37): > @Gwen has joined the channel
Rachel Eastwood (13:51:24): > @Rachel Eastwood has joined the channel
Jianhai Zhang (16:50:41): > @Jianhai Zhang has joined the channel
wenqiang he (22:11:23): > @wenqiang he has joined the channel
2020-10-16
Tusharkanti Ghosh (18:48:31): > @Tusharkanti Ghosh has joined the channel
2020-10-17
Kevin Blighe (08:23:40): > @Kevin Blighe has joined the channel
2020-10-18
Aaron Lun (00:16:52): > one of the downsides of having such a large monitor is that it just pumps out heat
Aaron Lun (00:17:07): > it’s a sauna in here
hiro (02:47:55): > @hiro has joined the channel
Aaron Lun (02:51:08): > just realized that I don’t have anything to do for my 12-1 programming slot
Aaron Lun (02:51:21): > guess I’ll work on the BiocFileCache PR.
Aaron Lun (02:52:00): > but, god, it really is warm in here. Wonder if this monitor has a low-power feature.
Dario Strbenac (04:00:20): > Is there an R function that applies a function to every combination (e.g. a pair) of elements of a vector? I am thinking about the shortest R command to calculate fold changes between all pairs of gene abundances in a numeric vector.
Aaron Lun (04:10:41): > > vec <- log2(runif(10)) > combs <- combn(length(vec), 2) > lfcs <- vec[combs[1,]] - vec[combs[2,]] > df <- data.frame(t(combs), LogFC=lfcs) >
Dario Strbenac (04:20:18): > Thanks. I was thinking there might be something even shorter using a functional programming function, akin toReduce.
Sudarshan (13:42:56): > @Sudarshan has joined the channel
Adele Barugahare (20:23:08): > @Adele Barugahare has joined the channel
2020-10-19
Eijy Nagai (04:23:00): > @Eijy Nagai has joined the channel
Suzy Downing (09:24:20): > @Suzy Downing has joined the channel
Elana Fertig (09:40:42): > All@Melanie Lothand I are noticing a boost error in theCoGAPSpackage that occurs only on******riesling1 ******Windows s**erver > > include/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] > failed ************************ (Pred::************************ > ^ > include/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] > failed ************************ (boost::mpl::not_<Pred>::************************ > > Has anyone seen this bbefore?
Elana Fertig (09:43:46): > seems to be a compiler error with boosthttps://stackoverflow.com/questions/57457659/gccs-warning-in-boost-source - Attachment (Stack Overflow): GCC’s Warning in Boost Source > I am using boost 1.63 and when I compile my application that includes #include <boost/algorithm/string.hpp>. GCC complains: In file included from /opt/boost/boost/mpl/aux_/na_assert.hpp:23,…
Dirk Eddelbuettel (09:43:47): > Yes. BH maintainer here (i.e.the package whose headers call this, if you useBHrather than system Boost). In general you would set options in the client package. But CRAN doesn’t let us.
Elana Fertig (09:44:07): > Thankns@Dirk Eddelbuettel
Elana Fertig (09:44:11): > any idea how we should fix?
Elana Fertig (09:44:25): > is there a widows specific flag to the complier we should include?
Dirk Eddelbuettel (09:45:15): > Locallyjust for you in~/.R/Makevarsadd all the flags listed with a ‘no’ (i.e.from above:-Wno-parenthesesto suppress that warning) toCXXFLAGS(orCXX11FLAGS).
Dirk Eddelbuettel (09:45:26): > BTW not a good topic for#random.
Elana Fertig (09:45:38): > sorry — wasnt sure which channel we shoudl use
Elana Fertig (09:45:41): > happy to move it
Elana Fertig (09:45:56): > the local solution doesn’t seem to help the Bioconductor isnstall errors for submission though
Dirk Eddelbuettel (09:46:03): > So I use something like this:
Dirk Eddelbuettel (09:47:24): - File (Shell): Untitled
Elana Fertig (09:47:51): > do you submit that with the package?
Dirk Eddelbuettel (09:47:57): > None of these areerrorsthough. Just extra extra tediouswarnings. If you have errors we need a new question.
Dirk Eddelbuettel (09:48:22): > No you do NOT at least not on CRAN which forbids “non-portable flags”:man-facepalming:
Elana Fertig (09:48:26): > it’s onnky on the reisling1 Windows server
Elana Fertig (09:48:44): > so for running on the linux / mac we use in the lab it’s not a problem
Elana Fertig (09:48:49): > but erroring in the Bioconductor builds
Dirk Eddelbuettel (09:48:55): > Probably Riesling (ie no ei) if named after the wine. Same with Wiener of his processes. Not “Weiner”.
Elana Fertig (09:49:02): > http://bioconductor.org/checkResults/devel/bioc-LATEST/CoGAPS/riesling1-install.html
Elana Fertig (09:49:17): > sorry, typing quickly
Elana Fertig (09:49:41): > with a newborn so my typos may be frequent:laughing:
Dirk Eddelbuettel (09:50:22): > Mine are now at college in 3rd and 5th year and I still type like crap. But slack lets me edit so I can sometimes look respectable:wink:
Elana Fertig (09:52:11): > so I guess the question is since it’s just this one compiler in this one system and working fine otherwise, and seems to be a dependency issue
Elana Fertig (09:52:17): > how do we address w/ the Bioc submission?
Elana Fertig (09:52:20): > to make error free?
Elana Fertig (09:53:07): > happy to move channels to discuss if that’s more appropraite
Dirk Eddelbuettel (09:55:51): > I just glanced at your HTML log. I see twounrelatedthings happening > * you a ton of warnings; all are harmless (apart from confusing you, see next point) but irritating; per the discussion above you can try to suppress some; I would consider add openmpifWindows has that (I just don’t know) > * a hard error … but that one, experience taught us, is often a C++ compilation resource issue –> not enough memory
Dirk Eddelbuettel (09:56:51): > If that analysis is correct then there is very littleyoucan do other than maybe trying to dial down optimisation levels for the compiler. We see these errors “all the time”e.g.on cloud instances with 512mb or 1gb ram. For serious C++, you need more. I think that is your issue here.
Elana Fertig (10:05:18): > So nothing we can do?
Elana Fertig (10:05:25): > Thanks for checking.
Alan O’C (10:05:53): > Worth asking in#bioc-buildswhat amount of memory is available on the riesling builder
Elana Fertig (10:06:04): > Thanks. Will do.
Elana Fertig (10:10:47): > Really appreciate both of your quick responses@Dirk Eddelbuettel@Alan O’C!
Alan O’C (10:11:29): > No worries, can be messy getting things to build on windows at the best of times
Kasper D. Hansen (10:20:34): > Seems like ti would be worthwhile to figure out a configure script that identifies the compiler and then conditional on the compiler, sets the flags. This comes up once in a while, and there must be some autoconf way of doing this (although this problem is on Windows, so we don’t have autoconf)
Dirk Eddelbuettel (10:22:53): > I don’t think you can. Flags seen are standard-O2 -Wallwhich come from R. The box is simply too small or doing too many other things.Sometimesthe error is also spurious, so hitting it on the side (kidding) and re-submitted has also worked…
Elana Fertig (10:23:59): > it woudl be nice if this were a Bioc solution vs left to the individual package builder
Dirk Eddelbuettel (10:24:50): > The build admins generally work very hard at these things. And “nobody leaves a $10 bill on the floor”. Most easy and cheap fixes have been made.
Kasper D. Hansen (10:38:34): > Yeah, so we need a configure script which detects the compiler and then modifies the FLAGS but only if the compiler understands them
Kasper D. Hansen (10:40:26): > something like this:https://github.com/sifive/verilator/blob/master/configure.ac#L175
Kasper D. Hansen (10:40:36): > (I think, just did a quick google)
Chris Chiu (23:23:34): > @Chris Chiu has joined the channel
2020-10-20
Mahmoud Ahmed (07:39:58): > @Mahmoud Ahmed has joined the channel
Amy Willis (11:57:50): > @Amy Willis has joined the channel
Renyu (18:47:15): > @Renyu has joined the channel
2020-10-21
Britta Velten (07:02:32): > @Britta Velten has joined the channel
Mikhael Manurung (16:18:20): > Hi, I have a question regarding managing multiple package environments in various devices. In a project that I am working on, I use both Python and R. Sometimes I work on my personal workstation and then there are times when I submit my jobs to a cluster. However, I realised that the package versions in my workstation and cluster are not similar – I do not update the packages in my cluster as often as in my workstation. How should I solve this? > > I am thinking of using singularity in both my personal workstation and cluster. Is this a good solution or an overkill?
Nitesh Turaga (16:21:23): > A good way to go about it is, use a container (docker or singularity) and then upon start of that container it pulls from your Github version control. That way you always have the updated package running. > > Another more “localized” way is to use virtualenvs in python and R. Basilisk package in R helps with this.
Aaron Lun (16:22:34): > At least for R, I used to have a cron job on the cluster that would just doBiocManger::install(ask=FALSE)every night.
Nitesh Turaga (16:30:23): > But maybe don’t complicate things. Just use version control (Git / Github), virtualenv for python and virtualenv for R (renv or packrat)
Dirk Eddelbuettel (16:30:49): > I never found it to be a real problem for R either and did what Aaron suggests: current packages. No issues.
Mikhael Manurung (16:39:24): > Thanks for the ideas especially re: the Github. Maybe I can just put my conda env.ymlthere and use it as the reference for all of my devices. Isrenvalso capable of generating a.ymlfile?
Mikhael Manurung (16:41:13) (in thread): > This is:fire:. Could you point me to a tutorial that can get me started with this? Thanks in advance!
Nitesh Turaga (16:41:58) (in thread): > https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html
Nitesh Turaga (16:42:19) (in thread): > No idea about the.ymlfile for renv.
Mikhael Manurung (16:43:49) (in thread): > I could not find an explanation on how to make a cron job in the link…
Aaron Lun (16:45:47) (in thread): > this is a fairly standard unix operation, google provides reasonably good tutorials.
Mikhael Manurung (16:48:34) (in thread): > Okay, I’ll try it out! Thanks again:smile:
Kevin Rue-Albrecht (17:03:36) (in thread): > renvgenerates arenv.lockfile, which is the equivalent of the conda.ymlfile
Alan O’C (17:55:46) (in thread): > I don’t think renv works nicely with bioc-devel at all fwiw
Burak Kutlu (18:30:08): > @Burak Kutlu has joined the channel
2020-10-22
Luke Zappia (02:37:38) (in thread): > I have usedrenvto manage both the R and Python environments for some projects. For me it has worked pretty well but I did sometimes need to fall back toBiocManagerto install things.
Christa Toenhake (06:00:35): > @Christa Toenhake has joined the channel
Lori Shepherd (09:40:23): > 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.
Iara Souza (10:02:35) (in thread): > When I have to work in multiple platforms, I use renv to control library versions. Also, I use DVC (https://dvc.org/) and git to sincronize my data in those multiple platforms. This way I can ensure I have the same data in different machines. - Attachment (dvc.org): Data Version Control · DVC > Open-source version control system for Data Science and Machine Learning projects. Git-like experience to organize your data, models, and experiments.
ImranF (11:38:56): > @ImranF has joined the channel
Lori Shepherd (13:09:59): > support site is back up and able to post. Please post issues, bugs, concerns togithub.com/Bioconductor/support.bioconductor.org/issues
Aaron Lun (13:11:04): > oh yeah
MEHADI HASAN (15:33:12): > @MEHADI HASAN has joined the channel
2020-10-23
Rebecca Howard (08:15:15): > @Rebecca Howard has joined the channel
Falola Dare (10:18:16): > @Falola Dare has joined the channel
chaimae samtal (14:05:09): > @chaimae samtal has joined the channel
2020-10-25
Leo Lahti (17:29:52): > I cannot find information on abstract length for EuroBioc conference website. Does anyone know if there are strict limits on the abstract length?
Nitesh Turaga (18:21:48): > There is probably a Bio Europe channel
Leo Lahti (18:47:54): > i did not find, this is why i put it here..
2020-10-26
Sean Davis (12:26:20): > Some BOOOOOOlean logic thanks to Jason H. Moore on twitter: - File (PNG): image.png
Hervé Pagès (13:19:01) (in thread): > How did you search the channels? I just searched for “euro” and found this:#eurobioc2020.
Leo Lahti (13:19:29) (in thread): > yep they said that they created it today..
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
Sean Davis (08:29:33): > Is anyone here using GitHub Enterprise? If so, how is your usage different from a standard GitHub experience (that is, how are you using Github Enterprise features)?
Michael Lawrence (11:11:13): > For us it’s not so much about the features but the support that comes with the product, particularly on the development side, where validation is so emphasized.
Kevin Rue-Albrecht (11:16:45): > I’m curious now,@Michael Lawrencehow much time would you estimate (roughly) is wasted figuring out things without the extra “support that comes with the product”, at least in the academic context?
Aaron Lun (11:17:33): > Unless you have super-secret stuff that needs to stay on-prem, I would say that you would have better value-for-money using the public instance.
Kevin Rue-Albrecht (11:20:21): > Ok. Considering I’ve got my habits and I’m using GH basically every day, I thought as much. Though there are times when it’d be nice to poke support to clarify things, but I’d say that’s rare enough
Michael Lawrence (11:37:03): > Since for obvious reasons we have an on-prem deployment, “support” is mostly about integrating it with our internal infrastructure and keeping it working. It’s not about getting help with using it.
Sean Davis (13:54:05): > Thx,@Michael Lawrence,@Aaron Lun, and@Kevin Rue-Albrechtfor the discussion.
Dirk Eddelbuettel (14:03:24): > (For completeness, there is even “middle ground”. U of I had a GHE pilot in the CS dept but is now testing a standard GH hosted “outside” yet accessed with a the same campus-wide single sign-on. So same user account, but properties (orgs, repos, …) you can only get to via SSO.)
Lori Shepherd (15:04:14): > 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
2020-10-29
Pinki Dey (01:38:32): > @Pinki Dey has joined the channel
2020-10-30
Mikhael Manurung (05:49:53): > Does anyone have ideas for fun activities during virtual casual group meeting? What have you tried so far? What worked and what didn’t? And does any of you successfully recreate a virtual version of small talk at the coffee machine?
Steve (07:34:02): > Our team has a weekly chat session where we show and tell a photo (or screenshot) from the week. No pressure to produce one if your week was boring. It started as being a photo from our lives, but quickly became a way to talk about anything of interest, including some obscure (but fascinating) hobbies some fo the team have. It’s extremely casual and relaxed.
Mike Smith (07:35:57): > I’m guessing from ‘casual’ this isn’t supposed to be work related. One thing I’ve found works well is to have a fairly open ended question that each person in the group can take turns answering. For example, recently someone asked “Where’s the first place you’d travel too if COVID cleared up tomorrow?” That’s broad enough that people can answer in many ways (you can cover hobbies, family, adaption to remote working, previous trips, etc) so you learn a bit about each other, and everyone is likely to have something to say.
Kevin Rue-Albrecht (08:13:49): > Hello community! > > The#eurobioc2020submission deadline is extended toMonday, November 16th! > > The organising committee welcomes submissions for: > * talks > * workshops > * posters > * birds-of-a-feather session topics > The scope for submissions is far from limited to Bioconductor packages; we welcome contributions as workflows, live demonstrations, interactive Shiny applications, data visualisations, new concepts, packages in development, calls for feedback and collaborations, … and all the many more hidden gems produced by the community; surprise us! > > Submit your contribution here
We look forward to seeing you all online for this stimulating and community-driven conference! - Attachment (OpenReview): EuroBioC 2020 Conference > Welcome to the OpenReview homepage for EuroBioC 2020 Conference
Mikhael Manurung (09:20:52) (in thread): > Yes! This is exactly what I’m looking for. Thanks:smile:
2020-11-03
Antonio Federico (05:58:59): > @Antonio Federico has joined the channel
2020-11-04
Kishore A (14:17:10): > @Kishore A has joined the channel
Regina Reynolds (15:51:23): > @Regina Reynolds has joined the channel
2020-11-05
Qi (09:33:36): > @Qi has joined the channel
2020-11-09
Mike O. (14:33:01): > @Mike O. has joined the channel
Aaron Lun (23:36:14): > Only tangentially related, but I was just thinking about Eurovision.
2020-11-10
Kevin Blighe (07:21:01): > They say that Ireland eventually sabotaged its own chances of winning Eurovision because they could no longer financially support hosting it… they won it too much
Alan O’C (07:48:22): > How can you say that when we sent Dustin the Turkey in 2008?
Federico Marini (10:26:55) (in thread): > I’m more like a Jeux Sans Frontieres kind
Aaron Lun (15:04:37) (in thread): > For some context: Youtube, in its infinite wisdom, decided to puthttps://www.youtube.com/watch?v=NvS351QKFV4on my automatically suggested playlist. - Attachment (YouTube): Dschinghis Khan - Moskau 1979
Aaron Lun (18:48:53) (in thread): > which is now stuck in my head.
Aaron Lun (18:49:00) (in thread): > moskau…
2020-11-11
watanabe_st (05:05:37): > @watanabe_st has joined the channel
Jaclyn Taroni (09:02:36): > @Jaclyn Taroni has joined the channel
Joshua Shapiro (09:06:49): > @Joshua Shapiro has joined the channel
2020-11-12
Abby Spangler (11:40:31): > @Abby Spangler has joined the channel
2020-11-13
Welliton de Souza (06:44:27): > @Welliton de Souza has joined the channel
2020-11-16
Carmen Abaurre (05:57:54): > @Carmen Abaurre has joined the channel
XinqiaoZhang (11:24:55): > @XinqiaoZhang has joined the channel
2020-11-17
Liliana Zięba (14:05:43): > @Liliana Zięba has joined the channel
Jeroen Ooms (18:23:14): > @Jeroen Ooms has joined the channel
Gabriel Becker (18:49:34): > @Gabriel Becker has joined the channel
2020-11-18
Aaron Lun (03:40:18): > oops,just realized I was 17 minutes into a 1 hour loop of the same song
Anna Rita Putignano (05:00:37): > @Anna Rita Putignano has joined the channel
Valeria Ranzani (05:02:57): > @Valeria Ranzani has joined the channel
eugenia.galeota (05:11:23): > @eugenia.galeota has joined the channel
2020-11-19
Kim Grummel (00:45:09): > @Kim Grummel has joined the channel
tain lan (03:19:35): > @tain lan has joined the channel
David Dittmar (08:27:33): > @David Dittmar has joined the channel
Jan Bartel (08:39:51): > @Jan Bartel has joined the channel
2020-11-20
Shruti Shah (17:59:29): > @Shruti Shah has joined the channel
2020-11-21
Fedik Rahimov (13:49:05): > @Fedik Rahimov has joined the channel
2020-11-22
Tuomas Borman (16:16:53): > @Tuomas Borman has joined the channel
2020-11-23
Dominique Paul (08:33:49): > @Dominique Paul has joined the channel
황석영 (09:18:19): > @황석영 has joined the channel
2020-11-25
Arsenij Ustjanzew (08:05:47): > @Arsenij Ustjanzew has joined the channel
Louise Huuki (11:16:56): > @Louise Huuki has joined the channel
Aoi Senju (16:16:17): > @Aoi Senju has joined the channel
2020-11-26
rohitsatyam102 (08:24:31): > Just a random musing!! Is there a way to convert a python script to a conda package??
Federica Eduati (10:27:18): > @Federica Eduati has joined the channel
Oscar Lapuente Santana (16:15:34): > @Oscar Lapuente Santana has joined the channel
2020-11-27
fcatalamoll (06:45:42): > @fcatalamoll has joined the channel
2020-11-28
Rory Stark (12:30:04): > @Rory Stark has joined the channel
2020-12-01
Glenn Morton (12:22:02): > @Glenn Morton has joined the channel
Jenny Drnevich (23:05:43): - File (PNG): image.png
2020-12-02
Chienju Chen (01:22:39): > @Chienju Chen has joined the channel
Elyas Heydari (12:17:49): > @Elyas Heydari has joined the channel
cottamma (16:06:26): > @cottamma has joined the channel
2020-12-03
Eva Kohnert (06:19:18): > @Eva Kohnert has joined the channel
Daniel Keitley (08:56:46): > @Daniel Keitley has joined the channel
Kate (10:55:58): > @Kate has joined the channel
2020-12-04
Ewan Buckingham (10:02:22): > @Ewan Buckingham has joined the channel
Greg Brittingham (13:55:26): > @Greg Brittingham has joined the channel
Kary Oetjen (20:12:16): > @Kary Oetjen has joined the channel
2020-12-05
Changrong Ge (23:18:26): > @Changrong Ge has joined the channel
2020-12-07
Ying Chen (20:08:33): > @Ying Chen has joined the channel
Frank (21:36:29): > @Frank has joined the channel
2020-12-09
Phil Xie (05:59:13): > @Phil Xie has joined the channel
Alan O’C (08:24:00): > apropos of nothing - File (JPEG): drake_meme-r.jpg
Ines de Santiago (11:13:29): > https://remoteclan.com/s/z8k5bp/remote_work_is_forcing_managers_work - Attachment (remoteclan.com): Remote work is forcing managers to work harder and they aren’t doing a good job already > 2 comments
2020-12-10
Steve (02:52:09): > Hi all. I’m an avid R coder, but not a biologist at all. I was curious to know if it’s possible to get someone’s genome sequence (i.e. via one of those tests available for a few hundred dollars), and use R to somehow understand the individual’s predisposition to long term consequences from concussion injuries? > > The reason for my interest: I observe sports people receive similar injuries (head knocks), yet some develop Alzheimer’s at age 40, yet others experience no long term problems. I wonder if the genome can tell us who may suffer the worst so that they can avoid contact sports and minimise their chances of long term implications. Any suggestions / advice greatly appreciated
Lambda Moses (02:59:35) (in thread): > You might not need the whole genome sequence. You can get select SNPs used for genome wide association studies (GWAS) and see which SNPs are associated with the predisposition. There might already be a GWAS for something related.
Steve (03:00:49) (in thread): > Thanks@Lambda Moses! This is all new to me, so I’ll start googling the terms you mention, thanks very much for the ideas
Lambda Moses (03:04:30) (in thread): > SNP means single nucleotide polymorphism, like single bits in the genome where people have different nucleotides. They can be associated with disease risk. Those tests most likely only checked some SNPs of interest instead of the whole genome, since the former is a lot cheaper than the latter.
Steve (03:08:03) (in thread): > Thanks a lot, I’ve already found some GWAS’s that look useful. I just realised the human genome is 100GB (at least according to google)!
Steve (03:08:30) (in thread): > I wonder if the $300 consumer tests provide a 100GB data file. I’m guessing they probably don’t. I’ll have to investigate
Ricardo Ramirez (08:18:09): > @Ricardo Ramirez has joined the channel
Abhijeet Sonawane (13:41:40): > @Abhijeet Sonawane has joined the channel
2020-12-11
Katharina Imkeller (09:31:27): > @Katharina Imkeller has joined the channel
2020-12-12
Huipeng Li (00:35:25): > @Huipeng Li has joined the channel
Aaron Lun (19:16:47): > quiet around here.
Aaron Lun (19:16:53): > everyone playing cyberpunk 2077?
Sridhar N (19:23:29): > no, quake it is!
Aaron Lun (23:13:28): > in the meantime, I had a lapse of discipline and accepted a few paper reviews. Old habits…
Aaron Lun (23:15:16) (in thread): > Well, I don’t thnk that’s right. The genome sequence shouldn’t be more than ~3 GB uncompressed. Even less compressed, and definitely less if you’re just getting variant calls in VCF files.
Dario Strbenac (23:15:35): > Your Christmas presents arrived early.
Aaron Lun (23:17:19): > I had sworn off reviewing papers but I got guilted into it.
Aaron Lun (23:18:28): > My new year’s resolution is going to be “no more peer reviews”.
Aaron Lun (23:18:34): > well, unless I get something in return.
Abhijeet Sonawane (23:20:37): > Maybe a basic question but does anyone know how do I install STAR aligner on MacOSx Catalina?
Aaron Lun (23:24:12): > probably best to ask on biostars or something.
Jared Andrews (23:25:07): > Use conda.
Aaron Lun (23:28:21): > ugh. I can’t do this, I’m watching cyberpunk playthroughs instead.
Jared Andrews (23:33:52): > i will give it the 3-8 years necessary to purchase it for <$10 and maybe give it a go then
Aaron Lun (23:52:20): > it’s pretty buggy, though the vision is there.
Dario Strbenac (23:55:23): > The game’s developers could turn to bioinformatics software next.
2020-12-13
Sridhar N (00:00:02): > EA Sports - Mutect 2021
Sridhar N (00:01:48): > i just hope they don’t associate insertions == spawning
Aaron Lun (01:39:32): > EA? Sounds like it’ll be pay to win.
Sridhar N (01:59:37): > Of-course?!?
Aaron Lun (04:40:18): > it’s over. Finally, after 5 hours of procrastinating, I have finished my review.
Alan O’C (06:16:32): > conda install cyberpunk-2077?
FelixErnst (06:16:57): > longest conda install ever
Alan O’C (06:17:24): > Probably less buggy than my last conda env on the hpc tho
FelixErnst (06:18:09): > I will bet against that. consoles users seam to be in a bit of a state
rohitsatyam102 (13:45:30) (in thread): > Try using Mamba. It significantly reduces time
FelixErnst (13:46:13) (in thread): > This was not about conda vs. mamba
Aaron Lun (14:50:08): > it’s a good excuse to finally buy a top-of-the-line machine.
Aaron Lun (14:50:27): > 64-core threadripper, > 100 GB RAM, 2 TB SSD, the best graphics card money can buy.
Aaron Lun (14:50:36): > For single-cell work, of course.
Aaron Lun (14:50:53): > just happen to play games on it while it’s not in use.
FelixErnst (14:51:15): > And then you have a monitor which has a weird widescreen resolution. Good for single-cell work, but the game won’t like it
Aaron Lun (14:51:44): > I’ll have even more peripheral vision, it’ll be immersive!
FelixErnst (14:51:49): > :slightly_smiling_face:
FelixErnst (14:52:48): > a game in full HD looks a bit weird on a 4K screen. That took some getting used to, at least for me. Luckily I have less time to play games
FelixErnst (14:53:04): > :expressionless:
Alan O’C (16:33:33): > I think I have the same res screen as Aaron (3440x1440) and it’s great for games actually
Alan O’C (16:33:54): > At least I think it was back in the days when I made time for gaming
Alan O’C (16:34:24): > Also as long as Cyberpunk doesn’t segfault on load it’s less buggy:slightly_smiling_face:
Aaron Lun (23:43:14): > well, I finished watching the playthrough of one of the endings, so I better get back to… yet another review.
Aaron Lun (23:59:15): > ugh. it’s more than 10 pages long!
2020-12-14
Aaron Lun (00:00:06): > and it’s got a million authors. I was looking through the list hoping to find someone I worked with, so I could excuse myself due to a conflict of interest. Alas…
Aaron Lun (01:32:25): > I can’t believe they sent me a review reminder on the weekend.
Aaron Lun (01:32:56): > So as an act of silent disobedience, I put down my country of origin as the DPRK.
Hector Climente (02:23:44): > @Hector Climente has left the channel
Aaron Lun (02:46:43): > 2 down, 1 to go. Final review of the weekend.
Pranavathiyani G (08:19:18): > @Pranavathiyani G has joined the channel
Roberto Malinverni (08:21:46): > @Roberto Malinverni has joined the channel
Jenny Brown (08:48:38): > @Jenny Brown has joined the channel
Fredrick E. Kakembo (08:49:31): > @Fredrick E. Kakembo has joined the channel
Thomas Naake (08:49:36): > @Thomas Naake has joined the channel
Nicole (11:06:12): > @Nicole has joined the channel
Davide Risso (13:37:13): > At the next conference we should do bingo cards:@Aaron Lun’s name came up already 3 times at#eurobioc2020(if I counted correctly) – his picture once!
FelixErnst (13:38:08): > Should he get drunk, or do we get drunk?:slightly_smiling_face:
Davide Risso (13:43:04): > I think we should have a shot everytime his name is mentioned?:wink:
FelixErnst (13:43:44): > I agree. That way everyone gets something out of it. On the other hand this can used to force a drunkeness level
Alsu Missarova (14:04:40): > @Alsu Missarova has joined the channel
2020-12-15
Francesc Català (04:12:01): > @Francesc Català has joined the channel
Demitra Ellina (04:41:32): > @Demitra Ellina has joined the channel
Vince Carey (19:45:55) (in thread): > A macosx binary is distributed at the main STAR github. I verified that it could be used on catalina, once one has opened it with finder, and confirmed desire to use, as it is not ‘verified’ software.
2020-12-16
Manojkumar Selvaraju (08:08:05): > @Manojkumar Selvaraju has joined the channel
Paul Myers (10:17:44): > @Paul Myers has joined the channel
Henrik Eckermann (11:07:13): > @Henrik Eckermann has joined the channel
mariadermit (13:04:52): > @mariadermit has joined the channel
Abhijeet Sonawane (14:21:24) (in thread): > Thanks Vince.
2020-12-17
Abel Torres Espin (13:49:18): > @Abel Torres Espin has joined the channel
2020-12-18
Arvind Mer (11:03:32): > @Arvind Mer has left the channel
Ciro Ramírez-Suástegui (11:20:15): > @Ciro Ramírez-Suástegui has joined the channel
Aaron Lun (11:30:04): > omg. Apparently I went to the same high school as one of the atlassian co-founders.
Aaron Lun (11:30:08): > Shame about their products.
Jared Andrews (11:33:02): > Confluence is a nightmare
Marion Shadbolt (11:34:55): > @Marion Shadbolt has joined the channel
Anne-Maud Ferreira (12:22:21): > @Anne-Maud Ferreira has joined the channel
António Domingues (12:29:46): > @António Domingues has joined the channel
Shirin Moossavi (12:29:48): > @Shirin Moossavi has joined the channel
Yue Pan (12:59:30): > @Yue Pan has joined the channel
Faris Naji (13:03:34): > @Faris Naji has joined the channel
Andy Lynch (13:11:56): > @Andy Lynch has joined the channel
Byunggil Yoo (13:39:01): > @Byunggil Yoo has joined the channel
Friederike Dündar (15:42:55): > Can anyone recommend a repository for FASTQ files with sequencing data from human donors/patients? Something that provides controlled access to scientists (like dbGAP, I don’t mind if it’s more user-friendly than dbGAP, but it shouldn’t just allow anyone to download the data) and will accept data from studies involving fewer than 100 participants?
Michael Prummer (16:15:21): > @Michael Prummer has joined the channel
Kasper D. Hansen (16:16:29): > what’s wrong with dbGap?
Kasper D. Hansen (16:16:48): > How about ENA? The european counterpart to dbGap
Eric Davis (17:18:15): > @Eric Davis has joined the channel
USLACKBOT (18:06:27): > This message was deleted.
Dario Strbenac (22:00:02) (in thread): > Is that a rhetorical question or are you waiting for someone to reply with “SRA Toolkit”?
2020-12-19
Soumya Banerjee (16:16:24): > @Soumya Banerjee has joined the channel
Kasper D. Hansen (17:19:07) (in thread): > I often complain about dbGap, but it isasolution to release protected data, which is very non-trivial in general.
Kasper D. Hansen (17:19:47): > Ah its EGA. The branding could be better here (or I could google first)
2020-12-20
Giacomo Antonello (11:24:53): > @Giacomo Antonello has joined the channel
Wancen Mu (23:05:01): > @Wancen Mu has joined the channel
2020-12-21
Aaron Lun (00:47:02): > Another day, another way discovered for basilisk to walk itself into a wall.
FelixErnst (03:40:18): > maybe you want to call these situations aHarry Potter?
Harithaa Anand (04:08:16): > @Harithaa Anand has joined the channel
FelixErnst (04:31:02) (in thread): > Anything to test/debug on a second system?
Luiz Gustavo dos Anjos Borges (07:58:16): > @Luiz Gustavo dos Anjos Borges has joined the channel
Aaron Lun (12:29:50) (in thread): > no, I thnk I figured it out.
2020-12-22
Maya Reed McDaniel (10:05:29): > @Maya Reed McDaniel has joined the channel
Friederike Dündar (16:52:59) (in thread): > Well, they seem to suggest that only large-scale studies are qualifying and it does seem like a lot of bureaucracy is involved for each upload. I work for a core, so typically see many different, completely unrelated projects from many different PIs, each usually not exceeding 20 patients or so.
Friederike Dündar (16:53:34) (in thread): > Say, I have RNA-seq from 5 cancer patients. Would you deposit that in dbGAP?
Friederike Dündar (16:54:23) (in thread): > Have you used EGA?
2020-12-23
jim rothstein (22:24:59): > @jim rothstein has joined the channel
2020-12-24
rohitsatyam102 (06:00:18): > Hi can anyone furnish resources to start with package development in R like from the basics. Any youtube channel for thar sake would be great.
Davide Risso (07:05:33): > Not a youtube channel but I find Hadley’s book great! It covers both basic and advanced topics:https://r-pkgs.org/
Davide Risso (07:07:36): > I also gave this tutorial for a NYC Bioconductor meetup a while ago:https://youtu.be/Io2P7fe88eE - Attachment (YouTube): NYC R/Bioconductor Meetup: Creating and Maintaining an R package
Jose Marie Antonio Miñoza (16:36:04): > @Jose Marie Antonio Miñoza has joined the channel
2020-12-25
Hervé Pagès (15:43:21): > Let’s not forget the “Writing R Extensions” manual:https://cran.r-project.org/doc/manuals/r-release/R-exts.htmlIt doesn’t read as a book, doesn’t have exercises, doesn’t have much on the S4 class system, doesn’t have an opinion on good software practices, but it’s the reference and the authority, so a must to have in your bookmarks. - Attachment (cran.r-project.org): Writing R Extensions > Writing R Extensions
António Domingues (17:36:09): > @rohitsatyam102I just made public a collection of links which might be useful:https://github.com/adomingues/create_r_apckages/tree/mainMind you this is my own personal list of resources. I use this very often as well:https://kbroman.org/pkg_primer/ - Attachment (kbroman.org): R package primer > A minimal tutorial on how to make an R package.
Aaron Lun (18:48:56): > Second the WRE. The true bible for R development.
Aaron Lun (18:49:37): > On an unrelated topic, I’ve finally done it. It took a lot of work, but I’ve finally reached number 1 on the BioC rankings. - File (PNG): Screenshot from 2020-12-25 15-48-33.png
Aaron Lun (18:49:51): > Who knew that Bumpy matrices could be so popular?
2020-12-26
Aaron Lun (00:11:54): > Truly an auspicious day. - File (PNG): Screenshot from 2020-12-25 17-48-18.png
rohitsatyam102 (01:46:35) (in thread): > Thanks@Davide Rissowill start with these.
rohitsatyam102 (01:49:19) (in thread): > Wow! This is so resourceful. Really appreciate your efforts…Will check them out as I want to be transit from user to Developer by the end of 2021 end (New Year resolution:grin:)
Lori Shepherd (11:02:44): > I’m on vacation until after New year’s but I’ll look at the rankings when i get back. There was an issue when the stats weren’t generating since we use those for rankings and thought I applied a patch to use whatever the most recent calculated ranking was if unavailable but seems like there is a bug somewhere.
Hervé Pagès (15:24:38): > Right,@Aaron Lunyou already brought this in the#bioc-buildschannel and I already explained there that the download stats were currently broken. All the scripts that compute the stats have now been moved to a new AWS instance with more disk space (lack of disk space was the reason the stats broke in the first place) and have been migrated to Python 3. The stats are almost entirely repaired except for the workflows which will be restored today.
Aaron Lun (17:33:12): > yes, I know. I knew all along. Geez, don’t even get a day to celebrate my rank-1 status… BumpyMatrix is back to 1914/1927…
Hervé Pagès (21:07:47): > ah, ok. Well, didn’t mean to be a kill joy, sorry…
2020-12-29
Soumya Banerjee (05:54:45) (in thread): > @Davide Rissothat was a great tutorial! thanks a ton
Davide Risso (06:43:40) (in thread): > You’re welcome! I’m glad you liked it!
2020-12-30
Jay Gillenwater (11:30:23): > @Jay Gillenwater has joined the channel
2020-12-31
Aaron Lun (03:41:01): > NYE!
Aaron Lun (14:33:17): > still 2020 in my part of the world
2021-01-01
Aaron Lun (03:02:33): > first!
Hervé Pagès (03:23:04): > 2nd!
Davide Risso (04:49:36): > And you’re the two in the westernmost time zone in here! Even more impressive!:clinking_glasses:
Manasa Chava (08:26:59): > @Manasa Chava has joined the channel
Bernd (13:59:17): > @Bernd has joined the channel
2021-01-04
Lluís Revilla (03:03:58): > Why does Bioconductor exists as separate repository than CRAN?https://twitter.com/ozjimbob/status/1345947982210818052 - Attachment (twitter): Attachment > Hey #rstats folks, why does BioConductor exist? It’s super helpful that there is just the occasional random package with one useful function that isn’t on CRAN but is just…somewhere else instead.
Jared Andrews (08:44:32): > Different standards, different review process, different goals.
Hervé Pagès (12:58:36): > also: 6-month release cycles + rapid push/build/propagate mechanism for the devel branch + an overall size of 140GB (mostly due to some really big data packages) that wouldn’t be compatible with CRAN policy
Aaron Lun (13:00:13): > some developer-level sentiments athttps://github.com/Bioconductor/MatrixGenerics/issues/21
Michael Lawrence (15:09:04): > It’s also worth pointing out that Bioc is a lot more than a repository, contrary to what that tweet implies.
2021-01-05
Ralf Weber (06:10:55): > @Ralf Weber has joined the channel
Malte Thodberg (06:14:28): > Bioconductor also encourages reuse of common S4-classses that are maintained and optimized by the core team. CRAN is more of a wild west of S3 (perhaps with the exception of tidyverse packages)
Alan O’C (06:39:17): > Even tidyverse is kind of a wild west. I think Hadley’s written about how they’ve got a mad mix of class systems (ggproto and reference classes for example)
Federico Marini (09:28:57): > I don’t know about you, but I don’t think CRAN has much of an interest in having interoperable packages - and thereforeimprove your package, if you want to see it like that. > The review you get there is only technical - and I guess pretty much based on the R CMD check output, with the extra “as-cran” flags on. > Every package submitted to Bioc gets a human-made (andfor humans) review, which normally elevates the package one or two steps more. And this is potentially priceless in the academic software devel panorama
Lori Shepherd (09:30:59): > And as mentioned above… much more than a repository . you get this; a whole community to tap into and ask for advice and help.
Kasper D. Hansen (10:11:47): > I would say a critical factor is the dependency tree which was apparant from the get-go would be much bigger than for CRAN. A bigger dependency tree has clear immediate implications for testing and release
Kasper D. Hansen (10:13:25): > You can see the same with the tidyverse now, where I would argue they are starting to suffer from their approach of just updating each package as necessary. But because there are so many packages, tidyverse is essentially updated all the time. Not great for reproducibility. You can then argue that it is the users responsibility of making it reproducible, but that’s really just punting on a complicated problem.
Aparna Krishnan (13:56:31): > @Aparna Krishnan has joined the channel
Casey Greene (15:05:45): > I know@Sean Daviswon’t toot his own horn but he has a new gig:slightly_smiling_face:https://twitter.com/GreeneScientist/status/1346548082549391365?s=20 - Attachment (twitter): Attachment > I am thrilled to be joined by @seandavis12 at @CUAnschutz @CUMedicalSchool @CUCancerCenter to work together at the intersection of AI and health! > > https://news.cuanschutz.edu/cancer-center/sean-davis-data-science-ai https://pbs.twimg.com/media/Eq_mF_wXEAATmoE.jpg
Aaron Lun (15:06:46): > damn, I didn’t know sean was a MD.
Aaron Lun (15:07:25): > I’ll remember that the next time we’re at a conference together and I sprain my ankle or something.
Lluís Revilla (15:18:53): > Thanks all for the input, but I was thinking (and I think OP too) more on the historical events that lead to the creation of Bioconductor.
Sean Davis (16:08:05) (in thread): > Thanks,@Casey Greene. I could not be more excited! (except if, perhaps, I could go to an office sometime soon, but….)
Vince Carey (17:36:11): > @Lluís RevillaI can only speak for my view of the history, but just about every one of the points that has been raised was a concern at the inception of the project with a modest number of packages, back around 2001. We needed packages dealing with annotation that were large and “strange” relative to CRAN packages. We needed stronger standards for documentation than were obligatory at CRAN (vignettes). We needed two maintenance streams (release for stability and devel for experimentation). We needed a fixed schedule for synchronization with changes to R and for interoperation of packages in the ecosystem. We needed that schedule to be rapid enough to accommodate rapid change in biotech and slow enough to permit stabilization of user code. I credit Rob Gentleman with seeing all of those issues, and Jeff Gentry and Jianhua Zhang with starting it off. I am surely forgetting others who set the groundwork – Tony Rossini was our first release manager and his rigorous approach to dealing with stability is memorable. It may be illuminating to read thishttps://genomebiology.biomedcentral.com/articles/10.1186/gb-2004-5-10-r80… very readable, and, IMHO, not that much has changed. - 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.
2021-01-06
Lluís Revilla (04:11:57) (in thread): > Many thanks for all the work since the beginning
2021-01-07
Elisabetta Mereu (03:59:30): > @Elisabetta Mereu has joined the channel
Julie Aubert (05:58:26): > @Julie Aubert has joined the channel
Friederike Dündar (08:52:12) (in thread): > And you’ve used it for small scale experiments, i.e. 5-20 samples?
Kasper D. Hansen (11:25:56): > One small historical clarification: vignettes is really something that Bioconductor started. They are now supported at CRAN.
Federico Marini (12:11:31): > How did peopleuse a package before that? (Yes, sure, the man pages, but that’s usinga function, not the whole package)
Lori Shepherd (12:13:02): > I’ve seen people do a pipeline in the package overview man page but vignettes with expanded explanation is far superior
Federico Marini (12:13:48): > Yes, let alone the fact you can just share the pdf of that document in a much better way/see its outputs and so
Kasper D. Hansen (16:16:27): > You can still find many CRAN packages without vignettes
Federico Marini (16:25:49): > I know - always annoying since we are somehow… spoiled by the feast-level of documentation here
2021-01-08
rohitsatyam102 (07:03:30): > I was wondering if there is any package wherein you input the NC ID of variants and it gives output about which ACMG attribute does the Variant qualifies for?
Vince Carey (08:38:06): > what is an NC ID?
rohitsatyam102 (16:14:33) (in thread): > I was referring to variant annotation using HGVS nomenclature. Here by NC ID i mean the chromosomal position of variant. More from here:http://varnomen.hgvs.org/recommendations/general/ - Attachment (varnomen.hgvs.org): Sequence Variant Nomenclature > General
rohitsatyam102 (16:20:57) (in thread): > For example with NC ID: NC_000011.9:g.111959625C>T I can tell if the variant is pathogenic or benign, but I wish to ask if there is a package that assign it if the variant corresponds to which of the 28 ACMG attributes. For examples attributes discussed in this figure
rohitsatyam102 (16:21:26) (in thread): - File (JPEG): Screenshot_2021-01-08-22-21-09-79.jpg
rohitsatyam102 (16:21:51) (in thread): > Literature based attributes
2021-01-10
Vince Carey (08:19:27) (in thread): > Could you have a look athttps://vjcitn.github.io/BiocOpenCRAVAT/articles/BiocOpenCRAVAT.html… I would like to do more to update Bioc variant annotation capabilities, and OpenCRAVAT (https://opencravat.org/) is extremely relevant. The case study 3 inhttps://www.biorxiv.org/content/10.1101/794297v1.full.pdfmentions the ACMG guidelines but I am not sure whether there is an annotator in OpenCRAVAT that uses those attributes. - Attachment (vjcitn.github.io): Annotating variants with OpenCRAVAT, using Bioconductor > BiocOpenCRAVAT
2021-01-11
Hugo Tavares (12:45:38): > @Hugo Tavares has joined the channel
2021-01-12
Aaron Lun (01:14:39): > broke my entire toolchain with a catalina update and had to rebuild from Xcode up… 4 hours later, my R installation is functional again.
Aaron Lun (01:15:41): > Used the heat and fan from the laptop to dry my laundry at the same time.
Robert Castelo (02:55:53): > speaking of macOS catalina, i use docker to work with bioc-devel and, without any image running, the docker-related processcom.docker.backendis working at 100% CPU, even without laundry to dry. i’ve tried the suggestions i found on google about restricting “Resources File sharing” to/Users,/privateand/tmpand CPUs to 1, but still doesn’t go away when docker should be idle. any suggestions besides shutting down docker when i don’t use it? (which is what i’m currently doing) - File (PNG): Screenshot 2021-01-12 at 08.49.12.png
Sridhar N (03:16:18): > known issue probably chime in herehttps://github.com/docker/for-mac/issues/3499
Sridhar N (03:16:43): > if you have not tried this yethttps://github.com/docker/for-mac/issues/3499#issuecomment-482646126
Robert Castelo (04:32:01): > i saw that thread, they say that with the last update of docker the issue was resolved, i have the last update of docker and still have the same problem:thinking_face:
Dr. Laurel Raffington (05:50:09): > @Dr. Laurel Raffington has joined the channel
Sridhar N (09:52:43): > yes its worth reopening that issue IMO.
2021-01-13
Espen Riskedal (08:28:34): > @Espen Riskedal has joined the channel
Mohmed Ahmed Abdel-Fattah (15:10:26): > @Mohmed Ahmed Abdel-Fattah has joined the channel
2021-01-14
Eduard P (04:47:17): > @Eduard P has joined the channel
Darren (09:04:32): > @Darren has joined the channel
Dario Strbenac (18:00:05): > Someone has proposed thatGenome Wide Association Study (GWAS) statistics should be stored in VCF format. > > To address these issues, we adapted the variant call format to store GWAS summary statistics (GWAS-VCF) and developed open-source tools to use this format in downstream analyses.
2021-01-15
Malte Thodberg (04:35:46): > That paper had me wondering: Is there a Bioconductor package that has developed infrastructure for storing and manipulating GWAS summary stats?
Dario Strbenac (06:00:04): > GWASToolsseems like the one you’re wondering about. The journal article about GWAS-VCF didn’t even mention its existence.
Malte Thodberg (06:23:42): > GWASTools seems to be storing actual genetic data for GWAS, I was thinking in terms of storing post-GWAS summary stats, like positions, rsID, effect/other allele, INFO, MAF, N, P-Value, Z-score, standard error, etc. Basically the type of data you would use for SNP heritability, finemapping and colocalization
2021-01-16
Aishwarya Mandava (17:18:53): > @Aishwarya Mandava has joined the channel
Brad Tremblay (20:00:10): > @Brad Tremblay has joined the channel
2021-01-17
rohitsatyam102 (10:07:31): > Hi everyone. I was curious if there are any remote/ virtual genomics internship intakes happening currently?
Vince Carey (20:20:44) (in thread): > @Malte Thodberg@Kevin BligheI have done a bit of work on “data warehousing” for multiple sets of GWAS summary statistics. The fields noted by Malte define records in SQLite databases. Should we identify some example summary statistics – for example, from the GIANT consortium – and start a package to tackle this problem? The colocalization task is of especial interest.
2021-01-18
Malte Thodberg (02:57:00): > Interesting: What are the advantages of using SQL? My immediate idea would be to use a RangedSummarizedExperiment, with a GPos as ranges and Z-scores/SEs/P-values stored as assays in some form of DelayedArray
Andrea Gobbini (03:33:14): > @Andrea Gobbini has joined the channel
Kasper D. Hansen (04:24:43): > There are some long term advantages to storing data in SQLite because it is OS independent and the file format is unlikely to change. In contrast, when we serialize R objects, we need to update them every time we change the class definition. This has started to become more of a burden. Now,@Malte Thodbergsuggestion makes total sense for the R representation of the database.
Kasper D. Hansen (04:27:03): > Having said that, Im not sure@Vince Carey’s suggestion was based on a careful analysis. Finally, there is the alternative to build of GWAS-VCF and use that to store stuff. Personally, I would probably start with writing code for ingesting GWAS-VCF because no matter what you would probably want to be able to access that data and once you have it, you have some example data to play with. But using GWAS-VCF as the defacto file format for this, might not be a great idea.
Malte Thodberg (04:35:32): > I wouldn’t mind something standardized like GWAS-VCF catching on: Most people use their own csv/tsv files. That quickly becomes tedious to work with with GWAS tracks with tens of millions of variants
Malte Thodberg (04:37:25): > Given so many usefull R-packages for post-GWAS analysis, like COLOC/MOLOC, hypRcoloc, susieR and gChromVar, it’s a shame they don’t use the same data representations
Kasper D. Hansen (05:07:13): > The lack of standardization in the GWAS world is surprising to me. However, it is not clear to me that the answer is GWAS-VCF which - only based on the abstract - reads as someone taking a fileformat they already work with and say “hey, let’s expand this”. But perhaps its good? At least I hope the data they provide is great, even if the file format is not.
Kasper D. Hansen (05:08:09): > In general I am a bit skeptic about these file formats. For example, IMO SAM/BAM was not great and I don’t have a great feeling about VCF but honestly I have only used it very little so I have no insight.
Vince Carey (06:11:29): > https://github.com/mrcieu/gwasglue/
Vince Carey (06:11:39): > That looks pretty amazing?
Malte Thodberg (06:11:55): > Also here:https://www.biorxiv.org/content/biorxiv/early/2020/10/23/2020.10.22.351221.full.pdf
Malte Thodberg (06:12:50): > Both these projects seem to tackle the issue of assembling GWAS summary stats + LD information into a single pipeline
Vince Carey (06:16:04): > Let’s deploy on AnVIL.
Malte Thodberg (06:20:11): > Would be super cool if Bioconductor had a parallel to these projects though, with standardized classes for holding GWAS summary stats and LD-information from various populations. Then one could simply plug-and-play whatever colocalization or finemapping tool was best in a given situation
Vince Carey (06:28:11): > Have you used any of these mrcieu resources?
Malte Thodberg (06:38:54): > Looked briefly at echolocator, but since I was already running all the R-packages, using the their wrappers didn’t seem worth the while
Vince Carey (07:30:45): > @Kasper D. Hansenthe gwasvcf doc includes: Querying by rsid is slow. If a large number of queries by rsid are to be performed then it could be worth generating an index which would speed up the querying. This approach uses SQLite to create a local database, linking rsid to chromosome and position. It strips out the ‘rs’ from the rs identifiers to make fast searchers by integer. The concept is based on that developed here: bioforensics/rsidx. … so it looks like this is a hybrid of tabix/bcftools/sqlite…. perhaps a strong standard has not emerged because such a standard would really be the purview of GA4GH (imho) and the sights seem set very high (https://vrs.ga4gh.org/en/stable/releases.html#id1)
Kasper D. Hansen (07:33:08): > Im just going to say that from where Im sitting, the GWAS community has failed to deliver on this for many years, so I would not hold my breath.
Kasper D. Hansen (07:33:44): > A good long term solution might also not be easy, for example with different reference genomes and different populations and structural variants.
Kasper D. Hansen (07:34:30): > But more immediate challenges, for example how to do a co-localization analysis well in R using standardized objects, seems doable.
Kasper D. Hansen (07:35:24): > This may be a situation where you should start with a few reachable and identified goals and focus on that. And not get distracted by a perfect solution until you have some experience with 1 iteration.
Vince Carey (07:50:29) (in thread): > We have to make good choices on representation and storage for the analyses to be performant. But it seems like you@Kevin Bligheare thinking more about individual-level contributions to GWAS. Even the summary statistics are proving to be unwieldy and need benchmarking and standardization. I’ll have a look at RegParallel….
Vince Carey (08:02:32): > The gwasglue seems to depend onhttps://github.com/explodecomputer/genetics.binaRies… which provides plink, bcftools, and gcta in binary format…. unwinding this could be laborious.
Malte Thodberg (08:14:09): > There’s quite a few very useful R packages for analyzing GWAS summary stats: > * COLOC:https://cran.r-project.org/web/packages/coloc/vignettes/vignette.html > * MOLOC:https://github.com/clagiamba/moloc > * HyPrColoc:https://github.com/jrs95/hyprcoloc > * susieR:https://github.com/jrs95/hyprcoloc > * mmbr:https://github.com/stephenslab/mmbr > * chromVar:http://www.bioconductor.org/packages/release/bioc/html/chromVAR.html > * gChromVar:https://caleblareau.github.io/gchromVAR/articles/gchromVAR_vignette.html
Malte Thodberg (08:15:42): > It seems obvious to use them together with GRanges. Main thing would be a class to store the summary stats, and then sum functions for easier merging.
Malte Thodberg (08:16:18): > For example, merging two GPos based on seqnames/pos/strand and effect/other allele.
Kasper D. Hansen (08:29:06): > There is also the locusZoom script which is widely used but is just one enourmous R script as far as I know
Malte Thodberg (08:31:53): > Never really liked LocusZoom, simply doesn’t produce very nice looking plot. We are currently working on a ggplot-based replacement:https://github.com/MalteThodberg/tidyGenomeBrowser
Vince Carey (09:08:46): > Maybe we should start a new channel for GWAS-related software in Bioc. But I will just dump out this concept: We are looking for a GRanges-oriented interface to an external store with columns of diverse types, IMHO. So really a DelayedDataFrame as the mcols of a GRanges… I don’t think we have that. Maybe recent work in TileDb is relevant; bigrquery also comes to mind. The restfulSE project is somewhat relevant – we have have a RangedSummarizedExperiment with a BigQuery back end … for both the assay and the colData IIRC. But handling the colData is complex. End of dump. bigdata-rep channel very relevant.
Martin Morgan (09:11:27): > @Qian Liuhas worked on DelayedDataFrame and also with gdsfmt ; perhaps she will provide some commentary
Martin Morgan (09:12:07): > http://bioconductor.org/packages/devel/bioc/html/DelayedDataFrame.html - Attachment (Bioconductor): DelayedDataFrame (development version) > Based on the standard DataFrame metaphor, we are trying to implement the feature of delayed operation on the DelayedDataFrame, with a slot of lazyIndex, which saves the mapping indexes for each column of DelayedDataFrame. Methods like show, validity check, [/[[ subsetting, rbind/cbind are implemented for DelayedDataFrame to be operated around lazyIndex. The listData slot stays untouched until a realization call e.g., DataFrame constructor OR as.list() is invoked.
Vince Carey (09:12:25): > right … i googled on that but did not see it … it is low in page rank for now
Qian Liu (09:20:14): > Thanks@Martin Morgangdsarray uses gdsfmt as the back end, which was originally designed by xiuwen Zheng for gwas data lazy representation. Delayeddatadrame is compatible with all delayedarray concepts including gdsarray.
Qian Liu (09:26:27): > Xiuwen has also developed several very useful bioc packages for analyzing big popular genomic data usinggdsfmt(core array). For example,SNPRelatefor analyzing GWAS data, andSeqArrayfor analyzing sequencing data (as an alternative to VCF). A new package calledSCArrayalso suggests that he is working to use gds format to lazily represent the SCRNA-seq data. He is also a co-author ofGWASTools. The series of packages for representing and analyzing GWAS/DNA-seq/scRNA-seq data using GDS format is well worth to explore.
Qian Liu (23:18:45): > Above message updated!
Qian Liu (23:20:36): > TheGDSArraypackage is currently a wrapper of GDS formats that corresponds to theSNPRelateandSEQArrayonly. There are more general gds formats that I will need to update theGDSArrayto accommodate.
Qian Liu (23:23:38): > For@Vince Careyconcept, theDelayedDataFrameis now extending theDataFrameand representsDelayedArraycolumns (e.g.,GDSArray,VCFArray) It should fit as mcols of GRanges.
2021-01-19
Aaron Lun (16:07:05): > Julia’s “all functions are methods” philosophy is pretty interesting. Basically every function is (or has the capability of being) equivalent to an S4 generic in R.
Alma Hernandez de Rojas (16:18:57): > @Alma Hernandez de Rojas has joined the channel
Spencer Nystrom (16:29:05) (in thread): > I spent a lot of time with pre-1.0 Julia and really loved this about it. Alas, the Biojulia project is not keeping pace over time as I’d like.Biocwins again.
Aaron Lun (16:40:49) (in thread): > As a learning experience/proof of concept, I’m going to see if I can replicate some of BioC’s core structures and generics in Julia. Probably will start with the SE and see how far I can go.
Spencer Nystrom (16:48:45) (in thread): > That would be really neat. I’ll be curious to hear your thoughts after you’ve spent some time with it, so do report back. I very much want to jump on the Julia hype train, but I got a little tired of having to implement everything from scratch just to get an analysis done. I’m sure if you get something working well the Biojulia folks would be interested. > > A major annoyance for me was theirGenomicFeatures.jlwhich is their attempt atGRanges, but it uses B-trees and the ergonomics of it aren’t quite the same, but maybe I just never grokked it correctly. Regardless, something more data.frame like in that space could really open up the genomics space.
Aaron Lun (16:54:28) (in thread): > I can already see one advantage of the Julia CLI over python’s; I can indent as haphazardly as I like and it’ll take it.
Spencer Nystrom (16:58:10) (in thread): > Performance of C, flexibility of python, indentation like a madman (if you want).
Hervé Pagès (16:59:28) (in thread): > This will be an interesting experiment@Aaron Lun. I had that itch for a long time now but never got the time to dedicate to it. Let us know how that goes.
Aaron Lun (17:18:37) (in thread): > Trickiest part is how to handle copies, and the fact that the class objects are not mutable by default. A philosophy generally closer to R than Python, I would say.
Michael Lawrence (19:05:22) (in thread): > GenomicFeatures.jlwas developed by Pete Haverty, formerly of our group here at GNE. It was directly inspired by Bioconductor, and made some interesting internal optimizations that we could adopt (not sure about back compat).
Michael Lawrence (19:09:03) (in thread): > Adding more Bioc equivalents is a good idea. Julia generics though are less constrained than S4 generics (the formals do not need to be consistent), which makes them less useful as an abstraction. Of course, a project could voluntarily put that constraint on itself.
Spencer Nystrom (19:09:08) (in thread): > Was that notGenomicVectors.jl?
Spencer Nystrom (19:09:45) (in thread): > I remember pete pointing me towards that one in the early dev phase.
Spencer Nystrom (19:10:11) (in thread): > I recall that one acting more similarly to Granges.
Michael Lawrence (19:10:44) (in thread): > Yea, that’s right, sorry.
Michael Lawrence (19:14:34) (in thread): > Julia would complement R in much the same way that C++ does, as a means of increasing performance, with the added benefit (over C++) of being a simpler high-level language. R would remain the primary user interface. From that perspective, it may be acceptable and even desirable for the Julia equivalent of Bioc to implement mutable data structures.
Aaron Lun (19:15:20) (in thread): > for that, we would need no-memory copies of data structures into Julia.
Aaron Lun (19:15:33) (in thread): > I don’t know whether the RJulia interface really supports that, or whether we have to do it ourselves.
Michael Lawrence (19:15:42) (in thread): > definitely doable; would be fun
Aaron Lun (19:15:49) (in thread): > juliacall
Michael Lawrence (19:21:05) (in thread): > Would still need COW at the interface layer, but mutable after initial (lazy) copy.
Aaron Lun (19:30:50) (in thread): > well, that’s the thing; do we? We could justunsafe_wrapthe input to create a Julia object that is understood by developers to be immutable. Provisioning the output is a bit trickier but could be done by calling into R to allocate the necessary memory.
2021-01-20
Aaron Lun (03:59:27) (in thread): > My god. I finally got this damn thing working. Uses Julia as an embedded language inside the C++ code of an R package.
Aaron Lun (04:05:45) (in thread): > Major hurdles with actual deployment as the embedding relies on dynamic linking. Also I keep on getting stack smashing errors when I close the R session, though that’s probably because I had to do some voodoodlopenwithout adlclosesomewhere.
Kasper D. Hansen (04:13:35) (in thread): > How are Julia doing now with packages? Last time I looked I felt that the package concept (installing from say Github) was much more developer friendly, but I think that is a huge mistake. One of the most powerful thing about R is actually the CRAN/Bioc gatekeeping insisting on minimal (and sometimes not so minimal) requirements.
Spencer Nystrom (07:16:05) (in thread): > My understanding is that what happens a bit is folks will form groups which host packages around a task, like BioJulia and the JuliaImage groups. These groups have their own standards. Of course, as you say, most things are hosted on GitHub, and there is a version of package registration, but nowhere like CRAN or bioc. The package manager, underwent a major rewrite years back to support many backends that are not GitHub.
2021-01-21
Aaron Lun (03:19:29) (in thread): > Still waiting for my SQLDataFrame that’s actually a DataFrame, by the way.
Robert Castelo (07:03:18): > Not sure this is the right channel (tell me otherwise), but is there any documentation out there on best practices in using BiocParallel and basilisk? i want to call a python program from an R/Bioc pkg. the python program takes one BAM file at a time, i want tobplapply()over BAM files recorded in a BamFileList object. i guess the two main options are: > 1. open parallelism before starting the basilisk run > > > bplapply(bfl, function(bf) { cl <- basiliskStart(env) ; out <- basiliskRun(cl, function() { ## call python }) ; basiliskStop(cl) } > > 2. open parallelism within the basilisk run > > cl <- basiliskStart(env) ; out <- basiliskRun(cl, function() { bplapply(bfl, function() { ## call python }) }) ; basiliskStop(cl) >
Aaron Lun (11:18:14): > the former is safer with respect to arbitrary BPPARAMs. The latter only works in shared memory contexts, and might not even achieve parallelization in some cases.
Martin Morgan (11:25:28): > It seems likeSnowParam()is going to be a better bet for these complicated types of situations, which is method 1.
Robert Castelo (11:47:36): > Thanks for the advice, i’ll follow method 1. One further question for@Aaron Lun, i looked up the code ofvelociraptor, expecting to maybe find an example of using BiocParallel andbasilisktogether, which i didn’t, but i noticed that the call tobasiliskRun()is not enclosed by thebasiliskStart()andbasiliskStop()calls. How velociraptor creates the Python environment withoutbasiliskStart()? What is the recommended use ofbasiliskStart()andbasiliskStop()?
Aaron Lun (11:48:17): > oh,basiliskRuncalls start/stop automatically if you specifyenvand don’t pass it aclobject.
Aaron Lun (11:48:38): > The explicit start/stop is useful if you have multiplebasiliskRuncalls in between them.
Robert Castelo (11:55:28): > i see, thanks for the clarification!!:blush:
Román Pérez (15:54:14): > @Román Pérez has joined the channel
Amarinder Singh Thind (20:01:37): > any recommendation of R packages for nanostring analyses
Alan O’C (21:42:32) (in thread): > Been a while but I believe this is well regarded for QC. Once you’ve got normalised expression values it depends what you want to do downstream but should mostly be able to treat it as any other expression matrixhttps://www.bioconductor.org/packages/release/bioc/html/NanoStringQCPro.html - Attachment (Bioconductor): NanoStringQCPro > NanoStringQCPro provides a set of quality metrics that can be used to assess the quality of NanoString mRNA gene expression data – i.e. to identify outlier probes and outlier samples. It also provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and an easily sharable html quality control output.
Amarinder Singh Thind (21:52:12) (in thread): > Thanks for sharing, but I can’t find a relevant article of this method. Recently, the normalization problem was reported in nanostring commercial pipeline.https://academic.oup.com/nar/article/47/12/6073/5494770and I am wondering if anyone has usedNanoNormIterhttps://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa163/5891144
2021-01-22
Hervé Pagès (00:12:29) (in thread): > Also, there is this package (from my neighbors at NanoString) that is still in the submission process:https://github.com/Bioconductor/Contributions/issues/1815 > > Description: Tools for NanoString Technologies nCounter Technology. Provides support for reading RCC files into an ExpressionSet derived object. Also includes methods for QC and normalizaztion of NanoString data. >
Jonathan Speh (05:08:37): > @Jonathan Speh has joined the channel
Annajiat Alim Rasel (15:38:41): > @Annajiat Alim Rasel has joined the channel
2021-01-23
rohitsatyam102 (15:15:43) (in thread): > I watched your video today and it really helped me get started. It completely answers all of my queries right from how to pitch in to how to host my package. I have one question however, would you suggest using shell commands while writing a function for your package. If yes do you have some exemplary packages that usessystem()function to run shell commands in R. I think parsing strings and joining the resulting chunks using cut, tr, awk etc in shell is way easier than doing it in R.
2021-01-24
rohitsatyam102 (05:30:19): > Is there a substitute for ensemblVEP in R?
Davide Risso (06:04:39) (in thread): > I would not recommend using shell commands inside R packages, as they will not work e.g. in Windows
Vince Carey (07:27:11): > Can you explain the question? Is there a problem withhttps://bioconductor.org/packages/release/bioc/vignettes/ensemblVEP/inst/doc/ensemblVEP.pdf
rohitsatyam102 (15:05:38): > yes it’sVEPFlags()is broken. Doesn’t work: > > `Error in validObject(.Object) : > invalid class "VEPFlags" object: Ensembl >=88 requires vep script (not variant_effect_predictor.pl)` >
Lori Shepherd (15:58:50): > What version of ensemble vep are you using?
2021-01-25
rohitsatyam102 (01:48:25): > 1.30
rohitsatyam102 (01:48:49): > Couldn’t install 1.32 in R4.03
Lori Shepherd (08:01:02): > and what version of vep do you have installed on your system? and you sessionInfo() – maybe open an issue on the ensemblVEP github page for Bioconductor so we don’t use this channel – Please open the issue and post your version of installed vep, sessionInfo(), and you said that 1.32 couldn’t install? could you please print the error you receive when trying to install the latest version – please post all of this at:https://github.com/Bioconductor/ensemblVEP/issues
Vince Carey (15:11:35): > The key here is to have a valid current version of Ensembl VEP. I can tell you that installing it will likely require nontrivial activities in your perl infrastructure. But once that is done, the ensemblVEP package passes check nicely.
Martin Morgan (15:17:47) (in thread): > Are the instructions at the top of the vignette helpful for diagnosing this? > > To use this package the Ensembl VEP perl script must be installed in your path. See the package README for details. > NOTE: As of Ensembl version 88 the VEP script has been renamed from variant effect predictor.pl to vep. The > ensemblVEP package code and documentation have been updated to reflect this change. > Downloads:[http://uswest.ensembl.org/info/docs/tools/vep/index.html](http://uswest.ensembl.org/info/docs/tools/vep/index.html)Complete documentation for runtime options:[http://uswest.ensembl.org/info/docs/tools/vep/script/vep_options](http://uswest.ensembl.org/info/docs/tools/vep/script/vep_options). > html > To test that Ensembl VEP is properly installed, enter the name of the script from the command line: > vep > > This is fromhttp://bioconductor.org/packages/release/bioc/vignettes/ensemblVEP/inst/doc/ensemblVEP.pdf; the README is athttps://bioconductor.org/packages/release/bioc/readmes/ensemblVEP/README. Both are linked from the package landing pagehttps://bioconductor.org/packages/ensemblVEP. > > Maybe a helper functionensemblVEP::valid()could provide diagnostics? - Attachment (Bioconductor): ensemblVEP > Query the Ensembl Variant Effect Predictor via the perl API.
2021-01-26
rohitsatyam102 (03:43:20) (in thread): > Yes I saw those line. However, I am doing this on windows. So how do I give the path of the perl script and where should I add this path? Sorry for sounding naive (in Linux maybe adding the path to bashrc would work)
rohitsatyam102 (03:43:37) (in thread): > But where to add the path in windows?
Dario Strbenac (22:00:08) (in thread): > Control Panel -> System and Securiry -> System -> Advanced system settings -> Click on Environment Variables … button.
2021-01-27
Aaron Lun (02:40:11): > Who wants to see a photograph of a single cell taken with a smartphone? Pretty high resolution, subcellular compartments are visible.
Aaron Lun (04:17:43): > I would say that the plentiful cilia on the apical surface are a particularly outstanding feature. - File (JPEG): IMG_2363.JPG
Nils Eling (04:21:40) (in thread): > :joy:I remember that! But what happened to the mitochondria?!
Chong Tang (04:38:04): > Hello everyone. I’m wondering whether the videos of the talks in EuroBioc2020 are uploaded somewhere? Sorry if I missed any important information here.
Davide Risso (05:54:54): > Hi@Chong Tangthe videos are being edited and will be posted on youtube soon.
Jonathan Griffiths (06:07:22) (in thread): > There was absolutley nothing wrong with the mitochondria@Nils Eling!
Nils Eling (06:15:04) (in thread): > Right:wink:
Chong Tang (06:45:50) (in thread): > Thank you, David!
Shannan Ho Sui (11:54:22): > @Shannan Ho Sui has joined the channel
rohitsatyam102 (13:11:17) (in thread): > Thanks will try it and get back to you
rohitsatyam102 (13:12:27): > Me trying to end the presentation in a Bernie Sanders way!!:fiesta_parrot: - File (PNG): image.png
Mahmoud Ahmed (20:16:42): > What is a good way to get feedback on a preprint before submitting it to a journal?
Jared Andrews (21:55:54): > bioRxiv + twitter. Getting colleagues to read/critique it.
Aaron Lun (22:02:25): > most labs have “that one guy” who is supercritical and pedantic. Useful stand-in for the reviewer experience.
Mahmoud Ahmed (22:53:00) (in thread): > I agree. And I have got some good commenta from colleagues in the lab. I was looking for more from thr outside
Mahmoud Ahmed (22:54:41) (in thread): > I posted the document on the bioarxive and tweeted the links. I am afraid it wasn’t enough to get much of comments on the work
2021-01-28
Lluís Revilla (02:57:15) (in thread): > Agree with Mahmoud, I had the same experience. I sent my manuscript to some people I was in touch with who are/were working on similar topics, and didn’t get any comment. Pre-print + twitter doesn’t always work
Aaron Lun (03:18:18) (in thread): > Damn, there you are@Nils Eling. Can you dig out your files for the sperm paper? I want to make it downloadable inscRNAseq.
Nils Eling (03:21:29) (in thread): > They should all be herehttps://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6946/and herehttps://github.com/MarioniLab/Spermatogenesis2018 - Attachment (ebi.ac.uk): E-MTAB-6946 < Browse < ArrayExpress < EMBL-EBI > EMBL-EBI
Aaron Lun (03:22:22) (in thread): > are there cell labels and such in there?
Nils Eling (03:22:26) (in thread): > Yes
Aaron Lun (03:22:41) (in thread): > excelletn
Magali Michaut (04:24:14): > @Magali Michaut has joined the channel
Mahmoud Ahmed (04:24:52) (in thread): > :100:
Mahmoud Ahmed (06:40:16) (in thread): > Okay. A related question. What do people think about peer review services likePeer Community In GenomicsorPeerage of science? - Attachment (PCIGenomics): PCI Genomics > Peer Community in Genomics
Alan O’C (08:31:59): > I was going to ask who that person was in the Marioni lab but I think Johnny’s answered for me:rolling_on_the_floor_laughing:
Jonathan Griffiths (08:35:23) (in thread): > To the extent that I can turn on such a mentality, it is 90% learned from Aaron
Jonathan Griffiths (08:35:40) (in thread): > and yet I suspect that I am only 10% as supercritical as he is!
Nicholas Cooley (11:45:06): > Hi all, does anyone have a favorite program/script/tool for taking a big fastq and slamming out a metagenome? This is kind of foreign to me, so simple is good. I just need to get from the fastq to the, i assume seperated fastas. I can do all the gene calling and taxonomy and annotation after that.
2021-01-29
Aaron Lun (01:43:07): > peeled a lemon, thinking it was an orange.
Aaron Lun (01:43:11): > Ate it anyway.
FelixErnst (02:50:22): > Any side effects?
Aaron Lun (02:51:59): > just got through two slices before giving up and putting the rest in the fridge
Aaron Lun (02:52:01): > I’ll eat it later
FelixErnst (02:53:05): > So I put this down as dose dependent intolerance
FelixErnst (02:53:46): > Next up would be a replication and a control study with the orange:grin:
Aaron Lun (02:56:49): > I do in fact have some limes
Aaron Lun (02:57:05): > so that will be the next test.
Aaron Lun (02:57:19): > but that’s a bit harder to blind myself
FelixErnst (02:57:26): > Wow, didn’t see that twist coming
Alan O’C (06:51:26): > Lemons can be quite nice I reckon
Alan O’C (06:51:34): > Or maybe I just ate some very odd ones
Federico Marini (09:44:43): - File (PNG): image.png
Federico Marini (09:45:40): > stumbled upon this by chance lately, and you brought it back out of the blue:smile:
Julia Wrobel (14:02:23): > @Julia Wrobel has joined the channel
2021-01-31
Yue Cao (05:34:42): > @Yue Cao has joined the channel
Naveen Luke (15:19:22): > @Naveen Luke has joined the channel
Amarinder Singh Thind (23:29:59) (in thread): > @Hervé Pagèsrequire R=4.1 which is dev version and having some bugs at the moments.
2021-02-01
Annekathrin Ludt (04:34:02): > @Annekathrin Ludt has joined the channel
Chris Williams (10:54:17): > @Chris Williams has joined the channel
2021-02-02
Aaron Lun (02:51:31) (in thread): > how come the emptyDrops versions of the count matrix lacks the Tc0 and Tc1 data?
Nils Eling (03:42:56) (in thread): > Ah, they were never relevant for the analysis. For the emptyDrops analysis we only used WT mice
gargi (13:36:19): > @gargi has joined the channel
2021-02-04
MARC SUBIRANA I GRANÉS (08:10:15): > @MARC SUBIRANA I GRANÉS has joined the channel
2021-02-05
Aaron Lun (03:04:19): > 23:59 and I hadn’t committed for the day…
Aaron Lun (03:05:44): > fortunately had some carry over commits from last night
Spencer Nystrom (08:58:42) (in thread): > Ah yes, pre-squashing your commits.
2021-02-07
Mikhael Manurung (11:10:14): > @Mikhael Manurung has left the channel
2021-02-08
Larry Cai (04:02:39): > @Larry Cai has joined the channel
2021-02-09
Andres Wokaty (12:09:55): > @Andres Wokaty has joined the channel
Yuki Yamashita (22:11:06): > @Yuki Yamashita has joined the channel
2021-02-10
Bhavesh Borate (11:13:41): > @Bhavesh Borate has joined the channel
2021-02-11
Hojae Lee (13:11:20): > @Hojae Lee has joined the channel
2021-02-12
Janani Ravi (15:50:34): > @Janani Ravi has joined the channel
Alison Greenlaw (20:07:57): > @Alison Greenlaw has joined the channel
2021-02-13
Wes W (12:12:16): > @Wes W has joined the channel
2021-02-14
Ellora Chua (23:20:51): > @Ellora Chua has left the channel
2021-02-16
raveancic (11:55:50): > @raveancic has joined the channel
2021-02-17
Dario Strbenac (00:00:06): > Does anyone know what happened toBioinformaticsjournal? Its latest issue was four months ago.
Jared Andrews (01:05:31): > My guess is they’re just behind on getting the “proper” issues together since they all get listed as “Advance articles” anyway. Pretty sure their printing/shipping was impacted by COVID. The latest issue was just shipped on January 11th. Pre-COVID, they were shipping every ~2 weeks - that’s fallen to about once a month since mid summer.
Archana Panche (01:18:57): > @Archana Panche has joined the channel
Federico Marini (03:16:55) (in thread): > their rss feed is also stuck somehow
David Fischer (06:52:48): > @David Fischer has joined the channel
abdullah hanta (15:46:49): > @abdullah hanta has joined the channel
Aaron Lun (16:28:56): > I thought they were still hungover from the new year
Aaron Lun (16:29:06): > you know the OUP motto: “publish hard, party harder”
Dan Bunis (16:49:32): > I’ve been meaning to reach out to them actually… all correspondence I’d gotten on the dittoSeq paper said Advance version would be days & main release would be ~2weeks after signing of licenses. Instead, Advance Access took somewhere around 1-2 weeks and was published Dec 12, but the full release version is still nowhere to be seen.
Dan Bunis (16:50:15): > I can report back if I learn anything useful.
Janani Ravi (18:17:05): > Hello, I’m writing to invite you all to our first event this Spring as part of theWomen+ Data Science Panel Discussions!:calendar:**** Feb 18, 2021; 3.30–5p:female-student:Topic:Data Science Careers****Surely, many of you are thinking about this and will find this useful.*****Third Thursdayof the Month,3:30p EST. > Feb 18:Data Science Careers:Life after grad school > * Mar 18:Data Science Persuasion:Bridging analytics and policy > * Apr 15:Data Science Collaboration:Navigating disciplinary boundaries > :raised_hands:Note:everyone is welcome.:ballot_box_with_ballot: Register here(for Zoom link):https://forms.gle/4RPELwFyeeHgJKUp6You can use the same URL to register for all the panels. > > Webpage:https://women-plus-datascience.github.ioEmail:women.plus.datascience@gmail.com
Doug Phanstiel (21:53:25): > @Doug Phanstiel has joined the channel
2021-02-18
Janani Ravi (08:57:54): > We also have a set of cool:rladies:events coming up!:rladies:**** R-Ladies East Lansing & R-Ladies Chicago ****MeetupsFourth Fridayof the Month,1:00 – 3:00p EST. All are invited to attend.:raised_hands: > * Feb 26:Writing R Functions(w/ ) > * Mar 26:R Package Development(w/ Maelle Salmon)**** **** > * Apr 23:Fun with R > :loudspeaker:interested in giving a:zap:talk (Fun w/R)? Sign up here:https://forms.gle/jnQrYSnimLvehRuD9:ballot_box_with_ballot:**** Register here:https://forms.gle/ZLo6XEUVrz9eCLrQ8(same URL for all RL events)Contact:eastlansing@rladies.org|rladies-eastlansing.github.io(old’ish**)
2021-02-19
Alex Yermanos (05:55:41): > @Alex Yermanos has joined the channel
anjana sundarrajan (11:02:12): > @anjana sundarrajan has joined the channel
2021-02-22
Ingrid Aulike (05:17:37): > @Ingrid Aulike has joined the channel
2021-02-23
Wynn Cheung (10:29:56): > @Wynn Cheung has joined the channel
2021-02-24
Kyle Alford (11:23:38): > @Kyle Alford has joined the channel
2021-02-25
amira (06:06:21): > @amira has joined the channel
margherita mutarelli (09:37:01): > @margherita mutarelli has joined the channel
Haichao Wang (10:28:30): > @Haichao Wang has joined the channel
2021-02-26
Diana Hendrickx (11:52:59): > @Diana Hendrickx has joined the channel
Scott Lipnick (13:37:05): > @Scott Lipnick has joined the channel
Lyra Sheu (22:52:04): > @Lyra Sheu has joined the channel
2021-02-28
Amarinder Singh Thind (22:53:24) (in thread): > @Hervé PagèsI can’t find a proper document, particularly how to interpret the geometric mean of the housekeeping plot. If it fails, does it mean hk genes frequently detected below the Limit of detection (LOD)? And in this case, i might be changing the hk genes, or if not, then I should exclude the sample with flags.
2021-03-01
Alice Johnstone (00:07:29): > @Alice Johnstone has joined the channel
Hervé Pagès (00:24:28) (in thread): > Sorry I have no experience with nanostring data. I only recommended that you take a look at the NanoStringNCTools package because it happens to have “nanostring” in its name, that’s all. I recommend you ask your question on our support site or contact the NanoStringNCTools’s authors directly.
Amarinder Singh Thind (00:25:23) (in thread): > Sure Thanks! no worries
Lea Rothörl (05:50:33): > @Lea Rothörl has joined the channel
Reto Gerber (09:24:15): > @Reto Gerber has joined the channel
Michael Benjamin (13:50:32): > @Michael Benjamin has joined the channel
2021-03-02
Samuele Notarbartolo (04:32:55): > @Samuele Notarbartolo has joined the channel
Lluís Revilla (08:21:04): > Free courses about ENSEMBL:https://www.ensembl.info/2021/02/26/free-ensembl-browser-and-rest-api-virtual-workshops-in-march/ - Attachment (Ensembl Blog): Free Ensembl Browser and REST API virtual workshops in March > We’ve got another round of the free virtual Ensembl workshops covering the genome browser and the REST API. The Browser workshop will be held between Tuesday 16th March – Thursday 18th …
Alan Murphy (08:56:43): > @Alan Murphy has joined the channel
Gowtham (12:58:32): > @Gowtham has joined the channel
Aizada Chinybayeva (14:57:56): > @Aizada Chinybayeva has joined the channel
2021-03-04
Steph Studniberg (01:23:28): > @Steph Studniberg has joined the channel
2021-03-05
Seema Sheth-Voss (13:00:20): > @Seema Sheth-Voss has joined the channel
2021-03-06
Faride Lamadrid Feris (14:05:10): > @Faride Lamadrid Feris has joined the channel
Dario Strbenac (22:00:14): > Does anyone have a computationally-efficient R script that groups variables into clusters, such that each cluster contains a group of variables where each variable has correlation of at least some number (e.g. 0.85) with all other variables within the same cluster? If so, may you share it with me?
Aaron Lun (22:01:54): > You could probably do the cosine normalization trick, thenBiocNeighbors::findNeighborsat a distance threshold corresponding to a correlation of 0.85, followed by clique discovery with ****igraph****.
Aaron Lun (22:02:17): > Should work decently well for a few thousand variables, depending on the dimensionality.
2021-03-08
Calli Dendrou (05:35:20): > @Calli Dendrou has joined the channel
Lauren Harmon (12:18:54): > @Lauren Harmon has joined the channel
2021-03-10
Jeremy Goecks (13:35:11): > @Jeremy Goecks has joined the channel
2021-03-11
Michael Lawrence (11:51:48): > I wonder if there could be a way for Slack (like via some sort of bot?) to recognize when people mention a Bioc package name and automatically highlight it, and make a link to the package page. That might also allow integration of Slack conversations with package metadata somewhere. Like, “what are people saying about this package?“.
Alan O’C (12:20:28) (in thread): > You probably would want some way to tag packages (eg, what R people do on twitter, {pkg}), to avoid the bot searching every word of every message on bioc. I’ve not written slackbots but I imagine it’d be pretty easy for someone (other than me) to do
Sridhar N (12:21:35): > There are quite a few bots that are floating around
Sridhar N (12:21:54): > but integration is PTA IMO
Sridhar N (12:22:11): > unless some one has down time and willing to incorporate it in here
Hervé Pagès (12:46:03): > PTA?
Alan O’C (12:47:20): > PITA?
Hervé Pagès (12:49:11) (in thread): > I agree that without specific tagging, we’d probably get too many false positives.
Michael Lawrence (12:56:15) (in thread): > Specific tagging sounds like a pragmatic solution; is it supported?
Sridhar N (13:07:23): > Yes
Sridhar N (13:07:24): > lol
Hervé Pagès (13:14:21) (in thread): > Don’t know, not a Slack expert. Now how many Slack users are actually going to use the specific tagging is another question.
Alan O’C (13:15:31) (in thread): > A bunch of existing bots filter/process the text of messages so I think it must be. Also agreed, it might be useful for the 5 people who use it (I would probably not bother lol)
Michael Lawrence (14:58:09) (in thread): > Well I’ve noticed people at least using simple markdown on GitHub issues, e.g., for code, so I’m optimistic. If we had special functionality like that, there could be a bot that informs people about it upon first joining the Slack.
2021-03-12
Julia Romanowska (14:49:36): > @Julia Romanowska has joined the channel
2021-03-15
Life Science Alliance (06:25:28): > @Life Science Alliance has joined the channel
2021-03-16
koki (00:16:19): > Many Bioconductor packages depending on Seurat 4.0.0 was unable to build or install.https://github.com/satijalab/seurat/issues/4226 - Attachment: #4226 Error: package or namespace load failed for ‘Seurat’: object ‘markvario’ is not exported by ‘namespace:spatstat’ > I recently installed Seurat 4.0 along with R 4.0.4 on my Macbook Pro running OSX Big Sur v11.1. > > I was able to load the Library(Seurat) and run multiple analyses.
> It worked well until I installed the “limma” package to speed up the find clusters, and I selected “Yes” when it asked, Do you want to install from sources the package which needs compilation? (Yes/no/cancel) > > Now I get the following error message when I try to load the Library(Seurat) > > Error: package or namespace load failed for ‘Seurat’:
> object ‘markvario’ is not exported by ‘namespace:spatstat’ > > I uninstalled R and re-installed and I re-installed R studio and re-installed Seurat and re-installed limma, but I’m still getting the error. > > How can I fix this?
Christian Panse (06:14:07): > @Christian Panse has joined the channel
Nathan Eastwood (15:27:47): > @Nathan Eastwood has joined the channel
Amarinder Singh Thind (19:16:46): > Looking for package which corrects the genes expression based on the tumor purity of the samples in DGE (RNAseq)
2021-03-17
MFei (17:59:09): > @MFei has joined the channel
2021-03-18
koki (22:17:43) (in thread): > This bug has been fixed in Seurat 4.0.1https://github.com/satijalab/seurat/blob/4e868fcde49dc0a3df47f94f5fb54a421bfdf7bc/NAMESPACE#L643https://cran.r-project.org/web/packages/Seurat/index.html
2021-03-19
Dan Bunis (01:33:41) (in thread): > Discussed some in#bioc-buildsin case you didn’t see.https://community-bioc.slack.com/archives/CEQ04GKEC/p1615972134004700(the inception lol, post of your post in a thread of your post) - Attachment: Attachment > Many Bioconductor packages depending on Seurat 4.0.0 was unable to build or install. > https://github.com/satijalab/seurat/issues/4226
koki (01:35:26) (in thread): > Thanks !
Dan Bunis (01:35:59) (in thread): > np!
Helen Miller (15:28:22): > @Helen Miller has joined the channel
2021-03-22
Sarah Williams (19:29:19): > @Sarah Williams has joined the channel
Komal Dolasia (21:19:05): > @Komal Dolasia has joined the channel
2021-03-23
Philipp Schäfer (12:49:18): > @Philipp Schäfer has joined the channel
Zizhen Song (15:53:52): > @Zizhen Song has joined the channel
2021-03-24
Jan Stanstrup (10:19:17): > @Jan Stanstrup has joined the channel
Gonçalo Graça (12:18:20): > @Gonçalo Graça has joined the channel
Chris Williams (16:40:01): > @Chris Williams has joined the channel
2021-03-25
Yile He (00:23:46): > @Yile He has joined the channel
Catherine Ross (11:37:32): > @Catherine Ross has joined the channel
2021-03-30
Katerina Kechris (22:07:40): > @Katerina Kechris has joined the channel
2021-03-31
Lisa Cao (12:49:09): > @Lisa Cao has joined the channel
Jean-Baptiste Morlot (15:05:47): > @Jean-Baptiste Morlot has joined the channel
2021-04-01
Lambda Moses (15:11:50): > I clicked “preorder”. This is an April Fool’s prank:https://stackoverflow.blog/2021/03/31/the-key-copy-paste/ - Attachment (Stack Overflow Blog): Introducing The Key - Stack Overflow Blog > Sometimes, everything just clicks into place.
2021-04-04
Hong Ju Pyo (04:43:04): > @Hong Ju Pyo has joined the channel
2021-04-05
Lindsay Hayes (23:37:50): > @Lindsay Hayes has joined the channel
2021-04-06
Estefania Mancini (10:35:40): > @Estefania Mancini has joined the channel
KP (13:53:12): > @KP has joined the channel
2021-04-07
Peter Allen (13:40:47): > @Peter Allen has joined the channel
dvereen (15:02:00): > @dvereen has joined the channel
2021-04-08
Regan Hamel (06:34:05): > @Regan Hamel has joined the channel
2021-04-11
Mark Swanson (11:50:44): > @Mark Swanson has joined the channel
2021-04-12
Naohisa Goto (00:24:24): > @Naohisa Goto has joined the channel
Dario Strbenac (02:00:06): > I don’t get it. > > > 1+!+1 > [1] 1 >
Martin Morgan (02:03:16): > Nice! > > > !1 > [1] FALSE > > 1 + FALSE > [1] 1 > > and also > > > 1 + ! + 1 + 1 > [1] 1 > > !1 + 1 > [1] FALSE > > ! + 1 + 1 > [1] FALSE > > 1 + ! + ! + 1 > [1] 2 >
Chengyang Ji (02:45:53): > What does “+” do here > > > !+TRUE > [1] FALSE >
Kasper D. Hansen (03:27:47): > probably the same as > > > +1 > [1] 1 >
Chengyang Ji (03:29:18): > Right. > And I think what might be happening here is that~~+booleantype tonumeric, and!can do the opposite. > > > !+1 > [1] FALSE > > +!1 > [1] 0 > > This might be more obvious if parenthesis are used to force operator precedence > > > (1+!)+1 > Error: unexpected ')' in "(1+!)" > > 1+(!+1) > [1] 1 > > And also in javascript, they allow+to convertstringtonumber
Chengyang Ji (03:35:43): > Like this > > Welcome to Node.js v14.15.1. > Type ".help" for more information. > > +"123" > 123 >
Alan O’C (05:50:16) (in thread): > usually - File (PNG): whydoesR.png
Marcel Ramos Pérez (10:13:23) (in thread): > converts to numeric > > > `+`(TRUE) > [1] 1 >
jmsimon (11:14:32): > @jmsimon has joined the channel
Dipanjan Dey (15:08:34): > @Dipanjan Dey has joined the channel
2021-04-14
Harshita Ojha bs17b012 (01:18:27): > @Harshita Ojha bs17b012 has joined the channel
Wei (23:13:28): > @Wei has joined the channel
2021-04-15
Enrica Calura (18:39:16): > @Enrica Calura has joined the channel
2021-04-16
Kevin Rue-Albrecht (10:17:28): > I’m close to solving an issue for theTVTBpackage, but I’m stuck on a ‘basic’ R code issue: > In the example below, the user wants an expression that returnsTRUEfor elements of the list that containany combinationof the target values. > At the moment, it is missing the first element of the listc("a", "b"), which contains both values, and should returnTRUE > > targets <- c("a", "b") > x <- list( > c("a", "b"), > "c", > "d", > "e", > "a", > "b" > ) > x %in% targets > # [1] FALSE FALSE FALSE FALSE TRUE TRUE > > I thought I’d try this friendly crowd before I head to SO on a Friday:wink:
Kevin Rue-Albrecht (10:18:21) (in thread): > Original issue:https://github.com/kevinrue/TVTB/issues/8 - Attachment: #8 Rules of accepting multiple filters > Hi there, I am new here
> I would like to know if I would like to keep entries in VCF to a specific set of filters.
> For example, I would accept variants with any combinations of the following filters: c("ASSEMBLY_BIAS", "ASSEMBLY_ONLY", "PASS", "PON")
> How should I specify the rules?
> I have tried several kinds of syntax such as > > > all_filters <- c("ASSEMBLY_BIAS", "ASSEMBLY_ONLY", "PASS", "PON") > customFilterRules <- VcfFixedRules( > exprs = list( > all = expression(FILTER %in% all_filters) > )) > > > > However, it doesn’t work.
> Is it required to have another customized function? Thank you.
Charlotte Soneson (10:22:03) (in thread): > vapply(x, function(y) any(y %in% targets), FALSE)?
Kevin Rue-Albrecht (10:22:52) (in thread): > riiiight, thanks! let’s see if that works as aFilterRulesexpression as well
Kevin Rue-Albrecht (10:29:10) (in thread): > Thanks both. My understanding of their issue is that@Charlotte Soneson’sanyis the right solution, not@Kevin Blighe’sall. We’ll see when they answer.
Kevin Rue-Albrecht (10:30:03) (in thread): > That said I still haven’t fully converted that into a anS4Vectors::FilterRulesthat behaves well inevalSeparately. I’m just a bit rusty I guess:smile:
Martin Morgan (10:30:52) (in thread): > alsovapply(relist(unlist(x) %in% targets, x), any, logical(1))which I think would be more efficient (maybe not!); in XVector-land you get any(CharacterList(x) %in% targets) which is fast and comprehensible
Kevin Rue-Albrecht (10:33:34) (in thread): > actually,@Kevin Blighe, you’re making reconsider that they were likely after your version, now that I read their post again
Michael Lawrence (11:09:07) (in thread): > > any(CharacterList(x) %in% targets) >
Kevin Rue-Albrecht (11:10:43) (in thread): > testing now, thanks! (in FilterRules expression)
Kevin Rue-Albrecht (11:11:27) (in thread): > yay!
Kevin Rue-Albrecht (11:13:49) (in thread): > Thanks all for your help, here’s my reply to their issue:https://github.com/kevinrue/TVTB/issues/8#issuecomment-821247079 - Attachment: Comment on #8 Rules of accepting multiple filters > Dear @hsiaoyi0504 > > I will split my answer in a few points. I hope they are all clear. > > Origin and solution to the error > > Having cross-posted your issue on the package that TVTB relies on to actually do the work:
> <https://github.com/Bioconductor/S4Vectors/issues/80#issuecomment-820623709|Bioconductor/S4Vectors#80 (comment)> > > I was made aware that the calling environment is not automatically passed to the filtering step. > > The solution to your issue is to pass the global environment (where the object all_filters is defined, to the evalSparately() function call, so that the object all_filters is visible in the environment where the expression is evaluated. > > > all_filters <- c("ASSEMBLY_BIAS", "ASSEMBLY_ONLY", "PASS", "PON") > customFilterRules <- VcfFixedRules( > exprs = list( > all = expression(FILTER %in% all_filters) > )) > summary(evalSeparately(customFilterRules, vcf)) # fails > summary(evalSeparately(customFilterRules, vcf, enclos = .GlobalEnv)) # succeeds > > > > To illustrate the point, I will note that another solution could be to define the vector of values in the expression itself, so that it is defined on the fly when the rule is evaluated. However, that is probably not convenient for a programmatic and dynamic approach. > > > customFilterRules [https://www.internationalgenome.org/wiki/Analysis/vcf4.0/](- VcfFixedRules( > exprs = list( > all = expression(FILTER %in% c("ASSEMBLY_BIAS", "ASSEMBLY_ONLY", "PASS", "PON")) > )) > summary(evalSeparately(customFilterRules, vcf)) > > > > Clarification about “combinations of a set of filters” > > I understand what you mean now. It is possible for the FILTER column to contain multiple values separated by semi-colon, e.g. “q10;s50” (https://www.internationalgenome.org/wiki/Analysis/vcf4.0/)). > > I’m just not sure whether you want: > > • records where the FILTER value contains any one of the target values > • records where the FILTER value contains all of the target values > > As the VariantAnnotation package does not split the FILTER value (it is read as a single string "q10;s50", it is not converted as a vector c("q10", "s50"), you need to do the splitting yourself. > > I have created an example file here: [https://gist.github.com/kevinrue/120d584b07834fc457ec1442fd72c5df](https://gist.github.com/kevinrue/120d584b07834fc457ec1442fd72c5df)
> My example code below refers to this file, if you wish to reproduce my code and outputs. > > First, load the file as a VCF object: > > > library(SummarizedExperiment) > library(TVTB) > > vcf <- VariantAnnotation::readVcf(file = "moderate.vcf") > > all_filters <- c("q10", "q20") > > > > Assuming this is what you want: > >). > > I’m just not sure whether you want: > > • records where the FILTER value contains any one of the target values > • records where the FILTER value contains all of the target values > > As the VariantAnnotation package does not split the FILTER value (it is read as a single string "q10;s50", it is not converted as a vector c("q10", "s50"), you need to do the splitting yourself. > > I have created an example file here: https://gist.github.com/kevinrue/120d584b07834fc457ec1442fd72c5df
> My example code below refers to this file, if you wish to reproduce my code and outputs. > > First, load the file as a VCF object: > > > library(SummarizedExperiment) > library(TVTB) > > vcf <- VariantAnnotation::readVcf(file = "moderate.vcf") > > all_filters <- c("q10", "q20") > > > > Assuming this is what you want: > > ) • records where the FILTER value contains all of the target values > > Then, the code would be: > > > customFilterRules <- VcfFixedRules( > exprs = list( > all2 = expression(unlist(lapply(strsplit(FILTER, ";"), function(x) all(all_filters %in% x)))) > )) > summary(evalSeparately(customFilterRules, vcf, enclos = .GlobalEnv)) > evalSeparately(customFilterRules, vcf, enclos = .GlobalEnv) > rowRanges(vcf)[eval(customFilterRules, vcf, enclos = .GlobalEnv)] > rowRanges(vcf) # compare with > > > > Assuming this is what you want: > > • records where the FILTER value contains any one of the target values > > then, the code would be > > > customFilterRules <- VcfFixedRules( > exprs = list( > all2 = expression(any(CharacterList(strsplit(FILTER, ";")) %in% all_filters)) > )) > > > > Let me know how it goes!
Kevin Rue-Albrecht (11:14:35) (in thread): > @Michael Lawrencedo you have the equivalent for matching “all” the target values? it’s not as simply as switchinganytoall:innocent:
Kevin Rue-Albrecht (11:15:29) (in thread): > (i think I almost got it though)
Kevin Rue-Albrecht (11:17:25) (in thread): > > unlist(lapply( > CharacterList(x), > function(y) all(targets %in% y) > )) > > though I just realise that in that case, it’s literally just converting from one type of list to another
Kevin Rue-Albrecht (11:18:02) (in thread): > damn, that’s worth a Friday beer:stuck_out_tongue_winking_eye:
Michael Lawrence (11:28:37) (in thread): > sum(unique(CharacterList(x)) %in% targets) == length(targets)
Michael Lawrence (11:31:59) (in thread): > all(CharacterList(targets) %in% CharacterList(x))
Michael Lawrence (11:33:30) (in thread): > That last one is a bit unintuitive because of the behavior ofCharacterList()on a list vs. vector, and then the recycling.
Kevin Rue-Albrecht (11:35:03) (in thread): > :exploding_head:
2021-04-17
rohitsatyam102 (16:08:25): > Thanks@Martin Morgan@Hervé Pagèsand other authors for making SummarizedExperiment package. I learnt about it in BioC2020 and now while writing a package and actually using it make it feels so sane and tidy.
2021-04-19
Tembi F (08:15:17): > @Tembi F has joined the channel
Jack Tierney (09:08:48): > @Jack Tierney has joined the channel
Michael Lawrence (10:05:07) (in thread): > I like how you used the word “tidy”
2021-04-21
Stephanie Hicks (11:26:21): > do people have a fav review article for the state-of-the-field of methods and software for the analysis of multiomics data (using bioc packages or not)?
Aaron Lun (11:28:01): > no, but I would really like someone to pick up the slack on the mumosa package.
Lluís Revilla (11:32:55): > Not a review but I go to@Michael Loverepo:https://github.com/mikelove/awesome-multi-omics
Lluís Revilla (11:32:58): > there is a section about reviews
Stephanie Hicks (11:40:43): > cool thanks@Lluís Revilla!
Elle Loughran (13:12:07): > @Elle Loughran has joined the channel
Michael Love (13:44:16): > thanks for the pointer@Lluís Revillaalso just to point out to folks here: it’s community maintained so if you see something missing, PR!
Michael Love (13:45:31): > something that shocked me when i started reading (some) stats multi-omics papers is that there’s not much inter-citation, a random paper by Foobar will just cite groundbreaking work by Foobar (1998) Foobar and Barfoo (2005) and recent developments by Barfoo and Foobar (2019)
Michael Love (13:46:09): > i’ll constantly find new L1 regularized CCA implementations out there
Aaron Lun (13:46:50): > if your group is actively working on any single cell stuff, do you want to take over mumosa?
Michael Love (13:47:08): > haha, not doing sc multi omics right now:slightly_smiling_face:nice try tho
Aaron Lun (13:47:12): > damn
Aaron Lun (13:47:19): > well, that’s an open invitation for anyone.
Michael Love (13:47:23): > MOFA folks could turn it into mumofasa?
Michael Love (13:47:38): > mosafamu
Michael Love (13:47:47): > mo omics mo problems
Kasper D. Hansen (13:52:24): > I think its a common weakness in the stats literature: very light citation practice
Federico Marini (15:13:25) (in thread): > mufasa:lion_face:
Ashwini Shanmugam (16:52:11): > @Ashwini Shanmugam has joined the channel
2021-04-22
Davide Risso (16:08:56): > This R behavior was surprising to me… > > > x <- seq(10) > > x[c(TRUE, FALSE)] > [1] 1 3 5 7 9 > > the surprise was that there is no warning that the two vectors are of different lengths… any idea what is the reason for the lack of warning? Am I missing something obvious?
Davide Risso (16:09:55): > I encounter this while reviewing this code: > > keepgenes <- !isOutlier(sce_cordblood$sum, type="lower", log=TRUE) > sce_cordblood <- sce_cordblood[keepgenes, ] > > Obviously the intent was to filter out cells, but R didn’t complain and the student didn’t realize they filtered out genes instead
Alan O’C (16:11:07): > Vector recycling, R never warns for that
Alan O’C (16:11:47): > Doesn’t even warn forx[c(T, F, T)]
Davide Risso (16:12:41): > yeah exactly, I used a wrong minimal example since 2 is a multiple of 10, but I assumed that when not a multiple of the vector length it would throw a warning, while it doesn’t
Alan O’C (16:12:50): > Well strictly speaking it will~warn~error if you try to add a column to a dataframe and the length of the vector isn’t a factor of the number of rows, and similar cases.
Alan O’C (16:14:20): - File (PNG): whydoesR.png
Davide Risso (16:15:46): > yeah I guess that I knew that R recycles vectors, I just never thought that it could lead to that type of easy-to-make mistake in matrix subsetting
Alan O’C (16:17:08): > That,match, and factors have each caused me immeasurable pain and embarrassment over the years
Hervé Pagès (16:24:07): > Yeah, weird that R doesn’t issue a warning forx[c(T, F, T)], especially since things likerep(TRUE, 10) & c(TRUE, FALSE, FALSE)or1:10 + c(TRUE, FALSE, FALSE)do issue one. You wish that vector recycling would behave consistently across a wide range of operations. And that would just be the case if the recycling code was implemented in one single place and shared but I’m not aware of anything like that. So it seems that every function needs to re-implement their own little recycling mechanism:disappointed:
Hervé Pagès (16:32:17): > Another famous exception to the rule: > > > paste0(letters, LETTERS[1:3]) > [1] "aA" "bB" "cC" "dA" "eB" "fC" "gA" "hB" "iC" "jA" "kB" "lC" "mA" "nB" "oC" > [16] "pA" "qB" "rC" "sA" "tB" "uC" "vA" "wB" "xC" "yA" "zB" > > No warning! > Also: > > > paste0(letters, LETTERS[0]) > [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" > [20] "t" "u" "v" "w" "x" "y" "z" > > Inconsistent with how binary arithmetic operations treat the zero-length case.
2021-04-23
Robert Castelo (02:11:32): > The only place whereRecycling rulesare referred to in the Rlang manual (here), where it is described that a warning is given when the longer vector is not a multiple of the shorter one, is the section onElementary arithmetic operations, so probably we cannot expect any specific behaviour for non-arithmetic operations. TheR infernofrom Patrick Burns contains another funny edge case of the recyling rule even in arithmetics, wheresomething plus nothing is … nothing! > > > 1 + NULL > numeric(0) >
FelixErnst (03:37:52) (in thread): > I always think ofNULLas a blackhole. It sucks in everything and even though you cannot see it, it is usually somewhere
Robert Castelo (04:15:53) (in thread): > Albert Einstein would have been an enthusiastic R user:zany_face:
FelixErnst (05:19:15) (in thread): > You are onto something:slightly_smiling_face:NAis the empty space: If you add something to that is still vast empty space. That should have added AE’s enthusiasm
Robert Castelo (05:53:21) (in thread): > If physicists would learn about this, they would all quit MATLAB, Maple and Mathematica and move into R:grin:… or maybe that’s the reason why so many physicists move into bioinformatics with R.
Alan O’C (11:36:21): > I’m part of a group in bonnie Scotland developing a short (2-day) carpentries-style course on high-dimensional statistics for biological and health data. If you’d be interested in taking that type of course it’d be helpful if you could fill out this form to give us ideas on what topics to coverhttps://forms.gle/yvA3fKyHkkJhYUTr7 - Attachment (Google Docs): Learners for high dimensional statistics > High dimensional stats in this context refers to methods you might apply (for example) to large sequencing data like RNAseq, scRNAseq, or genetic sequence data particularly of large cohorts. We might cover topics like dimensionality reduction, clustering, multiple testing, and some broader statistical concepts that can be useful for data like these. These are some questions to guide our development of a course on statistics for high-dimensional datasets, to choose what topics to cover and how to cover them. The course will be delivered in the latter half of 2021.
Alan O’C (12:24:36) (in thread): > Should mention: the course materials will be open and we’ll be happily encouraging others to use the materials. We may also be looking for external groups who would like to test out the course in the latter stages of development:slightly_smiling_face:
Henrik Bengtsson (13:59:10) (in thread): > > x[c(T, F, T)] > I’m pretty sure Section ‘Indexing’ in ‘R Language Definition’ (https://cran.r-project.org/doc/manuals/R-lang.html#Indexing) covers that case. We relied on that long section when implementing support for row and column subsetting inmatrixStatsand I remembering it as comprehensive and covering lots of corner cases.
Brandon Le (16:03:07): > @Brandon Le has joined the channel
Wes W (18:39:06) (in thread): > Happy to participate and would love to run your course here in Philly
2021-04-25
Steve (02:57:39): > Hi all. I love coding in R. I have zero knowledge of biology, but find it so fascinating. > > Has anyone paid to have their genome mapped? If so, were you able to download your sequenced genome? And could you import it into R? If the answer are all “yes”, (the important question) - what cool/interesting things could you do with it!?
2021-04-27
Bradford Winkelman (13:21:36): > @Bradford Winkelman has joined the channel
2021-04-28
sedreh Nassirnia (07:03:48): > @sedreh Nassirnia has joined the channel
Dario Strbenac (09:00:28): > Regarding mutations per megabase calculations, is it common to divide by the chromosome length in the genome database or the chromosome length times two (or whatever its ploidy is), if the chromosome is autosomal?
Stephen Chen (10:08:34): > @Stephen Chen has joined the channel
Mateusz Staniak (17:42:15): > @Mateusz Staniak has joined the channel
2021-04-29
Jovan Tanevski (04:22:31): > @Jovan Tanevski has joined the channel
Arjun Krishnan (06:46:44): > @Arjun Krishnan has joined the channel
Reagan Mogire (08:25:02): > @Reagan Mogire has joined the channel
Medhat Radi (09:46:04): > @Medhat Radi has joined the channel
JAVAN OKENDO (09:46:10): > @JAVAN OKENDO has joined the channel
Anita Ghansah (09:48:49): > @Anita Ghansah has joined the channel
Nihal Habib (09:53:41): > @Nihal Habib has joined the channel
Maureen Osano (09:53:52): > @Maureen Osano has joined the channel
Ibra Lujumba (10:17:44): > @Ibra Lujumba has joined the channel
Dalia mousa (10:26:20): > @Dalia mousa has joined the channel
Mulinge Martin (10:44:40): > @Mulinge Martin has joined the channel
Modibo K Goita (10:57:05): > @Modibo K Goita has joined the channel
Afolabi Owoloye (11:13:19): > @Afolabi Owoloye has joined the channel
Ijeoma Chinwe Uzoma (12:59:58): > @Ijeoma Chinwe Uzoma has joined the channel
2021-04-30
Winfred Gatua (10:32:19): > @Winfred Gatua has joined the channel
2021-05-01
Oluwaseyi Ashaka (05:01:44): > @Oluwaseyi Ashaka has joined the channel
2021-05-03
Jesús Vélez Santiago (10:32:17): > @Jesús Vélez Santiago has joined the channel
2021-05-04
kongmou (09:47:07): > @kongmou has joined the channel
Ka Yat Liu (17:31:26): > @Ka Yat Liu has joined the channel
2021-05-05
Emmanuel Olagbaju (09:41:16): > @Emmanuel Olagbaju has joined the channel
2021-05-06
Haichao Wang (08:51:35): > Hi guys, just to double confirm that pushing bug fix to RELEASE_3_12 is not accepted anymore right?
Haichao Wang (08:52:19): > my pushing to master branch is successful, but RELEASE_3_12 was rejected
Haichao Wang (08:53:42): > I saw the announced schedule here:http://bioconductor.org/developers/release-schedule/
Haichao Wang (08:54:10): > but not sure whether I understand it correctly, as this is my first package ( as a maintainer!)
Lori Shepherd (08:58:18): > yes. We freezed the RELEASE_3_12 branch to no longer accept changes. You may continue to push to master (Devel branch). When the release happens in another two weeks the core team will create the new RELEASE_3_13 branch from the current version of the master branch.
Haichao Wang (09:14:05): > will the RELEASE_3_12 be kept in the git repo as a branch? or it will be wiped completely after 3_13?
Lori Shepherd (09:22:26): > it will be kept for legacy and we keep the versions of the package to be able to download the appropriate version of the package for past versions of R
Lori Shepherd (09:22:45): > but you will not be able to push to ourgit.bioconductor.orgversion of the release_3_12 branch
Mike Smith (09:24:29): > If you look at a package that’s been in Bioconductor for a long time, you can see the available RELEASE branches go back a quite a way e.g.https://code.bioconductor.org/browse/biomaRt/
Pratheepa Jeganathan (10:37:28): > @Pratheepa Jeganathan has joined the channel
Haichao Wang (10:51:48): > thank you both Lori and Mike. still got another Q: will I be allowed delete the old RELEASE branches? (due to some special reasons …)
Lori Shepherd (10:55:27): > normally we would keep all branches ongit.bioconductor.orgfor legacy purposes and not delete anything – it would probably be better to have a private discussion over email if there were special circumstances for this request. I suggest maybe the maintainer atbioconductor.orgemail
Haichao Wang (14:17:58): > thanks Lori, appreciate your suggestion. I will emailmaintainer@bioconductor.orgabout this
Briha Ansari (17:41:53): > @Briha Ansari has joined the channel
2021-05-08
Prabhakaran (05:37:07): > @Prabhakaran has joined the channel
2021-05-09
Andrew Judell (03:15:29): > @Andrew Judell has joined the channel
Bisola (09:01:07): > @Bisola has joined the channel
keqiao li (18:40:29): > @keqiao li has joined the channel
2021-05-10
Aakash Mantri (08:10:35): > @Aakash Mantri has joined the channel
Jason Prasad (20:17:50): > @Jason Prasad has joined the channel
2021-05-11
Megha Lal (15:59:11): > @Megha Lal has joined the channel
Megha Lal (16:45:29): > @Megha Lal has left the channel
2021-05-12
Megha Lal (09:59:51): > @Megha Lal has joined the channel
Devon Kohler (17:52:07): > @Devon Kohler has joined the channel
Devon Kohler (17:57:08): > Hi all, I have a question about maintainer changes for bioconductor packages. I am trying to push an update for the 3.13 release but I am not currently the package maintainer. The current maintainer does not have access to a computer the rest of the day, but can send an email asking to add me. What is the fastest way we can swap maintainers so that the update can go through for the version 3.13 deadline today?
Hervé Pagès (18:05:14): > Maybe ask on the#bioc_gitchannel?
Devon Kohler (18:07:21): > thank you!
2021-05-13
Amol Shinde (05:14:22): > @Amol Shinde has joined the channel
Yagmur Simsek (08:42:42): > @Yagmur Simsek has joined the channel
MONAH ABOU ALEZZ (09:59:14): > @MONAH ABOU ALEZZ has joined the channel
Alan O’C (10:43:34): > Any ideas what licence GEO data is released under?
Casey Greene (10:46:47): > the “good luck” license
Casey Greene (10:46:50): > > Databases of molecular data on the NCBI Web site include such examples as nucleotide sequences (GenBank), protein sequences, macromolecular structures, molecular variation, gene expression, and mapping data. They are designed to provide and encourage access within the scientific community to sources of current and comprehensive information. Therefore, NCBI itself places no restrictions on the use or distribution of the data contained therein. Nor do we accept data when the submitter has requested restrictions on reuse or redistribution. However, some submitters of the original data (or the country of origin of such data) may claim patent, copyright, or other intellectual property rights in all or a portion of the data (that has been submitted). NCBI is not in a position to assess the validity of such claims and since there is no transfer of rights from submitters to NCBI, NCBI has no rights to transfer to a third party. Therefore, NCBI cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in the molecular databases.
Casey Greene (10:47:10): > key is:Nor do we accept data when the submitter has requested restrictions on reuse or redistribution.
Alan O’C (10:49:29): > Clear as mud
Alan O’C (10:49:44): > Thanks though, where’d you find it?
Casey Greene (10:50:45): > https://www.ncbi.nlm.nih.gov/home/about/policies/
Sean Davis (11:54:45): > Also, this:https://grants.nih.gov/grants/guide/notice-files/not-od-14-124.html - Attachment (grants.nih.gov): NOT-OD-14-124: NIH Genomic Data Sharing Policy > NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: NIH Genomic Data Sharing Policy NOT-OD-14-124. NIH
Alan O’C (12:47:33): > Thanks!
2021-05-15
Belinda Phipson (04:56:49): > Hi! I’m not sure where to ask this question or who to ask, but I was wondering whether it is possible to obtain the number of monthly visitors to a particular package’s page? I’m trying to collate some “impact” statistics about the minfi and missMethyl packages.
Belinda Phipson (07:35:09) (in thread): > Thanks Kevin, I’ve already downloaded all those statistics (avg # distinct IPs per month, rank etc). I guess I was thinking more of whether traffic to package landing pages is tracked.
Martin Morgan (09:35:50) (in thread): > We don’t publish landing page views, sorry. The unique IP download traffic is probably useful in a relative way (my package 1 is downloaded more frequently than my package 2…) but still quite problematic for a measure of ‘use’ for a number of reasons. Web page traffic would I think be even more problematic.
2021-05-16
Belinda Phipson (01:49:43) (in thread): > Thanks for replying Martin. It feels like a tricky task to assess/estimate the user base of software packages.
2021-05-17
Jovana Maksimovic (00:37:35): > Hi all, when/what year did Bioconductor switch from SVN to git? My memory is failing me and my searches of the website aren’t helping.
Charlotte Soneson (01:10:05) (in thread): > I think the timeline is outlined in this bioc-devel thread:https://stat.ethz.ch/pipermail/bioc-devel/2017-August/011280.html
Jovana Maksimovic (01:13:15) (in thread): > Thanks Charlotte:smiley:
Dario Strbenac (02:00:14): > Does anyone have a script for spiltting a FASTQ file by lane and flowcell into separate FASTQ files? The service provider delivered 100x whole genome sequencing samples concatenated into one file per read side, per sample, but I want to have meaningful@RGIDs that we had from the previous sequencing service provider.
Sean Davis (09:37:15) (in thread): > I don’t think there is a standard for how read names are formatted, so you may have to create a quick script yourself. In Bioconductor, take a look atShortRead::FastqStreamer. Inside the yield, you can segregate reads and concatenate to separate files.
Alexander Toenges (09:57:14) (in thread): > Feel free to ask atbiostars.orgincl an example how data look like right now. My gutfeeling says that there is a command from BBtools that can do that efficiently.
Hervé Pagès (14:23:56) (in thread): > Also if you look at the commit history of a long time Bioconductor package likeBiobase, you’ll see that all the commits from the SVN era have agit-svn-idline at the bottom: > > git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@129350 bc3139a8-67e5-0310-9ffc-ced21a209358 > > The last commit to have this line forBiobaseis commit 536f1371 from May 2, 2017. The next commit (from Oct 30, 2017) no longer has agit-svn-idline.
Henry Miller (15:05:07): > @Henry Miller has joined the channel
Krithika Bhuvanesh (17:22:23) (in thread): > Which machine is this ? I think Illumina may have a tool for this ? They have a tool to convert he BCL files into FASTQ files . You could also reach out to your service provider to provide the FASTQ files in the format you prefer.
Dario Strbenac (19:00:10) (in thread): > Thanks for good suggestions.FastqStreamermight be a convenient high-level function to use in Rscript. I have seena similar question with a similar answeron Biostars but I was not sure how to adapt Frédéric Mahé’s awk code to a more general case since I have only used awk a couple of times before and am very much a beginner. I think Illumina FASTQ files contain fairly standard read names. I checked with the service provider and they didn’t keep the separate FASTQ files, so they would need to convert BCL to FASTQ again and it’s for 100x coverage whole genome sequencing. I think I could split the files quicker than a BCL to FASTQ conversion would take.
2021-05-18
Aditi Kulkarni (09:22:44): > @Aditi Kulkarni has joined the channel
Olle Björkqvist (11:10:08): > @Olle Björkqvist has joined the channel
rohitsatyam102 (16:03:17): > Hi!! I was wondering if there is any cheatsheet to manipulate DFrame object, like subsetting rows based on row/col names, etc…?
Michael Lawrence (18:32:46): > It would be almost identical to a cheat sheet for data.frame.
Hervé Pagès (20:18:52): > With some additional capabilities like the possibility to use Rle or IRanges subscripts for subsetting. Note that all Vector derivatives should support this, not just DataFrames.
2021-05-19
rohitsatyam102 (07:17:43) (in thread): > I thought doing that. While using filter function to subset my DFrame object I got an error.
rohitsatyam102 (07:18:10) (in thread): > error in usemethod(“filter”) : no applicable method for ‘filter’ applied to an object of class “c(‘dframe’, ‘dataframe’, ‘datatable’, ‘simplelist’, ‘datatable_or_null’, ‘list’, ‘vector’, ‘list_or_list’, ‘annotated’, ‘vector_or_vector’)”
Michael Lawrence (11:05:05) (in thread): > To clarify, a base R data.frame cheat sheet. Not a tibble cheat sheet.
Andrea Waterstone (14:21:08): > @Andrea Waterstone has joined the channel
2021-05-20
Guido Barzaghi (07:45:11): > @Guido Barzaghi has joined the channel
2021-05-21
Sean Davis (11:17:55): > Anyone here have any experience setting up an organoid culture characterization program?
Lluís Revilla (11:59:13) (in thread): > On my lab we do organoid cultures and we have helped several labs to set up their own organoids culture. We characterize them by morphology and comparing the expression profile with fresh biopsies. My lab mates take lots of microscope images (with confocal microscopes too) to identify the spatial distribution of the cells with previously known markers.
2021-05-22
Moritz E. Beber (15:46:50): > @Moritz E. Beber has joined the channel
2021-05-23
Jonas Schulte-Schrepping (07:27:38): > @Jonas Schulte-Schrepping has joined the channel
2021-05-24
Ariel Hippen (12:23:30): > Is there any way to remove an assay from a singleCellExperiment object?
FelixErnst (12:24:05): > assay(se,"name") <- NULLwould be my guess
FelixErnst (12:27:05): > assays(se) <- assays(se)[!(name %in% assayNames(se))]works as well. That example can be reworked to exclude/include more than one assay in one step
Ariel Hippen (12:31:25) (in thread): > It works, thank you!
Leonardo Collado Torres (14:25:42): > Does anyone have some code or a function for exporting a counts matrix + gene/feature info in aRangedSummarizedExperimentobject into thegctfile format used by GTEx et al?https://rdrr.io/github/ctlab/phantasus/man/write.gct.htmlis something I found online > > (asking for a colleague of mine, thanks!) - Attachment (rdrr.io): write.gct: Saves ExpressionSet to a GCT file (version 1.3). in ctlab/phantasus: Visual and interactive gene expression analysis > Saves ExpressionSet to a GCT file (version 1.3).
Jovana Maksimovic (19:15:09) (in thread): > Thanks@Hervé Pagès, that’s good to know.
2021-05-25
Quang Nguyen (12:17:59): > @Quang Nguyen has joined the channel
Janani Ravi (17:43:29) (in thread): > I don’t remember the specifics now, but cmapr has a few gct-friendly functions or called upon packages that did.
2021-05-26
Gerhard Burger (15:13:11): > @Gerhard Burger has joined the channel
brian capaldo (20:28:40) (in thread): > Late to the party, but that’s basically the focus of the lab I am in. We have around 30 or so organoids and run them through a standard battery of assays including full NGS workup, single cell rna and atac with a “reference” single cell embedding
Sean Davis (22:34:09) (in thread): > Thanks,@brian capaldoand@Lluís Revilla. If we proceed with anything formal, we might reach out to compare notes.
2021-05-27
Aarthi Ravikrishnan (02:36:16): > @Aarthi Ravikrishnan has joined the channel
Aaron Lun (16:23:04): > What on earth happened to our the formatting of code chunks in our Rmarkdown vignettes? It looks hideous, e.g.,https://bioconductor.org/packages/release/bioc/vignettes/bluster/inst/doc/clusterRows.html
Aaron Lun (16:23:11): > is this a biocstyle problem?
2021-05-28
FelixErnst (03:17:26): > I don’t see any difference between 3.12 and 3.13. I also did go back to vignettes from other packages from 2019. They all look the same and my browser also doesn’t load external stylesheets…
Mike Smith (04:11:13): > Looks to me like the padding around code blocks has been removed e.g. 3.12 vs 3.13 - File (PNG): image.png
Mike Smith (04:12:54): > I suspect something has changed in the rmarkdown template, which tends to inject CSS into the header of the HTML and override our CSS. This happens semi-frequently e.g.https://github.com/Bioconductor/BiocStyle/issues/86
Aaron Lun (04:44:02): > I hope we can all agree that the one on the right is disgusting
Federico Marini (04:52:09): > It would save space when printing
Federico Marini (04:52:27): > Sometimes the ugliness is tightly related to not-being-used-to…
Lluís Revilla (04:55:13): > I actually like the more compacted one
Lluís Revilla (04:55:38): > I also use collapse = TRUE on my vignettes to “save” more space
Aaron Lun (04:56:33): > seriously guys? you think the one on the right is acceptable?!
Aaron Lun (04:56:51): > I can barely tell the difference between the code and the output
Aaron Lun (04:57:28): > especially when the commented output isn’t even in a different highlighting.
Aaron Lun (04:59:23): > it’s like saying that a circos plot is nice because it has the most information per pixel, that completely misses the point,
Aaron Lun (05:00:55): > strongly advise using knitr’s default athttps://cran.r-project.org/web/packages/knitr/vignettes/knitr-markdown.html, which is much more readable.
Kevin Rue-Albrecht (05:30:14): > I do prefer the former one (on the left), which gives a bit more breathing space to the code chunks
Alan O’C (05:54:00): > Output being distinct from code is separate from the padding but I agree it would make things much easier to read
Sharanya Manoharan (06:29:35): > @Sharanya Manoharan has joined the channel
Lluís Revilla (06:34:53): > The output has ## but maybe some class associated with a color or other font or style can be applied to differentiate input and output
Federico Marini (07:55:32) (in thread): > same. Visually, it gives more air to the document. Also cause these html docs are not really born to be printed
Alan O’C (08:10:02): > Yeah the knitr example Aaron linked is much easier to read for me - File (PNG): knitr.png
Federico Marini (08:24:21) (in thread): > “but it is round, and the human eye likes it”
Federico Marini (08:25:10): > I also fancy the fact that one is italic and the other one isn’t
Federico Marini (08:25:41): > it’s a low-effort-hi-impact thing to make the doc accessible, probably
Federico Marini (08:26:05): > And in teaching you can say “when you see something in italic, it is an output”
Jonathan Carroll (09:59:37) (in thread): > (late to the party) FYI:https://github.com/jonocarroll/DFplyr
Henrik Bengtsson (14:16:36) (in thread): > FWIW, you can customize CSS specifically to print media, so can be different from on screen rendering
Federico Marini (14:23:43) (in thread): > never tried yet, thanks!
Russell Fletcher (17:44:17): > @Russell Fletcher has joined the channel
skume (22:33:45): > @skume has joined the channel
2021-05-29
Kowo Cyril (00:29:17): > @Kowo Cyril has joined the channel
2021-05-31
Sridhar N (11:55:55): > Am i doing something wrong or Biomart archive is down for everyone else?
Sridhar N (11:55:59): > > listEnsemblArchives() > Error in getNodeSet(html, path = "//div[@class='plain-box float-right archive-box']")[[1]] : > subscript out of bounds >
Sridhar N (11:56:28): > > > package.version('bioMart') > [1] "2.42.1" >
Sridhar N (11:56:57): > have been trying to access mm10 mart and not GRCm39 which gets loaded by default
Federico Marini (12:05:32): > It is down, along with the mirrors, it seems
Sridhar N (12:07:02): > Thanks for checking, is it odd that this won’t return any error
Sridhar N (12:07:03): > > m = useEnsembl("ensembl", > dataset="mmusculus_gene_ensembl", > host ="[http://aug2020.archive.ensembl.org](http://aug2020.archive.ensembl.org)",mirror = "uswest") >
Sridhar N (12:08:56): > i see that usinggetBMonmreturns this > > Error in getNodeSet(html, path = "//div[@class='plain-box float-right archive-box']")[[1]] : > subscript out of bounds >
Sridhar N (12:27:09): > ahh i do see an issue related to thishttps://support.bioconductor.org/p/9135007/#9135008
Mike Smith (12:28:31): > It’s looking for a table of archive URLs and Ensembl versions, which are delimited by that<div>on the page. However, at the momentwww.ensembl.orgis unavailable, so it doesn’t find it. I’m working on a patch so that it will give a more helpful message, and maybe also check if one of the mirror sites is still available with the relevant information.
Federico Marini (12:29:10): > The main site says
Federico Marini (12:29:13): - File (PNG): image.png
Sridhar N (12:29:31): > Thanks Mike
2021-06-01
Mike Smith (05:58:00) (in thread): > Hopefully this is now addressed (https://support.bioconductor.org/p/9135007/#9137514)
Sridhar N (11:01:09) (in thread): > yes it seems to be back,,
Gurpreet Kaur (13:08:05): > @Gurpreet Kaur has joined the channel
Leonardo Collado Torres (13:09:12) (in thread): > thanks!
2021-06-03
Oliver Voogd (22:12:06): > @Oliver Voogd has joined the channel
2021-06-04
Flavio Lombardo (05:45:46): > @Flavio Lombardo has joined the channel
2021-06-06
Dario Strbenac (22:00:20): > A student showed me an example of R consistently crashing. I don’t work with single-cell data, so I don’t have experience with this, but what’s the solution to this? > > > mat <- counts(sceATAC) > > class(mat) > [1] "dgTMatrix" > > keep <- Matrix::rowSums(mat == 0) > 1000 > > ***** caught segfault ***** > address 0x7f123daf63c0, cause 'memory not mapped' > > Traceback: > 1: .Call(dgeMatrix_colsums, x, na.rm, FALSE, FALSE) > 2: .local(x, na.rm, dims, ...) > 3: rowSums(x = x) > 4: rowSums(x = x) >
Dario Strbenac (22:05:36): > I think that addresses a different question. I think she’s looking for rows with at least 1000 zeros. > > > dim(mat) > [1] 190937 34774 >
Dario Strbenac (22:21:08): > temp <- mat == 0only uses 30 GB on a 768 GB RAM server and the error isn’t triggered there. ApplyingrowSumstriggers the error and only 103 GB is used with about 400 GB free. I think I can now make a reproducible example.
Chengyang Ji (23:56:09): > It says herehttps://stackoverflow.com/a/50163562the compiler incompabilities can cause segfault. SinceMatrixis a built-in package, maybe an upgrade could help? - Attachment (Stack Overflow): caught segfault - ‘memory not mapped’ error in R > I have a problem running some R scripts on our cluster. The problems appeared suddenly (all the scripts were working just fine but one day they started giving a caught segfault error). I cannot pro…
2021-06-07
Chengyang Ji (00:00:06): > The souce code for the culprit functiondgeMatrix_colsumslooks really innocent and couldn’t possibly go wrong (I think)https://github.com/cran/Matrix/blob/65c37738919156f6bbb682a1d8198d715a82a19f/src/dgeMatrix.c#L839
Stuart Lee (00:11:59) (in thread): > sparseMatrixStats::rowCountsmight be useful here
Alan O’C (05:26:13): > OOM has never segfaulted for me. I would tend towards updating packages as well, that usually fixes those memory not mapped errors when I’m working on the HPC
Kasper D. Hansen (07:35:29): > Running our of memoery is different from a segfault
Mike Smith (11:17:37): > I agree. If this was an out of memory error I’d expect to seeError: cannot allocate vector of size XX Gb
USLACKBOT (11:20:58): > This message was deleted.
Michael Lawrence (12:06:01): > Probably just integer overflow
Mike Smith (12:35:10) (in thread): > One option might be to dotemp <- as(mat, "lsparseMatrix")which I think creates a logical sparse matrix is the equivalent ofmat == 0and then doingsparseMatrixStats::rowSums2( temp ) > 1000. That way everything should stay sparse.
Hervé Pagès (13:14:18) (in thread): > A program cannot try to allocate memory that is not available. Memory allocation is done via system calls likemalloc(),calloc(),realloc(), and AFAIK these system calls won’t segfault if there’s not enough memory available. What they will do in this case is return a NULL pointer instead of the address of the allocated memory and it’s the responsibility of the program to check that. However poorly written C code doesn’t always check that and then tries to write to the NULL address which causes a segfault. So yeah, using a system with more memory will avoid running into that problem but the program is buggy nonetheless and should be fixed.
Henrik Bengtsson (14:31:11) (in thread): > Please report this to the maintainer ofMatrix(Martin Mächler), because this is a (serious) bug inMatrix- anything that causes R to segfault is a bug. Don’t forget to reportsessionInfo().
Dario Strbenac (17:00:06) (in thread): > I reported it to R-devel yesterday and I guess that he’ll see it if he’s not on holidays.
2021-06-08
Lorenzo Bonaguro (07:56:36): > @Lorenzo Bonaguro has joined the channel
2021-06-09
Jin (09:37:26): > @Jin has joined the channel
Lluís Revilla (13:10:31): > Perhaps someone from the core or boards wants to participate on this survey?https://sustainable-open-science-and-software.github.io/ - Attachment (sustainable-open-science-and-software.github.io): Study - Sustainability in Open Source Projects > Recruitment site for a study run by Yo Yehudi, EngD student at the University of Manchester.
2021-06-11
Mercedeh Javanbakht Movassagh (11:22:09): > @Mercedeh Javanbakht Movassagh has joined the channel
Haichao Wang (14:29:16): > Hi , I am using TxDb.Hsapiens.UCSC.hg19.KnownGene, and found that the gene_id is pure numbers (this is the ncbi gene_id style,right?) , how to convert them to ENCODE style?
Haichao Wang (14:29:22): - File (PNG): image.png
Haichao Wang (14:30:11): > i.e. how to convert the ‘1’ in gene_id col to something like ‘ENSG00000…’
Lluís Revilla (14:49:41) (in thread): > Look at thesupport.bioconductor.orgsite.
Lluís Revilla (14:50:01) (in thread): > Probably it has been already answered there
Haichao Wang (14:50:10) (in thread): > ok thanks
Jared Andrews (15:03:31): > Several options listed here:https://www.biostars.org/p/9461782/
2021-06-12
Haichao Wang (11:47:16) (in thread): > this is SUPER helpful, thanks Jared.
2021-06-14
James MacDonald (11:09:18) (in thread): > If you need Ensembl IDs, you should start with anEnsDbobject rather than trying to convert.
Haichao Wang (11:14:52) (in thread): > thx
GuandongShang (22:48:47): > @GuandongShang has joined the channel
2021-06-15
Mike Smith (06:52:29): > Does anyone know when/where the {packname} convention for mentioning R packages started? I swear I hadn’t seen it before about 2 weeks ago, and now my twitter feed is full of {knitr} and {ggplot2} etc. Is it just a twitter thing?
Lluís Revilla (06:57:30): > I think it was started by Colin Fay he explained in a tweet he took it from the help pages, on the top left corner the package name is with curly parenthesis:usethis-package {usethis},select {dplyr},org.Hs.eg.db {org.Hs.eg.db}, …
Mike Smith (08:30:21): > Well, he tweets a lot! But here were are:https://twitter.com/_ColinFay/status/934740425956569088?s=20Definitely not just the last two weeks. - Attachment (twitter): Attachment > @dataandme @juliasilge @drob This is the how it is written on the online R help :) > I find it helpful to make it clear I’m referring to a package :package: https://pbs.twimg.com/media/DPjddcpWsAE0NFh.jpg
Mike Smith (08:30:58): > Took me a while to realise that was the HTML help. It looks different in a terminal - File (PNG): image.png
Alan O’C (08:31:53): > Yeah I did not recognise it for the same reason
mahmod suliman (14:46:53): > @mahmod suliman has joined the channel
GuandongShang (23:40:09): > Hi, I am writing @examples in my packages, and loading TxDb.Athaliana.BioMart.plantsmart28 in examples in every function. But I think each library(TxDb.Athaliana.BioMart.plantsmart28) will take some times, so I am wondering whether some one can give me some advice about it. > > my examples code like it > function 1 > > #' @examples > #' data("RNA_normCount") > #' data("ATAC_normCount") > #' > #' library(TxDb.Athaliana.BioMart.plantsmart28) > #' Txdb <- TxDb.Athaliana.BioMart.plantsmart28 > #' seqlevels(Txdb) <- c(paste0("Chr", 1:5), "M", "C") > > function 2 > > #' @examples > #' data("ATAC_normCount") > #' data("input_genes") > #' library(TxDb.Athaliana.BioMart.plantsmart28) > #' Txdb <- TxDb.Athaliana.BioMart.plantsmart28 > #' seqlevels(Txdb) <- c(paste0("Chr", 1:5), "M", "C") > #' > #' peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2") > #' peak_GR <- loadPeakFile(peak_path) > #' > #' ChIP_peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2") > #' ChIP_peak_GR <- loadPeakFile(ChIP_peak_path) > #' ChIP_peak_GR$TF_id <- "AT1G28300" >
2021-06-16
Dario Strbenac (02:00:09): > You shouldn’t immediately load packages in examples because data packages should be inSuggests:part of DESCRIPTION file and might not be installed on a user’s computer unless they did a comprehensive install. Examples should test if the package is available before doing some analysis. > > if(require(dataPackage)) > { > # Do analysis. > } > > See Section 2.8 ofPackage Development Guidelinesfor information.
Mike Smith (04:25:53): > I agree with Dario thatrequire()is more appropriate, and that you want the package load statement in each example to make it clear to the user what’s required. > > I think it’s also worth noting that when the examples are tested inR CMD checkthey’re actually all concatenated together into a single file before being run. So even if you have lots of repeatedrequire()orlibrary()calls across many examples, you don’t suffer from excessive load times during the package check process. > > You can verify this by taking a look in the<PKG>.Rcheckfolder produced byR CMD check, where there should be a file called<PKG>-Ex.Rthat contains all your examples.
GuandongShang (04:26:39) (in thread): > Thanks for your suggestion ! This is helpful. I am correcting it
GuandongShang (04:27:27) (in thread): > got it. Thanks for your reply, I will see the Rcheck.
Kasper D. Hansen (04:27:46): > You could consider the concatenation to be a bug however
GuandongShang (04:29:26): > I am sorry, what’s the meaning ofconcatenation to be a bug?
Kasper D. Hansen (04:33:30): > The fact that R - at the moment - concatenates all examples into a single R which is then executed, is something I claim you could consider a bug or at least not a great design. You can argue that having a fresh environment for each example is much better, but this will also be much slower
GuandongShang (04:35:51): > Thanks, I get it : ).
Kasper D. Hansen (04:36:13): > This is more of a meta comment. What concerns you is that repeated calls does not slow down checking - at the moment.
Kasper D. Hansen (04:36:32): > And you should follow therequireadvice
Mike Smith (05:27:29): > I think what I said previously holds true, but R does run the functioncleanEx()between each example. That function doesn’t seem to be documented anywhere (I think it’s thishttps://github.com/wch/r-source/blob/79298c499218846d14500255efd622b5021c10ec/share/R/examples-header.R#L37-L75), so it’s a bit mysterious. At first read it looks to me like it will remove created variables, and detach any loaded packages, but not unload them.
Kasper D. Hansen (05:38:28): > interesting
Heather Turner (08:18:12): > :wave:Hi Folks! We are looking for volunteers to serve as a Zoom Host at useR! 2021 (5-9 July). > > What does a Zoom Host do? Manage the running of talk or tutorial sessions, to take the technical burden off the session chair or tutor. You will work in pairs and be responsible for a certain time block between you (~8 hours). > > You will be given training by experienced community organizers in the week of June 21st. You need to be available to run conference rehearsals one week before the conference, at exactly the same time as during the conference. > > Since this is quite a commitment, Zoom Hosts are offereda stipend of USD 100for their help. We’re also happy to offer**** conference fee waivers**for volunteers if required (https://user2021.r-project.org/participation/faq/#waiver). > > Interested? Please fill in this doodle asap
. It would be helpful if you fill it out with “your name - Bioconductor” to know which community you’re coming from:bioc:
Heather Turner (08:23:32): > We’re looking for ~50 hosts to cover the whole schedule, so please still respond even though several have already volunteered!
Hervé Pagès (12:55:48) (in thread): > I didn’t know about thecleanEx()feature and I wonder how long it’s been around. I remember seeing some packages with examples failing in the context ofR CMD checknot so long ago where trying to run the problematic examples interactively would not trigger the error. After some digging around, this situation turned out to be a side-effect ofR CMD checkconcatenating all the examples in one single file. These events are rare andcleanEx()probably helps making them even more rare but it’s not perfect either. More generally speaking I don’t think there’s an easy way to reset the state of an R session to a clean slate except by restarting R.
2021-06-17
청전 (03:53:49): > @청전 has joined the channel
2021-06-18
Kozo Nishida (23:41:11): > Does anyone know how to deploy a package usinginteractiveDisplayBasetoshinyapps.io? > I want to deploy a webserver toshinyapps.iothat is started by thedisplayfunction of AnnotationHub. - Attachment (Bioconductor): interactiveDisplayBase > The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.
2021-06-19
Marcel Ramos Pérez (14:54:08) (in thread): > Try using the RStudio Connect interface. There should be a button available to deploy to ashinyapps.ioafter you run the shiny app within Rstudio
Kozo Nishida (15:25:35) (in thread): > I think the button only appears in Shiny apps launched withrunApp(). The button does not appear because(?) the display of interactiveDisplayBase (that is, AnnotationHub) is started withd <- display(AnnotationHub()). - File (PNG): image.png
2021-06-20
Vince Carey (18:39:41) (in thread): > @Marcel Ramos Pérezit looks like you’ve done the last non-trivial changes to interactiveDisplayBase. To get this to work withshinyapps.io, as far as I can tell, we need to have a function that hands back the list(ui, server) that interactiveDisplayBase produces. The relevant function seems to be .dataFrame3, which is not exported. So we’ll need to discuss what should be exported from the package so that@Kozo Nishidacan achieve his aim.
2021-06-21
Steve (05:55:13): > I built a site where to make it easy for clients or students to book you for consulting or R tuition by the hour. It’s called Hangswith. I’m cultivating a modern and intellectual culture (as opposed to other sites which can be ‘fluffy’ in nature). Pease check it out if you have a moment, feel free to create a profile if you feel so inclined! (it’s completely free to sign up / create a profile).https://www.hangswith.com/All feedback very welcome. I’m learning daily!
Sebastian Worms (06:02:43): > That’s sounds nice! I was considering signing up on upwork to do similar things. What do you see as your platform’s edge? Being more people focued and less task focused?
Steve (06:13:51): > That’s a great question, I’m figuring that out myself:slightly_smiling_face:I’d say the two strongest bits of feedback I’ve had so far is > 1. More honest/transparent pricing than similar sites, which hit both sides of the transaction with hidden fees. > 2. It’s been great in cases where someone receives a lot of inquiries, and ends up doing a lot of unpaid work (via email etc) - hangswith lets you take a booking straight over the web, and have it paid for by the client/student up front. In other words, instead of 10 inquiries leading to 1 hour of actual work, you only get notifiedaftersomeone’s already booked and paid. That puts more responsibility on the consultant/tutor, but relives them of all the rigmarole arranging it. Although they do have to send a zoom link, but that’s not a huge burden:slightly_smiling_face:
Marcel Ramos Pérez (09:58:43) (in thread): > Yes, I can look into this. One thing aboutshinyapps.iois that the monthly compute hours are limited so if the app gets quite some use, we may have to think about alternative solutions for hosting.
Marcel Ramos Pérez (12:22:42) (in thread): > Here is a rough draft of theshinyapps.iohosted app.https://mramos.shinyapps.io/AnnotationHubShiny/The send button doesn’t work because it is hosted on a server which we don’t have access to other than for running the app. I could look into adding a panel for the data.frame return after clickingSend.
Marcel Ramos Pérez (12:28:36) (in thread): > see the source repository herehttps://github.com/LiNk-NY/AnnotationHubShiny
Vince Carey (19:12:06) (in thread): > We could use a download control instead of the send-to-session action. I will have a look and try to produce a PR
2021-06-23
Kozo Nishida (02:57:23) (in thread): > Thank you@Marcel Ramos Pérez!.https://mramos.shinyapps.io/AnnotationHubShiny/is what I wanted to see!
Ayushi (14:31:03): > @Ayushi has joined the channel
Stephen Mosher (14:57:34): > @Stephen Mosher has joined the channel
2021-06-24
Ilaria Billato (08:13:21): > @Ilaria Billato has joined the channel
2021-06-25
Heather Turner (03:41:25): > https://twitter.com/_useRconf/status/1408319045905141760 - Attachment (twitter): Attachment > :hatching_chick: useR! 2021 Incubator > > The role of the R community in the RSE movement > > A participatory session on Research Software Engineering and R > > #RSE #RStats > > :date: Tuesday July 6, 2021 > :clock1: 4:00pm – 5:00pm UTC > :link: https://teamup.com/event/show/id/UD6yzXFjJ9VAdmHv58K9DVYkhxKmwp https://pbs.twimg.com/media/E4recX2XEAguq-j.jpg
Heather Turner (03:41:43): > :memo:Register for useR! if you’d like to join the RSE incubator: deadline today
:bulb:Next week we will share a way for you to view proposed topics for the breakout rooms and to add further topics for discussion!
Sean Davis (08:21:50): > Thanks to@C. Mirzayi (please do not tag this account)for pointing this out:https://education.github.com/pack
Sean Davis (08:22:42): - File (PNG): image.png
2021-06-26
Kasper D. Hansen (04:14:04): > If you’re not a student they still have educational accounts with a .edu email I think. You need to apply for it, but its relatively easy
Tom Kelly (08:25:59): > @Tom Kelly has joined the channel
2021-06-28
Alan O’C (06:11:07): > Similar forac.ukemails I believe
Mirko Brüggemann (10:21:39): > @Mirko Brüggemann has joined the channel
2021-06-29
Himel Mallick (04:22:22): > @Himel Mallick has joined the channel
Simone Montalbano (07:23:22): > @Simone Montalbano has joined the channel
2021-07-01
SP (06:56:22): > @SP has joined the channel
2021-07-02
Chouaib Benchraka (04:34:03): > @Chouaib Benchraka has joined the channel
Heather Turner (07:58:31) (in thread): > We have gathered a list of topics to be discussed at the RSE + R incubator here:https://docs.google.com/spreadsheets/d/1-3fyUrmUf7ged5Y4pAnu0u8oSsP8ZX5bm4qch7OS6UE/edit. Please take a look and comment on existing ideas/add further suggestions before Monday 07:30am UTC!
2021-07-05
Danielle Harris (07:06:18): > @Danielle Harris has joined the channel
2021-07-06
João Malato (07:25:39): > @João Malato has joined the channel
2021-07-07
Tom Sinden (10:06:33): > @Tom Sinden has joined the channel
Ben Story (10:33:39) (in thread): > Hi just to double check this I’m trying to render an Rmd file in RStudio using the old style but setting\VignetteEngine{knitr::knitr}doesn’t seem to be sufficient? Is there another way to force the old format?
Vladimir Lialine (19:45:55): > @Vladimir Lialine has joined the channel
2021-07-08
Abbey Thorpe (17:51:49): > @Abbey Thorpe has joined the channel
2021-07-09
Federico Marini (09:15:59): - File (PNG): image.png
Federico Marini (09:16:38): > Bioconductor featured in the R-universe keynote at useR!2021:tada:cc@Michael Love
Andrea Álvarez (09:36:20): > @Andrea Álvarez has joined the channel
2021-07-10
Kent Johnson (11:16:54): > @Kent Johnson has joined the channel
2021-07-11
Marloes Hoogstad (14:36:29): > @Marloes Hoogstad has joined the channel
ChiaSin (23:35:42): > @ChiaSin has joined the channel
2021-07-12
Aline Dantas (05:21:20): > @Aline Dantas has joined the channel
Harpo MAxx (11:51:30): > @Harpo MAxx has joined the channel
Sophie Arogbonlo (14:03:30): > @Sophie Arogbonlo has joined the channel
2021-07-16
Oscar Díaz (17:27:32): > @Oscar Díaz has joined the channel
Diego Montesinos V. (17:37:42): > @Diego Montesinos V. has joined the channel
Maria Ponce (17:51:30): > @Maria Ponce has joined the channel
MARIA TERESA ORTIZ MELO (19:02:16): > @MARIA TERESA ORTIZ MELO has joined the channel
2021-07-17
Lady Johanna Forero Rodríguez (11:46:44): > @Lady Johanna Forero Rodríguez has joined the channel
2021-07-19
Leo Lahti (17:04:01): > There is no channel for general announcements for relevant phd study or research positions in this Bioc Slack - should we have?
Ludwig Geistlinger (17:05:45) (in thread): > How about#jobs?
Marcel Ramos Pérez (17:11:33) (in thread): > And maybe#education-and-training?
Leo Lahti (17:36:55) (in thread): > Ah thanks, I missed#jobs, and yes right perhaps#education-and-trainingwould do as well
2021-07-21
Konrad J. Debski (13:31:47): > @Konrad J. Debski has joined the channel
Amir Shams (16:41:23): > @Amir Shams has joined the channel
2021-07-23
Batool Almarzouq (15:50:27): > @Batool Almarzouq has joined the channel
2021-07-27
Mercedes Guerrero-Murillo (08:56:25): > @Mercedes Guerrero-Murillo has joined the channel
2021-07-28
Stephanie Hicks (07:36:14): > This seems usefulhttps://twitter.com/natfriedman/status/1420122675813441540 - Attachment (twitter): Attachment > We’ve just added built-in citation support to GitHub so researchers and scientists can more easily receive acknowledgments for their contributions to software. > > Just push a CITATION.cff file and we’ll add a handy widget to the repo sidebar for you. > > Enjoy! :tada: https://pbs.twimg.com/media/E7VJ5FbWUAYithw.jpg
Alan O’C (08:42:42) (in thread): > Sadly it’s just to cite the actual repo so far, can’t have a paper in there. Which for R packages means you may get people citing the R package (before CITATION is added), people citing the paper, and people citing the repo
Stephanie Hicks (10:13:04) (in thread): > oh wow, seriously??
Stephanie Hicks (10:13:28) (in thread): > that’s not helpful
Alan O’C (10:14:19) (in thread): > Unless I misunderstand, yeah. I went from 100 to 0 pretty fast. I think the idea is you archive a version (which version???) in Zenodo and then people cite that…https://docs.github.com/en/github/creating-cloning-and-archiving-repositories/creating-a-repository-on-github/about-citation-files#citation-formats
Alan O’C (10:16:35) (in thread): > Or I guess part of the dev workflow would be push new version -> push to Zenodo -> update the cff
Alan O’C (10:17:18) (in thread): > Having said all that, they are aware of the issuehttps://twitter.com/natfriedman/status/1420300898903994371 - Attachment (twitter): Attachment > @tgamblin Will do
Kasper D. Hansen (11:57:39) (in thread): > I am also baffled (like others on twitter) why we need a new format. It is already irritating that CITATION has its own format and now another one … Small complaint, but its death by a thousand cuts
Sean Taylor (13:30:39): > @Sean Taylor has joined the channel
Max Qiu (15:28:29): > @Max Qiu has joined the channel
lalchung nungabt (18:22:02): > @lalchung nungabt has joined the channel
2021-07-30
Charlotte Soneson (03:02:44) (in thread): > Seems that v1.2.0 will support adding a preferred citation:https://twitter.com/stdruskat/status/1420289082211672064?s=20 - Attachment (twitter): Attachment > @arfon @OriolAbril @diehlpk @JOSS_TheOJ Yes, the shortly forthcoming version 1.2.0 of CFF will introduce a preferred-citation field which can hold just that, a preferred citation (such as a JOSS paper). This way you won’t have to hack the message field to provide this information, although it will also be slightly
Lamar Fleming (17:56:24): > @Lamar Fleming has joined the channel
2021-08-01
Robert M Flight (20:29:08): > @Robert M Flight has joined the channel
2021-08-03
NABISUBI PATRICIA (04:28:29): > Hello guys, > I am having P.faliciparum genomes sequenced using sanger and i would like to do variant calling. How do I go about it. > I am not sure whether this is the right platform but who ever has ever encountered this please help.
Alexander Toenges (04:32:26) (in thread): > I would search the web first for previous questions on this, and if this does not fully answer it then consider dropping a question over at e.g.biostars.org. Bioc is more for specific technical support towards its packages.
NABISUBI PATRICIA (04:33:19) (in thread): > I have done so
Moein Khalighi (06:32:49): > @Moein Khalighi has joined the channel
Edie Crosse (13:18:56): > @Edie Crosse has joined the channel
Rosalina Tincopa Marca (13:57:01): > @Rosalina Tincopa Marca has joined the channel
Maggie Marshall (15:41:46): > @Maggie Marshall has joined the channel
Pratiik Kaushik (15:43:09): > @Pratiik Kaushik has joined the channel
2021-08-04
Jonah Librach (01:13:10): > @Jonah Librach has joined the channel
John Lee (01:29:05): > @John Lee has joined the channel
Valerio Licursi (08:22:57): > @Valerio Licursi has joined the channel
Hosna Baniadam (08:25:09): > @Hosna Baniadam has joined the channel
Caroline Schreiber (08:25:18): > @Caroline Schreiber has joined the channel
Nicole Kramer (08:25:24): > @Nicole Kramer has joined the channel
Van Dien Nguyen (08:25:35): > @Van Dien Nguyen has joined the channel
Jirawat I. (08:25:36): > @Jirawat I. has joined the channel
shristi shrestha (08:25:59): > @shristi shrestha has joined the channel
Khaled Bin Satter (08:26:00): > @Khaled Bin Satter has joined the channel
Julia Philipp (08:26:11): > @Julia Philipp has joined the channel
Kirsty McCann (08:26:14): > @Kirsty McCann has joined the channel
Mike Sportiello (08:26:18): > @Mike Sportiello has joined the channel
Darin Takemoto (08:26:18): > @Darin Takemoto has joined the channel
Ambarish S. Ghatpande (08:26:42): > @Ambarish S. Ghatpande has joined the channel
Jamal Ud Din (08:26:48): > @Jamal Ud Din has joined the channel
shashank saini (08:26:59): > @shashank saini has joined the channel
eric_galvez (08:27:19): > @eric_galvez has joined the channel
Alice Chiodi (08:27:27): > @Alice Chiodi has joined the channel
Ayush Aggarwal (08:27:39): > @Ayush Aggarwal has joined the channel
Gürkan Bal (08:27:47): > @Gürkan Bal has joined the channel
Vy Nguyen (08:27:54): > @Vy Nguyen has joined the channel
Prateek Arora (08:27:56): > @Prateek Arora has joined the channel
Matt McElheron (08:28:22): > @Matt McElheron has joined the channel
Beatriz Calvo Serra (08:28:23): > @Beatriz Calvo Serra has joined the channel
Krutik Patel (08:28:36): > @Krutik Patel has joined the channel
Lakni Weerakoon (08:29:08): > @Lakni Weerakoon has joined the channel
Jaydutt Bhalshankar (08:29:18): > @Jaydutt Bhalshankar has joined the channel
Nick (08:29:49): > @Nick has joined the channel
Dinesh Sharma (08:30:05): > @Dinesh Sharma has joined the channel
Madhubani Dey (08:30:22): > @Madhubani Dey has joined the channel
Liesa Salzer (08:31:22): > @Liesa Salzer has joined the channel
Marianna Foos (08:32:29): > @Marianna Foos has joined the channel
Archana Jayaraman (08:32:44): > @Archana Jayaraman has joined the channel
Snehasudha Subhadarsini Sahoo (08:33:43): > @Snehasudha Subhadarsini Sahoo has joined the channel
Liisa Veerus (she/her) (08:34:25): > @Liisa Veerus (she/her) has joined the channel
ping hu (08:34:26): > @ping hu has joined the channel
Madhavi Tippani (08:34:49): > @Madhavi Tippani has joined the channel
Adit Wiryadana (08:36:55): > @Adit Wiryadana has joined the channel
Niraj Khemka (08:38:36): > @Niraj Khemka has joined the channel
Janick (08:38:49): > @Janick has joined the channel
Rasha Shraim (08:39:04): > @Rasha Shraim has joined the channel
Robin Lu (08:39:39): > @Robin Lu has joined the channel
emanuela iovino (08:41:29): > @emanuela iovino has joined the channel
sonali patekar (08:42:28): > @sonali patekar has joined the channel
Tulasi Marrapu (08:47:13): > @Tulasi Marrapu has joined the channel
Elisabetta Mereu (08:53:51): > Hi! For those interested in doing a PhD insingle-cellandspatial transcriptomics, we offer a nice computational position in Barcelona:https://www.carrerasresearch.org/en/phd-student-cellular-systems-genomics-endothelial-pathobiology-and-microenvironment_185615. Contact with me atemereu@carrerasresearch.orgfor informal requests or apply directly.
Jun Yu (08:54:47): > @Jun Yu has joined the channel
Lori Shepherd (08:54:51) (in thread): > You might consider also posting in the#jobschannel as well Cheers!
Elisabetta Mereu (08:55:31) (in thread): > right! Sorry, I was not aware of it
Elisabetta Mereu (08:55:37) (in thread): > thanks!
Lori Shepherd (08:55:53) (in thread): > Not a problem at all. Just want to make sure you get good visibility
Elisabetta Mereu (08:56:49) (in thread): > That’s nice of you! Actually, I was really feeling bad for posting something in the OT channel!:slightly_smiling_face:
Gianni Monaco (09:06:23): > @Gianni Monaco has joined the channel
Ghazala Sultan (09:35:50): > @Ghazala Sultan has joined the channel
Marcel Ramos Pérez (09:59:05) (in thread): > Also try the#education-and-training
Ivo Kwee (10:40:40): > @Ivo Kwee has joined the channel
Tamas Schauer (12:11:12): > @Tamas Schauer has joined the channel
Vivi Ssen (12:11:19): > @Vivi Ssen has joined the channel
TimNieuwenhuis (12:11:29): > @TimNieuwenhuis has joined the channel
Lurian Caetano David (12:14:20): > @Lurian Caetano David has joined the channel
Steph Matoian (12:18:53): > @Steph Matoian has joined the channel
Chun Wu (12:29:31): > @Chun Wu has joined the channel
James Hibbard (15:25:16): > @James Hibbard has joined the channel
Darin Takemoto (15:52:57) (in thread): > With the disclaimer that I haven’t worked with Sanger sequencing data in over a decade, it would depend on what the issues you are having with variant calling and why. If it is detection of low-frequency variants that don’t fit the normal diploid model, there are variant callers made for cancer genomics and viral sequencing that can detect lower-frequency variants (this white paper suggests down to 5%):https://assets.thermofisher.com/TFS-Assets/LSG/Application-Notes/variant-detection-tumor-ffpe-samples-sanger-sequencing.pdf
Darin Takemoto (15:54:44) (in thread): > If the issue is more heterogeneity, one would have to deconvolute the trace, which is something I personally have never done. Here is a paper describing software to do this for ABI Sanger sequencing data:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557274/ - Attachment (PubMed Central (PMC)): Base-Calling Algorithm with Vocabulary (BCV) Method for Analyzing Population Sequencing Chromatograms > Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens …
Darin Takemoto (15:55:44) (in thread): > The BCV software package itself is here:http://bioinf.fbb.msu.ru:8080/bcviss/index/index.gsp
Sowmya Parthiban (16:13:11): > @Sowmya Parthiban has joined the channel
Maddy Griswold (16:29:46): > @Maddy Griswold has joined the channel
2021-08-05
NABISUBI PATRICIA (03:03:44) (in thread): > Thanks
Felix M (11:38:40): > @Felix M has joined the channel
M Phan (11:51:34): > @M Phan has joined the channel
Eleni (12:38:37): > @Eleni has joined the channel
PeterJ (17:51:41): > @PeterJ has joined the channel
Fabricio Almeida-Silva (17:56:37): > @Fabricio Almeida-Silva has joined the channel
Greg Tucker-Kellogg (22:19:38): > @Greg Tucker-Kellogg has joined the channel
2021-08-06
Wanmin Dai (01:08:24): > @Wanmin Dai has joined the channel
Dario Strbenac (02:00:26): > Have I been thinking about S4 method dispatch wrongly all these years? > > setGeneric("aClass", function(x, y, ...) {standardGeneric("aClass")}) > setMethod("aClass", numeric(0), function() {message("Empty")}) > setMethod("aClass", c("numeric", "character"), function(x, y = "G'day") {message("Both")}) > > aClass(9) > Empty > > How do I create the empty constructor for an S4 class that’s only dispatched if the constructor the user specifies isaClass()?
Alan O’C (03:23:22): > missing()?
Alan O’C (03:23:34): > or rather,"missing"?
Dario Strbenac (05:00:05): > Ah, true.
Hervé Pagès (09:18:29) (in thread): > > setMethod("aClass", c("missing", "missing"), function(x, y) message("Empty")) > > 2 notes: > 1. It’s better to not put curly brackets around the call tostandardGeneric(). This allows R to identify the function as astandard generic(with the curly brackets, R identifies the function as a non-standard generic). > 2. All your methods must at least have thexandyarguments. Also, for clarity, the signature of all the methods should be a length-2 character vector.
Jenny Drnevich (10:32:46): > Poll: how do you pronounce “tSNE”? Tiz-ny rhymes with Disney, or tee-sin-ee? I first learned the former but then saw 10X people saying the latter, but I’ve seen more of the former at Bioc2021. Anybody know if there is a definitive authority on the pronunciation?
Kevin Rue-Albrecht (10:35:13): > i think it should really be tee-ess-en-eee even though I tend to say tee-snee
Kevin Rue-Albrecht (10:36:38): > But I’ve heard every possible way I think, and I don’t know where to find the definitive authority:sweat_smile:
Jenny Drnevich (10:38:01): > I could abuse my authority and put up a poll in the Single Cell Genomics Talk but I think we will be short on time.
Alexander Toenges (10:38:03): > tee-snee, that is how the developer pronounces it, hear him at 5:08 ofhttps://www.youtube.com/watch?v=bCkXxaoeFZ8&t=308s - Attachment (YouTube): BioTuring Webinar | Using t SNE for Data Analysis: A Quick Introduction | Laurens van der Maaten
Jenny Drnevich (10:45:46): > Although I admit I find tiz-ny more fun and easier to say.:face_with_hand_over_mouth:
Kevin Blighe (10:58:39): > I usually say T S N E, but just now on the presentation I think that I said tiz-nee:expressionless:
Luke Zappia (11:07:56): > Hidden advantage of UMAP, much easier to pronounce. I am yet to hear someone say um-ap but it’s probably only a matter of time.
Jenny Drnevich (11:11:46): > Sadly, I think Bioconductor people will forever mispronounce BiocSwirl as “bio-cee” is hardwired into our brains. The developers pronounce it “bi-ock” swirl.
Jared Andrews (11:25:23): > I had never heard the “bio-cee” pronunciation until yesterday, I always went with “bi-ock”.
Jenny Drnevich (11:27:10): > Maybe it’s just me??? “bi-ock” is closer to “bio-konductor”
Kevin Rue-Albrecht (11:49:06): > … but then why is the C capitalised in BioC if not to pronounce bio-cee??:exploding_head:
Charlotte Soneson (11:56:26): > https://support.bioconductor.org/p/130998/
Kasper D. Hansen (11:57:29): > BioC is the conference
Kasper D. Hansen (11:59:13): > That is my impression of the standardization efforts.
Kasper D. Hansen (12:00:19): > You should use Bioc in package names like BiocParallel and Bioconductor when it’s spelled out.
Emily Schwenger (12:12:14): > @Emily Schwenger has joined the channel
Ambarish S. Ghatpande (14:36:50): > Hi all, newbie here, enjoying BioC2021 a lot. M1-mac: I am currently using RSwitch to switch between R 4.1 for intel based macs or R 4.1 for M1 macs on my M1 mac. I then launch RStudio to switch to any given project that depends on Bioconductor or not. I thought this was a clever fix! Do you see drawbacks?
2021-08-07
Octavio Morante-Palacios (03:56:57): > @Octavio Morante-Palacios has joined the channel
Sean Davis (09:27:54): > https://datascience.cancer.gov/news-events/blog/love-data-drs-kibbe-and-almeida-discuss-how-data-help-reveal-our-natural-world
2021-08-09
Chris Uyehara (10:43:02): > @Chris Uyehara has joined the channel
wang (14:34:46): > @wang has joined the channel
Shuxiong Wang (15:26:46): > @Shuxiong Wang has joined the channel
2021-08-10
Woo (08:12:24): > @Woo has joined the channel
Hervé Pagès (13:54:42) (in thread): > I’m curious what’s the benefits of having this dual setup. Is R 4.1 for M1 really that faster than R 4.1 for intel? Only drawback I see is that you need to download and install many packages twice.
Ambarish S. Ghatpande (14:39:45) (in thread): > It’s not such a big deal at all. I saw a few queries on SO and maybe the bioc support forum with people asking for workarounds. People with m1 macs shouldn’t feel like they can’t use Bioconductor, that’s all. > In terms of difference, the memory use seems to be quite different between the two versions The one needing Rosetta seems to hog much more of it. > Honestly I hadn’t thought of having to install many packages twice, although most R packages seem small in size compared to hard drive capacity.
Hervé Pagès (15:28:04) (in thread): > > People with m1 macs shouldn’t feel like they can’t use Bioconductor, that’s all. > Not sure why people with m1 macs would feel that way. Just to clarify Bioconductor is 100% compatible with m1 macs as long as you install R 4.1 for intel. > > I’m really surprised by your claim that R 4.1 for intel seems to hog much more memory. I would expect maybe a slight difference in speed, even though not something really significant. But a big difference in memory consumption is unexpected and hard to explain.
2021-08-11
Ambarish S. Ghatpande (10:53:00) (in thread): - File (PNG): Screen Shot 2021-08-11 at 10.44.49 AM.png - File (PNG): Screen Shot 2021-08-11 at 10.42.35 AM.png
Ambarish S. Ghatpande (10:57:31) (in thread): > the stats in the 2 screenshots above is what I meant. Note the memory used by the “session” under the x86 platform is close to 1 GB whereas the same under the aarch64 platform is ~ 226 MB. Not really sure we can compare speed since the most relevant packages (Bioconductor based) dont work un the aarch64 platform. Like I said, could be acrcane stuff, not really a big deal for a user like me.
Mónica Padilla Gálvez (19:56:03): > @Mónica Padilla Gálvez has joined the channel
2021-08-12
Hervé Pagès (14:46:15) (in thread): > Yes that’s a big difference! Interesting. It’s still hard for me to believe that this is only due to the different architectures or to a Rosetta inefficiency. I can see a lot of discussion and benchmarks on internet for Intel+Rosetta vs M1 but didn’t see anything about difference in memory consumption. This tends to suggest that maybe what you see is an R/RStudio thing even though I didn’t see anything like this reported on the R-SIG-Mac mailing list (didn’t check the RStudio mailing lists/forums). Could it be that something changed between R 4.1.0 and R 4.1.0 Patched r80661 that explains this? It would certainly deserve a little bit more investigation.
2021-08-15
Olga Malkova (18:38:39): > @Olga Malkova has joined the channel
Anna Quaglieri (she/her) (20:29:49): > @Anna Quaglieri (she/her) has joined the channel
2021-08-16
Alvaro Sanchez (06:17:08): > @Alvaro Sanchez has joined the channel
Lou Woodley (12:02:06): > @Lou Woodley has joined the channel
2021-08-19
Jean-Philippe Villemin (09:10:53): > @Jean-Philippe Villemin has joined the channel
rohitsatyam102 (11:09:39): > @Levi Waldron@Markus RiesterI came across HGNChelper package today and I was thinking if there is an extensive vignette that demonstrate usage of all functions except this one:https://cran.r-project.org/web/packages/HGNChelper/vignettes/index.html
Ava Hoffman (she/her) (11:31:28): > @Ava Hoffman (she/her) has joined the channel
Levi Waldron (17:32:13) (in thread): > That’s all there is, but the pkgdown page (https://waldronlab.io/HGNChelper/) does also have the man pages for the other functions. I think the other functions besides checkGeneSymbols are mostly of historical curiosity, but they also seem harmless enough not to warrant deprecation. I could be convinced to add something to the vignette or to deprecate them if you want to make a case for it… - Attachment (waldronlab.io): Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols > Contains functions for identifying and correcting HGNC human gene symbols and MGI mouse gene symbols which have been converted to date format by Excel, withdrawn, or aliased. Also contains functions for reversibly converting between HGNC symbols and valid R names.
2021-08-20
Stephanie Hicks (06:46:35) (in thread): > Updates in this spacehttps://twitter.com/arfon/status/1428395832030683139 - Attachment (twitter): Attachment > Thanks for all the feedback over the last few weeks :sparkles:. Since @natfriedman’s tweet a few weeks ago, we’ve been making a number of improvements including detecting BibTeX files, R (inst/CITATION) files, and citing papers. Check out the docs to learn more: docs.github.com/en/github/crea… twitter.com/github/status/… - Attachment (twitter): Attachment > We’ve added enhanced citation support so academics and researchers can easily receive acknowledgments for their contributions to software with citation links in the common APA or BibTeX styles. > > github.blog/2021-08-19-enh…
Kozo Nishida (07:06:10): > I would like to put a badge on the README of my Bioconductor package’s GitHub repo to indicate that the repository is a Bioconductor package. Does Bioconductor already have such a badge?
Kozo Nishida (07:10:41): > For example, rOpenSci seems to have a badge like this. - File (PNG): image.png
Charlotte Soneson (07:11:50) (in thread): > There may be others, but would the badge showing how long the package has been in Bioc be an option? E.g.https://bioconductor.org/shields/years-in-bioc/iSEE.svg
Kozo Nishida (07:12:57) (in thread): > Thank you for the information. I think it can be used. I’ll give it a try.
Kozo Nishida (07:17:48): > I have just found that I can add topic information to a GitHub repository. > Adding topic information to your Bioconductor package repository may help with visibility of Bioconductor packages on GitHub. - File (PNG): image.png
rohitsatyam102 (09:08:37) (in thread): > Thanks Levi. This is helpful!!
Kozo Nishida (11:00:24): > This conference may not be unrelated to Bioconductor.https://twitter.com/NumFOCUS/status/1428727541226000386Bioconda, for example, has Bioconductor packages. > It seems that the Conda Bioconductor packages do not need to be built and can be installed quickly. > > It may be good for the Bioconductor community if someone who is deeply involved in the packaging system attends this conference. - Attachment (twitter): Attachment > :package:Announcing PackagingCon 2021:package: > November 9th+10th, 2021 > > PackagingCon is a two-day virtual conference for developers of software package management software, as well as software packagers and communities! > > CFP is open now, closes on August 31st! > > packaging-con.org https://pbs.twimg.com/media/E9PcDmoXoAEx1v6.jpg
Vince Carey (13:10:17): > @Nitesh Turaga^^
Vince Carey (13:20:35): > It will be nice to hear about other packaging systems’ approaches to preventing supply-chain attacks.
Andres Wokaty (13:22:23): > I agree
Hervé Pagès (13:25:41) (in thread): > Not a badge but most of the packages maintained by the Core Team include the Bioconductor logo in their README file:https://github.com/Bioconductor/Biobase#readme
2021-08-21
Linda Araya (11:02:39): > @Linda Araya has joined the channel
2021-08-26
Wanchha Maurya (02:32:44): > @Wanchha Maurya has joined the channel
Priyanka Singh (03:00:19): > @Priyanka Singh has joined the channel
Prashant Gaikwad (04:07:25): > @Prashant Gaikwad has joined the channel
Afsha Khan (04:52:30): > @Afsha Khan has joined the channel
Chetana Tamadaddi (05:47:52): > @Chetana Tamadaddi has joined the channel
wang (13:48:04): - File (PDF): 来自 Android 的文件
2021-08-31
Yoweri Taremwa (16:38:52): > @Yoweri Taremwa has joined the channel
2021-09-01
A Silva (10:28:49): > @A Silva has joined the channel
Katie Saund (14:40:28): > @Katie Saund has joined the channel
2021-09-03
Jenny Drnevich (11:14:40): > Came across this tutorial that almost exclusively uses->instead of<-. It’s breaking my brain:confounded:https://www.bioinformatics.babraham.ac.uk/training/10XRNASeq/seurat_workflow.html
Kevin Blighe (11:27:20) (in thread): > Never even seen that before!
Jenny Drnevich (11:28:23) (in thread): > I knew that->existed but never really saw it in practice before.
James MacDonald (11:29:48) (in thread): > It’s a logical extension of mgrittr (sp?) pipes, where you do > > this %>% that %>% the_other > > And the result is the last thing piped thataway ->
Jenny Drnevich (11:35:47) (in thread): > I agree that it’s a logical extension and even teach it as a “fun fact” in my intro R when I teach pipes. But then I say the convention it to always put the assignment at the beginning of the line of code.
James MacDonald (11:35:55) (in thread): > Although if you want to go full tidyverse, isn’t it really > > huh %<>% this %>% that %>% the_other >
James MacDonald (11:36:34) (in thread): > Which I believe pipes everything back into thehuhobject? Obviously?
Jenny Drnevich (11:36:42) (in thread): > Never go full tidyverse!
James MacDonald (11:37:01) (in thread): > No, I’ve seen Tropic Thunder. I know better than that.
Alan O’C (11:57:29) (in thread): > > apply( > mat, > 2, > function(x) stuff(x) > ) -> variable >
Alan O’C (11:57:48) (in thread): > That is so cursed
Martin Morgan (12:04:18) (in thread): > x <- 2 -> yis also fun for this — kind of splitting a number between two variables, like the atom…
Alan O’C (12:05:06) (in thread): > I prefer to do2 -> x <- 3:laughing:
Simina Boca (13:36:07) (in thread): > I wonder if folks who write right-to-left have a preference? (eg Hebrew, Arabic, Farsi speakers/writers)
2021-09-04
Rosalina Tincopa Marca (14:45:53): > Hi Everybody:beret-parrot:
Rosalina Tincopa Marca (14:46:25): > Please, somebody can help me with this script
Rosalina Tincopa Marca (14:47:06): - File (R): testfC319.R
Rosalina Tincopa Marca (14:47:14): > i got this error
Rosalina Tincopa Marca (14:47:38): > Error in normalizePath(files, mustWork = mustWork) : > path[1]=“/home/rosi/Thesis/featureCounts/aug3.1_Ptep_genome.gft”: No such file or directory
Lluís Revilla (14:51:07) (in thread): > The error means that that file is missing. Did you check visually if on that folder do you have your file aug3.1_Ptep_genome.gft?
2021-09-06
沙洲 (05:55:53): > @沙洲 has joined the channel
Eddie (08:20:00): > @Eddie has joined the channel
2021-09-07
Rosalina Tincopa Marca (16:38:02) (in thread): > Thank you Lluís, yes you are right. I made a mistake and I put in the Rscript gft instead of gtf as the format of the file is
Lluís Revilla (16:40:35) (in thread): > Great! You found the solution:muscle:
2021-09-08
Mikhail Dozmorov (12:47:00): > I may be missing something obvious, but why the following regexp returns TRUE for the second string? > > strings <- c('abd', 'dabc', 'abcabc') > grepl("a*d", strings) > #> [1] TRUE TRUE FALSE > > And why the following gives all TRUEs? > > grepl("d*a", strings) > #> [1] TRUE TRUE TRUE > > Happened during the live demo in class, and I have no explanation why.
Aaron Lun (12:48:37): > well, the last string doesn’t have ad, but all strings have ana.
Mikhail Dozmorov (13:01:03) (in thread): > I considered “d*a” regexp as a substring starting with “d” and ending with “a”, with any characters in between. Is it not correct?
Alan O’C (13:01:44) (in thread): > d*ameans “zero or more instances of d, followed by one a”
Alan O’C (13:02:40) (in thread): > d.*ais “d, then zero or more of any character, then a”
Mikhail Dozmorov (13:03:33) (in thread): > Ah, the “zero” part is where I blanked:slightly_smiling_face:Lessons learned. All correct, thanks,@Alan O’C!
Alan O’C (13:04:18) (in thread): > No worries, behaviour of*is a bit different in regex vs globs:slightly_smiling_face:
Sean Davis (13:13:06) (in thread): > Great thread. Thanks!
Marcel Ramos Pérez (13:31:56) (in thread): > “starting with d and ending with a with any characters in between” corresponds to"^d.*a$"
Alan O’C (14:39:45) (in thread): > In case anybody is bored, I find this fun (I’m stuck at abba, though)https://alf.nu/RegexGolf
Mikhail Dozmorov (14:59:35) (in thread): > Added to my references: > * Curated Regular Expression Resources > * Learn regex the easy way > * All about Regular Expressions > * Preview your regex > * Play Regex Golf
2021-09-10
Rosalina Tincopa Marca (02:25:42): > Hi Everybody:beret-parrot:
Rosalina Tincopa Marca (02:26:19): > Is somebody who has used the DESeq2 package?
Kevin Blighe (07:39:08) (in thread): > Hi! There will be plenty of people here who have used it. You have a specific question about its usage? > You can also post questions on the support site and add thedeseq2tag, if needed.https://support.bioconductor.org/
Amy Guillaumet (14:58:27): > @Amy Guillaumet has joined the channel
2021-09-15
Kozo Nishida (04:05:43): > https://github.blog/changelog/2021-09-14-readmes-for-organization-profiles/ - Attachment (The GitHub Blog): READMEs for organization profiles > READMEs for organization profiles
kent riemondy (18:19:41): > @kent riemondy has joined the channel
2021-09-16
Lara Jakubowski (13:46:03): > @Lara Jakubowski has joined the channel
2021-09-17
Aarti (16:30:51): > @Aarti has joined the channel
2021-09-19
Bhavisha Doshi (18:48:06): > @Bhavisha Doshi has joined the channel
Natsume Kirito (22:13:04): > @Natsume Kirito has joined the channel
2021-09-20
alexandria kouri (04:53:40): > @alexandria kouri has joined the channel
2021-09-21
Konstantinos Geles (Constantinos Yeles) (08:02:22): > Dear all, > EOSC(European Open Science Cloud) Future launched aUser Surveyto identify the needs and requirements of the EOSC from the users’ point of view, to ensure the EOSC responds to real-life needs and expectations. The survey will stay open until30 September 2021. > It would be great if you participate in the survey! > In the following, the link to the survey:https://eosc-portal.eu/eosc-user-personas-surveyFeel free to share it with your colleagues!
jiye (21:10:58): > @jiye has joined the channel
2021-09-23
Joseph Paulson (09:21:50): > @Joseph Paulson has joined the channel
2021-09-25
Mikey C (19:04:02): > @Mikey C has joined the channel
2021-09-28
Kevin Rue-Albrecht (10:14:54): > Writing a side point about bioconductor in a lesson. Does anyone remember what happens upon acceptance of a new package that was submitted with a major version different from 0 ? Does it get incremented by 1 or is the version forced to 1.0.0 ?
Laurent Gatto (10:22:13): > As far as I know, new submissions should always be 0.99.z and any updates increment z.
Kasper D. Hansen (10:25:41): > If you’re teaching this, I think the lesson is this: if you want to use Bioc just accept and use the package version numbering scheme we use. There are many philosophies around version numbers, but forget about it and just embrace the Bioconductor way. Specifically, you should NOT follow the recommendations in “R Packages” by Wickham.
Martin Morgan (10:41:29): > I thinkx.99.zgets added to devel as-is, and bumped tox+1.0.0at the release. Package versions can never go backward, so if say your package had been on CRAN or GitHub or otherwise distributed at version 3.1-2 your only choice is3.99.0… If you use0.99.0theninstall.packages()(which is whatBiocManager::install()uses) would say ’oh, there’s a newer version installed, so I won’t update.
Kevin Rue-Albrecht (10:45:39): > thanks both
Laurent Gatto (11:34:30) (in thread): > Given the name requirement, would it even be possible to submit a CRAN package to Bioconductor?
Martin Morgan (12:35:56) (in thread): > Usually it’s moving a CRAN package to Bioconductor, which involves submitting / review / accepting under Bioconductor standards, then notifying CRAN to remove the package. So it’s available in CRAN but not Bioconductor before acceptance by Bioconductor, and Bioconductor but not CRAN after acceptance. > > This is how it works in practice, but I wouldn’t say that I endorse changing repositories as a good thing to do.
Chang Yin (15:35:48): > @Chang Yin has joined the channel
2021-09-29
Jianqiang Sun (22:00:56): > @Jianqiang Sun has joined the channel
2021-09-30
Kozo Nishida (07:37:11): > Is it possible to get statistics on which country the package is downloaded from? > I’d like to show that the number of Japanese Bioconductorusersis not small (although there are few Bioconductordevelopersin Japan). > If it can be shown, it can be said that the barrier in Japan is that the information fordevelopersis not available (or accessible==language barrier?).
2021-10-04
Alex Wolfe (19:37:14): > @Alex Wolfe has joined the channel
2021-10-05
Rahul Bhadani (22:52:29): > @Rahul Bhadani has joined the channel
2021-10-06
claudiozanettini (14:12:48): > @claudiozanettini has joined the channel
2021-10-08
Marcel Ramos Pérez (11:15:58) (in thread): > Note thatcleanEx()can be sidestepped by assigning an object to theCheckExEnvenvironment. It not a good thing to do but it still possible:shrug:
2021-10-10
Dongze He (20:57:07): > @Dongze He has joined the channel
2021-10-11
İrem B. Gündüz (07:40:15): > @İrem B. Gündüz has joined the channel
Maria Angeles Martinez Rodriguez (07:50:37): > @Maria Angeles Martinez Rodriguez has joined the channel
FM Kerckhof (08:26:51): > @FM Kerckhof has joined the channel
David Mateo García (13:45:51): > @David Mateo García has joined the channel
2021-10-12
Jalal Laaraj (00:29:18): > @Jalal Laaraj has joined the channel
2021-10-13
Nicholas Cooley (16:28:52): > I’ve got an odd question for the random crowd here: has anyone ever experiencedreadDNAStringSet()only pulling part of a fasta when talking to an ftp address? > > In my case, it pulled pretty much half of a normal-ish sized bacterial genome in a single instance and I’m struggling replicating the conditions or behavior.
2021-10-14
Gabe Mednick (01:21:42): > @Gabe Mednick has joined the channel
Hervé Pagès (13:10:55): > Interesting conversation on the CZI Science Community Slack (random channel) about reproducible science and containers.
Henrik Bengtsson (15:05:40) (in thread): > Link:https://cziscience.slack.com/archives/C8LL284EL/p1632784031025900
Hervé Pagès (15:36:25) (in thread): > Thanks Henrik. Glad someone finally mentioned R+CRAN+Bioconductor:wink:
2021-10-15
Vince Carey (14:58:10) (in thread): > Struggling to replicate means that you have succeeded in getting the whole sequence, but in one attempt it silently returned a truncated sequence? Any additional details may be helpful.
Nicholas Cooley (22:27:37) (in thread): > That’s exactly the case, a job on the open science grid pulled a truncated sequence from an address on the ncbi ftp site, but trying to grab the sequence myself -using the same address the job on the grid was referencing- from my local machine in any circumstances results in getting the full sequence as expected.
Nicholas Cooley (22:34:39) (in thread): > Sorry, i was traveling today and just checked slack. There is one caveat to this, and that’s the code on the grid looks like:try(readDNAStringSet(<myftpaddress.fna.gz>), silent = TRUE)
2021-10-16
Babette Jakobi (07:54:21): > @Babette Jakobi has joined the channel
HaNguyen (21:09:49): > @HaNguyen has joined the channel
2021-10-17
Aris Budiman (10:45:28): > @Aris Budiman has joined the channel
2021-10-18
John Kerl (09:12:22): > @John Kerl has joined the channel
Rodger Zou (13:44:05): > @Rodger Zou has joined the channel
Natalie Kucher (14:30:35): > @Natalie Kucher has joined the channel
2021-10-21
Emily Collins (14:26:51): > @Emily Collins has joined the channel
JP Cartailler (16:45:11): > @JP Cartailler has joined the channel
2021-10-23
Sébastien Vigneau (12:06:18): > @Sébastien Vigneau has joined the channel
2021-10-24
Gavin Tomlins (20:02:28): > @Gavin Tomlins has joined the channel
2021-10-26
George Avar (08:28:36): > @George Avar has joined the channel
2021-10-27
Harald Sager Voehringer (08:59:00): > @Harald Sager Voehringer has joined the channel
funda ipekten (09:44:58): > @funda ipekten has joined the channel
Lori Shepherd (16:57:13): > Bioconductor 3.14 is Released!! Thank you to all developers and community members for contributing to the project. See fullBioconductor 3.14 Release Announcement
2021-10-28
itTan (02:48:08): > @itTan has joined the channel
2021-10-29
Enrico Ferrero (13:14:54): > @Enrico Ferrero has joined the channel
2021-11-01
onur öztornacı (07:22:59): > @onur öztornacı has joined the channel
Mohammad Jaffery (19:53:45): > @Mohammad Jaffery has joined the channel
2021-11-02
Keisuke Sekine (02:57:11): > @Keisuke Sekine has joined the channel
ChiaSin (16:55:43): > Hi, I am not sure if this is the right channel to ask this. Does anyone have experience doing power analysis on bulk RNA-Seq? I found the packageSSPAon Bioconductor but it’s deprecated since Bioc3.13. Any suggestion/pointer is welcome! Many thanks in advance:pray:
Doug Phanstiel (18:25:32) (in thread): > We use RNASeqPowerhttps://www.bioconductor.org/packages/release/bioc/html/RNASeqPower.html - Attachment (Bioconductor): RNASeqPower > RNA-seq, sample size
ChiaSin (19:25:10) (in thread): > Thanks! I will check it out:slightly_smiling_face:
2021-11-05
Marc Elosua (12:14:16): > @Marc Elosua has joined the channel
2021-11-08
Paula Nieto García (03:18:08): > @Paula Nieto García has joined the channel
Ramon Massoni-Badosa (06:22:38): > @Ramon Massoni-Badosa has joined the channel
Mahmoud Ahmed (23:09:49): > Any specific reason why thedownstreamis set to 200 in theGenomicFeatures::promotersfunction?
Hervé Pagès (23:57:08): > This is just a default value that was set to be consistent withGenomicFeatures::getPromoterSeq(). Paul Shannon is the original author ofgetPromoterSeq(). I don’t know if Paul is on this slack but if you ask on our support site you might get a response from him.
2021-11-09
Mahmoud Ahmed (00:15:49) (in thread): > Okay. Thanks
Kasper D. Hansen (10:12:34): > What you use as promoter depends quite a bit on what you want to do with it
Mahmoud Ahmed (20:45:57): > Indeed. I was just curious as to why the specific default value
2021-11-10
Jill Lundell (10:46:19): > @Jill Lundell has joined the channel
2021-11-11
Shilpa Garg (09:26:21): > @Shilpa Garg has joined the channel
2021-11-15
Lluís Revilla (06:00:23): > Hi all, I want to change the password for my user onsupport.bioconductor.orgbut I couldn’t find a way. Did I miss some documentation or this is not possible?
Lori Shepherd (07:10:17): > Can you post to the#support-sitechannel please
joe mcconnell (22:23:03): > @joe mcconnell has joined the channel
2021-11-16
Hervé Pagès (04:04:26) (in thread): > @Aaron Lun@Qian LiuIt’s around the corner:https://github.com/Bioconductor/SQLDataFrame/pull/5
2021-11-17
Brenda de Santiago (11:21:09): > @Brenda de Santiago has joined the channel
2021-11-18
Sara Yones (09:57:49): > @Sara Yones has joined the channel
Vince Carey (11:07:49): > pretty quiet here. back to regular expressions? given > > > names(cs) > [1] "Case ID" "Secondary \nor Recurrent" > [3] "Age at \nProcedure" "Gender" > [5] "Path Dx" "MGMT Status" > [7] "2012 \nMethylation\n Class" "G-CIMP\n methylation" > [9] "IDH1\n status" "Expression\nSubclass" > [11] "Therapy Class" "Vital Status" > [13] "OS (days)" "Progression Status" > [15] "PFS (days)" "V16" > > produce > > [1] "Case_ID" "Secondary_or_Recurrent" "Age_at_Procedure" > [4] "Gender" "Path_Dx" "MGMT_Status" > [7] "2012_Methylation_Class" "G_CIMP_methylation" "IDH1_status" > [10] "Expression_Subclass" "Therapy_Class" "Vital_Status" > [13] "OS_days" "Progression_Status" "PFS_days" > [16] "V16" > > My solution involves 2 gsubs.
Alan O’C (11:11:36) (in thread): > I would probably justgsubonmake.names, although that’s probably not in the spirit of the question
Kevin Rue-Albrecht (11:20:41) (in thread): > @Vince Carey: Can you give the output ofcat(deparse(names(cs)))so that we can recreate the vector easily in an R session please?
Alan O’C (11:21:25) (in thread): > Aye, I was gonna suggestdput
Kevin Rue-Albrecht (11:21:54) (in thread): > ohh… didn’t know that one!
Vince Carey (11:22:00): > > c("Case ID", "Secondary \nor Recurrent", "Age at \nProcedure", > "Gender", "Path Dx", "MGMT Status", "2012 \nMethylation\n Class", > "G-CIMP\n methylation", "IDH1\n status", "Expression\nSubclass", > "Therapy Class", "Vital Status", "OS (days)", "Progression Status", > "PFS (days)", "V16") >
Vince Carey (11:25:34) (in thread): > @Alan O’CI hadn’t thought of make.names … it is certainly useful but produces lots of dots.
Alan O’C (11:28:45) (in thread): > Yeah, the lazy way of sanitising is to dogsub("\\.+", "_", make.names(x)), although that leaves some trailing_and some leadingXs
Kevin Rue-Albrecht (11:29:44) (in thread): > with magrittr I got super close, with the issue of the prefixXintroduced bymake.names(): > > make.names(x) %>% gsub("^.", "", .) %>% gsub(".$", "", .) %>% gsub("[.]+", "_", .) > > There is only one failure for this approach: the field “2012_Methylation_Class” because it gets an “X” prefix
Kevin Rue-Albrecht (11:30:31) (in thread): > my issue with that is that I’m not so keen to trim X’s from the left, since some variables might have a genuine X there
Kevin Rue-Albrecht (11:32:26) (in thread): > hold that though, I got an idea
Kevin Rue-Albrecht (11:34:39) (in thread): > arf - not yet, maybe with a bit more time:sweat_smile:
Marcel Ramos Pérez (11:36:27): > gsub("\\s\\((\\w+)\\)|(\\s\\(**|\\s**\\\n\\s*)|(-)", "_\\1", names(cs))
Kevin Rue-Albrecht (11:39:43) (in thread): > OK, so… I wish I could say “tadaaaa”:tada:but I’ll admit that it is fairly convoluted: > > x %>% > paste0("_", .) %>% > make.names() %>% > gsub("^[.]", "", .) %>% > gsub("[.]$", "", .) %>% > gsub("[.]+", "_", .) %>% > gsub("^X_", "", .) >
Kevin Rue-Albrecht (11:41:19) (in thread): > Happy to explain the reason for individual bits if needed. I can’t say that I’d be as happy to go down the “single regex” road for that one:laughing:
Kevin Rue-Albrecht (11:44:06) (in thread): > why do I getcharacter(0)when I run that?
Marcel Ramos Pérez (11:45:15) (in thread): > You can try it on > > cs <- c("Case ID", "Secondary \nor Recurrent", "Age at \nProcedure", > "Gender", "Path Dx", "MGMT Status", "2012 \nMethylation\n Class", > "G-CIMP\n methylation", "IDH1\n status", "Expression\nSubclass", > "Therapy Class", "Vital Status", "OS (days)", "Progression Status", > "PFS (days)", "V16") >
Kevin Rue-Albrecht (11:45:47) (in thread): > > > cs <- c("Case ID", "Secondary \nor Recurrent", "Age at \nProcedure", > + "Gender", "Path Dx", "MGMT Status", "2012 \nMethylation\n Class", > + "G-CIMP\n methylation", "IDH1\n status", "Expression\nSubclass", > + "Therapy Class", "Vital Status", "OS (days)", "Progression Status", > + "PFS (days)", "V16") > > gsub("\\s\\((\\w+)\\)|(\\s\\(**|\\s**\\\n\\s*)|(-)", "_\\1", names(cs)) > character(0) >
Kevin Rue-Albrecht (11:45:55) (in thread): > weird, right?
Marcel Ramos Pérez (11:46:34) (in thread): > No, there are no names. I was trying to emulate the original example. But you can also do > > cs <- setNames(nm = cs) >
Kevin Rue-Albrecht (11:47:15) (in thread): > omg, i’m blind:sweat_smile:
Kevin Rue-Albrecht (11:47:32) (in thread): > working now ^^
Vince Carey (11:54:02): > Wow. I need to study that@Marcel Ramos Pérez. > > > all.equal( gsub("\\s\\((\\w+)\\)|(\\s\\(**|\\s**\\\n\\s*)|(-)", "*\\1", names(cs)), gsub("\\(|\\)", "", gsub("( )**(\\n| |-)( )**", "*", names(cs)))) > [1] TRUE >
Martin Morgan (13:31:09): > sub("*$", "", gsub("[[:space:][:punct:]]+", "*", cs)); these ‘character classes’ are described in?regexand can improve readability — match one or more characters from the set of characters including[:space:]or[:punct:]; the outersub()replaces trailing_in entries likeOS (days)there’s only one end of each entry, sosub()instead ofgsub(). A variant isgsub("[[:space:]]+", "_", gsub("[[:punct:]]+", "", cs))Hmm, and taking@Michael Lawrence’s suggestion to heart, might as well make the intentions explicit, at least in english > > remove_punctuation <- function(x) > gsub("[[:punct:]]+", "", x) > > replace_whitespace <- function(x, with) > gsub("[[:space:]]+", with, x) > > cs |> > remove_punctuation() |> > replace_whitespace(with = "_") >
Michael Lawrence (13:31:44) (in thread): > I think it would be better code to be more explicit about the intent, i.e., usingstrsplit()andunstrsplit().
Peter Hickey (16:16:23) (in thread): > cheating by using a package, butjanitor::clean_names()is great for this sort of task (https://www.rdocumentation.org/packages/janitor/versions/1.2.0/topics/clean_names)
2021-11-19
Christian Arnold (05:06:22): > @Christian Arnold has joined the channel
Vince Carey (08:51:18) (in thread): > A defect here is that “-” is mapped to ““, so we get”GCIMP” instead of “G_CIMP”
takashi watanabe (09:07:22): > @takashi watanabe has joined the channel
Martin Morgan (10:17:28) (in thread): > bummer, I guess one loses the use of[:punct:]and gains the use of escaped parentheses\\( > > remove_parentheses <- function(x) > gsub("[\\(\\)]+", "", x) > > replace_whitespace_and_dash <- function(x, with) > gsub("[-[:space:]]+", with, x) > ## alternative pattern: "[- \n]+" > > cs |> > remove_parentheses() |> > replace_whitespace_and_dash(with = "_") > > Also using the stringr package > > cs |> > str_remove_all("[\\(\\)]") |> > str_replace_all("[- \n]+", "_") > > I guess this is just Vince’s two-gsub solution with maybe a little cleaner(?) regular expressions…
Martin Morgan (10:38:53) (in thread): > I wonder if using R string literalsr"{...}"would make this any more readable? > > > re = r"{\s\((\w+)\)|(\s\(**|\s**\n\s*)|(-)}" > > gsub(re, "_\\1", names(cs)) > > Maybe not!
Gabe Mednick (15:56:39): > Hi folks, > It’s an honor to be here with so many legends of Bioconductor! > I have a question regarding theyeastNagalakshmipackage: > I am trying to create an RNA-seq post using the said data package. I used the yeastTxDbobject to get exons by gene and then used theGenomicAlignments::summarizeOverlaps()to get gene counts. My question is what should the meta data and design arguments look like if I am trying to useDESeq2::DESeqDataSetFromMatrix()? Please correct me if I am not thinking about this in the right way. Also, are there any example posts where theyeastNagalakshmipackage is used? Much thanks in advance.
Marcel Ramos Pérez (19:49:16) (in thread): > I was going for the one liner:stuck_out_tongue:but if it had to go in package code, I would go with your option of making it more readable. The sequence in my mind would be to first remove unwanted characters (\nand()) and then replace all spaces and dashes with_. Thanks for providing a more legible solution
2021-11-20
Zachary DeBruine (16:19:14): > @Zachary DeBruine has joined the channel
Microglia1983 (19:58:19): > @Microglia1983 has joined the channel
2021-11-23
Tyler Gorrie-Stone (09:30:38): > @Tyler Gorrie-Stone has joined the channel
Heather Bouzek (17:15:25): > @Heather Bouzek has joined the channel
2021-11-24
Pablo Rodriguez (06:29:45): > Question for the people behindBiocParallel: the progressbar is gone, instead there is a message that says “iteration:” plus a number (that i assume is related to some step inside the function one parallelizes. Is this intended? > > Example: > > > fun <- function(v) { > + message("working") ## 10 tasks > + sqrt(v) > + } > > bplapply(1:10, fun, BPPARAM=MulticoreParam(workers=2, progressbar=TRUE)) > iteration: 1working > > 2working > > 3working > > 4working > > 5working > > 6working > > 7working > > 8working > > 9working > > 10working > > ## here comes the result > > Same happens forBPPARAM = SerialParam(progressbar=TRUE)
Martin Morgan (07:25:49): > This is unintentional and I opened an issue athttps://github.com/Bioconductor/BiocParallel/issues/172thanks for the report!
Helge Hecht (13:08:37): > @Helge Hecht has joined the channel
2021-11-26
Francesc Català (06:43:56): > @Francesc Català has left the channel
Chris Vanderaa (10:36:21): > Do you have an explanation for this? > > > any(logical(0)) > [1] FALSE > > all(logical(0)) > [1] TRUE > > I’m completely confused:exploding_head:: > 1. How can an empty vector return TRUE/FALSE? I would have expectedNULLor at leastNA > 2. The above also holds fornumeric(0)(ok, R can interpret/coerce numeric to logical) andcharacter(0)(:dizzy_face:) > 3. How can all be TRUE if any is FALSE ?
Alan O’C (10:43:40) (in thread): > From the documentation, it’s a greedy function. > > The value returned is ‘TRUE’ if all of the values in ‘x’ are ‘TRUE’ (including if there are no values), and ‘FALSE’ if at least one of the values in ‘x’ is ‘FALSE’.
Alan O’C (10:45:33) (in thread): > ie it’s doing something close to!any(!x)
Chris Vanderaa (10:48:30) (in thread): > Ok thanks for the pointer, I hadn’t caught that in the docs! In practice, I find this still very confusing. Luckily, I rarely deal with empty vectors:smile:
Alan O’C (10:49:29) (in thread): > Yeah it’s a nasty one for sure! Length zero (or zero row/column) objects are an endless source of errors
Martin Morgan (15:48:38) (in thread): > I think it’s deeper than a help page or greedy function definition.any()andall()are union and intersection operations on sets of (e.g.,) logical values, respectively. A set containing the single valueTRUE(henceall(TRUE) == TRUE) can be written as the union of the empty set and the setTRUE, soall(union of empty set and TRUE) == TRUE. But for that to be the case, it must be thatall(empty set) == TRUE. It is analogous to role played by 0 in arithmetic operations+and*on, e.g., non-negative integers,0 + 1 == 1and`0 * 1 = 0``
2021-11-27
Chris Vanderaa (17:39:44) (in thread): > OK that makes sense! Haha, this is yet another example where logic and (my) intuition disagree:laughing:. Thanks for the demonstration, I will sleep a little less ignorant tonight:wink:
2021-11-29
Yao-Chung Chen (07:59:37): > @Yao-Chung Chen has joined the channel
David Slater (14:46:27): > @David Slater has joined the channel
Hervé Pagès (16:10:46) (in thread): > If I say “everybody in this room is wearing a pink shirt” and you want to prove me wrong, you need to show me someone in the room that is not wearing a pink shirt. Can you do this if the room is empty? No. So I was not lying if the room is empty. Same if I say “everybody in this room was born on Mars”.:wink:
2021-12-01
Alexander Bender (11:20:19): > @Alexander Bender has joined the channel
Amy Houseman (16:42:46): > @Amy Houseman has joined the channel
2021-12-02
Brendan F Kohrn (15:46:10): > @Brendan F Kohrn has joined the channel
2021-12-04
Loc Tran (05:31:04): > @Loc Tran has joined the channel
2021-12-06
Sachintha Wijegunasekara (09:14:23): > @Sachintha Wijegunasekara has joined the channel
2021-12-07
Castro Mbithi (02:28:51): > @Castro Mbithi has joined the channel
Castro Mbithi (02:39:01): > I wanted to share a little piece we wrote as part of this whole fixed price vs hourly struggle that affects remote work. > > We used to hire developers on Upwork a lot in the past. We always had trouble deciding whether to pick “fixed price” or “hourly”. Fixed price is alluring since you only pay for quality work that you are satisfied with. But, it’s unfair to developers since estimating time precisely is a notoriously difficult thing to do. Moreover, we often found ourselves in the position where we kept having to add little bonuses to keep developers motivated to stick to a project rather than abandon it. So, we switched to hiring people by the hour. But we found developers were annoyed that the time tracking software was capturing their screen. And, some developers tracked exaggerated amounts of time to game the system. > > Inspired by the Pomodoro technique, we came up with a new technique of tracking time, that works well with our existing tools, namely Slack. I wanted to share the idea and get the community’s feedback on it:https://blog.learningdollars.com/2020/03/31/developer-time-tracking-using-slack-beyond-fixed-price-vs-hourly/ - Attachment (LD Talent Blog): Developer Time Tracking using Slack - beyond Fixed Price vs Hourly > Slack Work Sessions are a novel method for Developer Time Tracking. It resolves 2 issues: Developers prefer hourly pay, but clients want to pay for results.
Castro Mbithi (02:39:35) (in thread): > The second half of this video talks about how to execute projects on tight budgets - I hope it helps:https://www.youtube.com/watch?v=iuEKqJbm9O8(9 mins @ 2X speed) - in particular pay attention to the slack based work sessions for transparency part. The “transparent work sessions” part of the GIF is the TL;DR. - Attachment (YouTube): LD Talent - Find and Manage Vetted Remote Developers - Stanford Team Disrupts Upwork and Recruiters - File (GIF): aldgif-2FPS.gif
2021-12-08
Sean Davis (13:31:48): > https://www.microsoft.com/en-us/research/publication/the-influence-of-organizational-structure-on-software-quality-an-empirical-case-study/ - Attachment (Microsoft Research): The Influence of Organizational Structure On Software Quality: An Empirical Case Study - Microsoft Research > Often software systems are developed by organizations consisting of many teams of individuals working together. Brooks states in the Mythical Man Month book that product quality is strongly affected by organization structure. Unfortunately there has been little empirical evidence to date to substantiate this assertion. In this paper we present a metric scheme to quantify […]
Hervé Pagès (14:09:19) (in thread): > From a friend of mine who worked on Windows Vista at the time: “Windows Vista was intentionally engineered to perform poorly on the average PC of the time to force people into buying new machines. It was a deal between Microsoft and some hardware manufacturers.” Too bad those guys didn’t factor this into their study on software quality:laughing:
2021-12-09
Alex Mahmoud (01:24:41): > @Alex Mahmoud has joined the channel
Vince Carey (09:43:45) (in thread): > “The results indicate that a team of size 30 engineers and three levels of depth should be sufficient to collect the organizational metrics to predict failure-proneness.” The metrics are certainly interesting to ponder though.
Hervé Pagès (12:04:02) (in thread): > I don’t know. I find it ironical that they’ve picked up Windows Vista for their case study on software quality when it’s notorious that the ultimate goal for that OS was not to achieve quality.
2021-12-10
William Hart (08:38:50): > @William Hart has joined the channel
2021-12-11
Asiye (13:25:30): > @Asiye has joined the channel
2021-12-13
Leonardo Collado Torres (23:40:30): > https://twitter.com/paleogenomics/status/1468799893779238914?s=21 - Attachment (twitter): Attachment > Today we filed the response to the lawsuit that the sexual harasser in this story filed against me (yes, he sued me for defamation!). This fight has a long road ahead, but I’m hopeful that justice will be served & look forward to the day I can go back to be in peace. #MeToo 1/n https://twitter.com/paleogenomics/status/1443769016854659072 - Attachment (twitter): Attachment > This story by @emiliano_mega in @ScienceMagazine is finally out. It describes my experience confronting a sexual harasser, along with that of other brave scientists who were victims/survivors. 1/6 > https://www.science.org/content/article/women-accuse-famed-plant-geneticist-sexual-harassment
Leonardo Collado Torres (23:41:24): > https://twitter.com/paleogenomics/status/1468799897210134531?s=21 - Attachment (twitter): Attachment > For those who have asked how to support, my extraordinary friends and colleagues @daniela_oaks and @mgschiavon put together this fundraiser to help cover my legal costs: > https://donadora.org/campanas/help-maria 2/n
2021-12-14
Shinichi (19:43:24): > @Shinichi has joined the channel
Chirag Parsania (21:28:00): > @Chirag Parsania has joined the channel
2021-12-15
Roger Vargas (11:12:25): > @Roger Vargas has joined the channel
2021-12-17
Arun Karnani Khemlani (09:06:36): > @Arun Karnani Khemlani has joined the channel
Sean Davis (12:53:59): > [offtopic–even for#random] A lot of us struggle with writing job descriptions and many of us have little to no training in doing so to effectively attract diverse and innovative talent. LinkedIn has a collection of reviews and blog posts that might interest folks:https://www.linkedin.com/business/talent/blog/job-descriptions - Attachment (linkedin.com): Job descriptions
2022-01-02
Oumar Ndiaye (15:34:47): > @Oumar Ndiaye has joined the channel
2022-01-03
Sean Davis (13:07:53): > For those who haven’t seen it and are interested in or working with single-cell data:https://github.com/seandavi/awesome-single-cell.
Kurt Showmaker (17:01:30): > @Kurt Showmaker has joined the channel
2022-01-04
Nicholas Cooley (11:55:48): > This seems like as good a place to ask as any, so here goes: > > Does anyone know why there are domains listed in the PGAP evidence table that have no associated HMM or seed alignment?
Taylor Zimmermann (18:17:59): > @Taylor Zimmermann has joined the channel
2022-01-06
Daniel Finlay (18:12:54): > @Daniel Finlay has joined the channel
2022-01-07
Mark Keller (08:48:25): > @Mark Keller has joined the channel
Noriaki Sato (21:06:44): > @Noriaki Sato has joined the channel
2022-01-11
Koustav Pal (04:55:20): > @Koustav Pal has joined the channel
Nils Hoffmann (10:37:00): > @Nils Hoffmann has joined the channel
2022-01-13
Meriem Bahda (12:57:12): > @Meriem Bahda has joined the channel
2022-01-15
tatjana (17:33:05): > @tatjana has joined the channel
2022-01-18
andrea.komljenovic (10:09:20): > @andrea.komljenovic has joined the channel
2022-01-19
Linda A. (17:42:19): > @Linda A. has joined the channel
Samuel Gamboa (23:29:26): > @Samuel Gamboa has joined the channel
2022-01-20
hillel brukental (02:13:46): > @hillel brukental has joined the channel
Michael Lynch (08:45:50): > @Michael Lynch has joined the channel
brian capaldo (10:00:05): > Getting really weird error when trying to runvoomwithvarianceParition > > > dim(design) > [1] 67 2 > > dim(pdxos) > [1] 1055949 67 > > vobjGenes <- voom(pdxos, design) > Error in lmFit(y, design, block = block, correlation = correlation, weights = weights) : > row dimension of design doesn't match column dimension of data object >
Alan O’C (10:12:23): > What class ispdxos?
brian capaldo (10:22:36): > > > class(pdxos) > [1] "DGEList" > attr(,"package") > [1] "edgeR" >
Alan O’C (10:28:56): > AnyNAin design?
brian capaldo (10:35:56): > nope
Alan O’C (10:51:50): > :shrug:
2022-01-24
Erwann SCAON (03:42:55): > @Erwann SCAON has joined the channel
Daniel Adediran (10:12:15): > @Daniel Adediran has joined the channel
2022-01-25
Asaduzzaman Asad (23:46:20): > @Asaduzzaman Asad has joined the channel
2022-01-27
Brianna Wasik (12:24:59): > @Brianna Wasik has joined the channel
2022-01-28
Megha Lal (11:14:17): > @Megha Lal has left the channel
2022-01-31
Lindsay Clark (10:00:57): > @Lindsay Clark has joined the channel
Jared Slosberg (10:45:08): > @Jared Slosberg has joined the channel
Garth Kong (20:17:13): > @Garth Kong has joined the channel
Thai Nguyen (20:45:06): > @Thai Nguyen has joined the channel
John Cheney (20:46:52): > @John Cheney has joined the channel
Wesley Rosales (21:09:18): > @Wesley Rosales has joined the channel
Anjali Panikar (22:49:27): > @Anjali Panikar has joined the channel
2022-02-01
Jeanette Johnson (20:10:11): > @Jeanette Johnson has joined the channel
Madelyn Carlson (22:24:33): > @Madelyn Carlson has joined the channel
2022-02-03
Juseong (02:28:03): > @Juseong has joined the channel
2022-02-04
Sergiy Getlin (13:00:43): > @Sergiy Getlin has joined the channel
Paulina Paiz (16:46:38): > @Paulina Paiz has joined the channel
2022-02-07
Paul Heinrich (08:28:16): > @Paul Heinrich has joined the channel
Ning Shen (17:42:51): > @Ning Shen has joined the channel
2022-02-10
Susanna (03:42:58): > @Susanna has joined the channel
Koji Yoshida (10:42:47): > @Koji Yoshida has joined the channel
Krithika Bhuvanesh (12:11:16): > Hello everyone ! If you have an interest inHEALTH DATA SCIENCE ,this one-year career-ready Masters program may be of interest to you. We offer part time and full time options. More details and our brochure below:The ******Health Informatics and Data Science (HIDS)******* Masters program at *******Georgetown University******* is designed to help students develop core competencies in data science, health-related data, predictive analytics, machine learning (ML), Artificial Intelligence (AI), and other advanced technologies. Through the program, students will be prepared to successfully take on a wide range of opportunities in health care organizations and related industries including, health technology developers, device manufacturers, pharma/biotech, academic medical centers, and management consulting firms. We help our students build critical skills for this growing sector to lead the evolution of healthcare.*Join one of our virtual information sessions in the coming weeks and talk to us about how the Georgetown-HIDS program fits into your academic and professional goals. > February 25, 10:00 am ESThttps://buff.ly/3KXLrsj - Attachment (gradapply.georgetown.edu): Georgetown University Health Informatics & Data Science Virtual Info Session > - File (PDF): 2022_Georgetown-HIDS_Brochure_sharing.pdf
Fariborz Soroush (12:52:23): > @Fariborz Soroush has joined the channel
Hannes Oberreiter (13:08:14): > @Hannes Oberreiter has joined the channel
Gene Cutler (17:21:13): > @Gene Cutler has joined the channel
Kozo Nishida (18:09:21): > Is there a full-text search system (like Google) for******all******Bioconductor vignettes? > I tried to see if the search box at the top right ofhttps://bioconductor.org/had that feature, but it didn’t seem to be the case.
Lluís Revilla (18:21:02): > Perhaps this is helpfulhttps://code.bioconductor.org/search/? - Attachment (code.bioconductor.org): Bioconductor Code: Search > Search source code across all Bioconductor packages
Kozo Nishida (18:45:12): > Thank you for information. However, it seemed that only the code was searched. - File (PNG): image.png
Lluís Revilla (19:17:09): > You can restrict to file type/folder such as usingfile:vignettes/* file:Rmd metagenomic microbiome species
Kozo Nishida (19:30:55): > Thank you for information. But it doesn’t seem to return Google(page-rank?)-like search results. > It seems difficult to use it instead of a full-text search system. - File (PNG): image.png
Alan O’C (19:33:51): > If you want google results you can probably use google to searchcode.bioconductor.org. I say “probably” but I mean “definitely”
Kozo Nishida (19:41:56): > Do you intend to search below? > This did not return any search results. - File (PNG): image.png
Kozo Nishida (19:52:05): > If we want to do a full-text search in natural language, we may need some kind of intelligent system. > (And Bioconductor vignettes contain a lot of useful information, so it may be worth considering it.)
Kozo Nishida (19:56:01): > I thought it fromthis. - Attachment: Attachment > @mirna pathview is not in metagenomics biocViews, but it may be suitable for you. I found the following in the vignette of pathview. > Notebaly, it can be directly used for metagenomic, microbiome or unknown species data when the data are mapped to KEGG ortholog pathways (Subsection 8.5). > I think there are other cases like this, so it would be nice to have some advice from other people.
Alan O’C (20:10:11): > Odd, maybe can be indexed
Alan O’C (20:10:35): > If you’re looking for a string like that, you should quote it, otherwise you’re searching the individual words
Alan O’C (20:11:01): > iefile:vignettes/* file:Rmd "the sentence I'm looking for"
Alan O’C (20:14:20): > ah, interesting. Even with quotes it doesn’t like linebreaks either.
2022-02-11
Kozo Nishida (02:34:24): > Thank you for information. > But beginners may find it difficult to do a pro-like search. > (There are many things to consider, such as that Rmd is not the only text source for vignette. etc.)
Mike Smith (05:25:34): > You can combined search terms using regular expression syntax e.g. to find files that have extension .Rmd or .Rnw you can usefile:(Rmd|Rnw)$
Kozo Nishida (05:59:48): > Thank you. However, the problem I feel is not only that, but there is no system for natural language search that users can use without explicitly specifying it. > (It’s like we don’t use Google that way.)
Kozo Nishida (06:14:43): > @Mike SmithWhat is used for full-text search oncode.bioconductor.org? > Is it using a full-text search engine like Elasticsearch/Lucene/Solr or something? > If such a full-text search engine is already in use, I feel that I have said something impossible. > If not, I would like to create a full-text search system for vignette pdf and html. (not for code.) > (This is hope, and I doubt if I can make time for it …)
Mike Smith (07:05:52) (in thread): > The code search is powered byhttps://github.com/google/zoektI haven’t made any modifications to the tool, just added a new theme to the results, but if you can see that it does what you want with some tweaks or alternative settings then I’m happy to update the site.
Nour El kazwini (10:25:24): > @Nour El kazwini has joined the channel
2022-02-13
Xin Fang (15:02:38): > @Xin Fang has joined the channel
2022-02-14
Antonio Cembellin Prieto (02:01:07): > @Antonio Cembellin Prieto has joined the channel
Sean Davis (14:48:56) (in thread): > Just a note that the Search Box on the Bioconductor website does search all the stuff on the Bioconductor website. The search string you used,@Kozo Nishida, pulls up the pdf vignette as the top hit. (http://bioconductor.org/help/search/index.html?q=Notebaly%2C+it+can+be+directly+used[…]data+are+mapped+to+KEGG+ortholog+pathways+(Subsection+8.5)./)
Kozo Nishida (15:15:42) (in thread): > Exactly. Thank you for letting me know. > Sorry, I may have misrepresented the search accuracy.
Alexa Juarez (17:25:07): > @Alexa Juarez has joined the channel
2022-02-15
Manuel Barrios Izás (23:29:46): > @Manuel Barrios Izás has joined the channel
2022-02-18
Abhilash Dasari (03:37:28): > @Abhilash Dasari has joined the channel
Zehra Korkusuz (11:51:27): > @Zehra Korkusuz has joined the channel
Haining Lin (15:26:56): > @Haining Lin has joined the channel
2022-02-19
Jiefei Wang (09:59:24): > @Jiefei Wang has joined the channel
2022-02-21
rohitsatyam102 (16:18:50): > Hi everyone. I was trying to make a table withformattablein R but couldn’t get rid ofNAas converting NA to zeros will makex>0condition true thereby adding:arrow_up:arrow to these cells. Any thoughts?? > > formattable(tt, list( > area(col = clus_6:clus_2) ~ formatter( > "span", > style = x ~ style(color = ifelse(x < 0 , "red", "green")), > x ~ icontext(ifelse(x < 0, "arrow-down", "arrow-up"), x)) > ) > - File (PNG): image.png
Gene Cutler (16:27:31) (in thread): > Instead ofifelse, try using a 3-case test: > > case_when( > x < 0 ~ "arrow-down", > x > 0 ~ "arrow-up", > is.na(x) | x == 0 ~ "" > ) >
Gene Cutler (16:28:29) (in thread): > I don’t know if the empty string is what you want for the blank, so you can play with that.
2022-02-22
rohitsatyam102 (02:27:43) (in thread): > Wow, it worked like magic. I almost forgot aboutcase_whencoz I useifelse/if/forstatements in routine and using multiple if else here was only evaluating first two conditions here. Many many thanks for saving the day. Here is the code that worked > and here is how the output looks like. > > formattable(tt, list( > area(col = clus_6:clus_2) ~ formatter( > "span", > style = x ~ style(color = case_when( > x < 0 ~ "red", > x > 0 ~ "green", > x == 0 ~ "white" > )), > x ~ icontext(case_when( > x < 0 ~ "arrow-down", > x > 0 ~ "arrow-up", > is.na(x) | x == 0 ~ "" > ), x)) > ) > - File (PNG): image.png
2022-02-23
Susanna (12:06:30): > Hi! Kind of a long shot, but does anyone know of a method to predict whether a regulatory variant impact gene expression?
Jared Andrews (12:09:56): > Tough question, but funseq2 may be useful to you:http://funseq2.gersteinlab.org/
Susanna (12:13:39) (in thread): > Thanks for the suggestion, but unfortunately funseq2 is for cancer data only and that’s not what I’m working on
Jared Andrews (12:15:32) (in thread): > Well, kind of a few steps removed, but you could consider using something like motifbreakR to see if a variant impacts TF motifs, which may help prioritize those that disrupt regulatory potential.https://bioconductor.org/packages/release/bioc/html/motifbreakR.html
Susanna (12:20:44) (in thread): > Yes, that’s a good one. I’ve used it already but wondered if there was something else I could try
2022-02-24
Daniel Finlay (13:24:34): > @Daniel Finlay has left the channel
Alexandru-Ioan Voda (13:31:18): > @Alexandru-Ioan Voda has joined the channel
Mirana Ramialison (16:09:22): > @Mirana Ramialison has joined the channel
Quan Nguyen (16:10:33): > @Quan Nguyen has joined the channel
Chenhao Zhou (17:40:06): > @Chenhao Zhou has joined the channel
Guiyan Ni (18:03:58): > @Guiyan Ni has joined the channel
Natalie charitakis (18:05:31): > @Natalie charitakis has joined the channel
Minh (19:10:07): > @Minh has joined the channel
Solal C (19:51:45): > @Solal C has joined the channel
Amelia Dunstone (23:18:59): > @Amelia Dunstone has joined the channel
2022-02-27
GuandongShang (04:00:45) (in thread): > I have some thoughts if you have some genes you are interested in. maybe you can find the eQTL which is related with you gene set. Then you can use the motifBreak to predict whether the eQTL will break some TF motif.
2022-02-28
Gali Bai (13:18:54): > @Gali Bai has joined the channel
2022-03-01
Carolina Hager (16:42:27): > @Carolina Hager has joined the channel
2022-03-02
Pedro Sanchez (12:11:55): > @Pedro Sanchez has joined the channel
2022-03-03
Helen Lindsay (03:43:16): > @Helen Lindsay has joined the channel
Bernat Bramon (03:45:54): > @Bernat Bramon has joined the channel
Emily Isenhart (12:44:44): > @Emily Isenhart has joined the channel
2022-03-04
Jared Andrews (12:16:28): > @Aaron LunIs there a way to perform system/CLI calls that utilize software installed into a basilisk-created environment (non-python programs)? The only way I could think of was to do something goofy like:https://stackoverflow.com/a/60699389/4438552
Aaron Lun (12:20:43): > hm. if you have the environment object, you could dobasilisk:::.obtainEnvironmentPathto get the path, and from there you should be able to find and execute the relevant binaries. If you’re lucky you won’t have to do any environment activation, otherwise you’ll have to protect yoursystemcalls withactivateEnvironmentanddeactivateEnvironment.
Jared Andrews (12:22:58): > Hmm, okay, will have to do some testing. Thanks.
Ernest (14:06:42): > @Ernest has joined the channel
2022-03-05
Giulio Benedetti (07:15:26): > @Giulio Benedetti has joined the channel
Giulio Benedetti (07:32:57): > @Giulio Benedetti has joined the channel
Anshul Kundaje (20:25:01): > @Anshul Kundaje has joined the channel
2022-03-07
Zhaoyang Qin (11:29:29): > @Zhaoyang Qin has joined the channel
Buu Truong (11:38:38): > @Buu Truong has joined the channel
2022-03-09
Fabricio Almeida-Silva (02:52:35): > @Fabricio Almeida-Silva has joined the channel
Oscar Parrish (13:15:51): > @Oscar Parrish has joined the channel
2022-03-11
Christina Simoglou Karali (09:09:48): > @Christina Simoglou Karali has joined the channel
2022-03-14
Nikos Pechlivanis (03:41:04): > @Nikos Pechlivanis has joined the channel
Kristy Tracer (14:41:37): > @Kristy Tracer has joined the channel
2022-03-15
Ruslan Rust (08:39:22): > @Ruslan Rust has joined the channel
Lori Shepherd (10:39:08): > BiocAwards 2022 nomination is now open. Please seehttp://bioconductor.org/about/awards/
2022-03-18
Alessandro Davini (03:53:36): > @Alessandro Davini has joined the channel
Janet Young (14:36:32): > @Janet Young has joined the channel
2022-03-20
Wadschma (11:26:23): > @Wadschma has joined the channel
Sarvesh Nikumbh (21:37:02): > @Sarvesh Nikumbh has joined the channel
2022-03-21
Alison Merikangas (15:48:21): > @Alison Merikangas has joined the channel
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
2022-03-28
Jovan Isma (08:17:58): > @Jovan Isma has joined the channel
Susanna (08:25:55): > Hi there! I’m working on gene expression data and wonder if anyone know how to convert RPKM to TPM? Thank you!
Alexandru-Ioan Voda (09:01:55) (in thread): > It’s probably easier to convert raw read counts to TPM? Do you only have access to RPKM?
Rob Patro (09:16:41): > TPM is just normalized RPKM * 1000000, so TPM_i = ( RPKM_i / sum_j RPKM_j ) * 1000000.
Rob Patro (09:17:26): > Of course, there is the standard question of why you specifically want to convert RPKM to TPM here.
Susanna (09:52:43) (in thread): > Yes, I’m afraid I only have RPKM
Alexandru-Ioan Voda (10:02:49) (in thread): > sorry I was mistaken when I said “easier”, Rob Patro’s answer is correct and is just as easy as anything else
Alexandru-Ioan Voda (10:03:15) (in thread): > Good luck with work:four_leaf_clover:^_^
Artem Sokolov (10:31:38): > Keep in mind that if your gene expression data was collected by a 3’ sequencing method [e.g.,https://www.nature.com/articles/nmeth.f.376], you do NOT want to normalize by gene length. 3’-seq methods produce a single read per transcript, and normalization will skew gene expression values.
Alexandru-Ioan Voda (10:36:05) (in thread): > Although I assume that if Susanna had access to some RPKM matrix from public sources (since there was no access to raw counts, maybe just BAMs), that the sources didn’t publish an RPKM-norm of 3’-seq.
Susanna (13:00:19) (in thread): > Thank you, Artem. > Correct Alexandru:+1:
Alexandru-Ioan Voda (15:37:37): > Hi all! Curious, is there a package or suggested-R-function that can simulate having lower sequencing depth (lower library size, by subsampling), given a count matrix?
Marc Elosua (15:46:47) (in thread): > Maybe you can tryDropletUtilsdownsampleReads()!
Peter Hickey (17:38:46) (in thread): > scuttle::downsampleMatrix()will do what you describe
2022-03-29
Oby Egeolu (12:11:33): > @Oby Egeolu has joined the channel
2022-03-30
sarah i (10:02:29): > @sarah i has joined the channel
Sergio Oller (23:02:12): > @Sergio Oller has joined the channel
2022-03-31
Nicole Ortogero (22:24:51): > @Nicole Ortogero has joined the channel
2022-04-01
Theodore Vichos (03:52:48): > @Theodore Vichos has joined the channel
2022-04-05
Alan Murphy (07:41:31): > Hey! Apologies but not sure where to ask this question regarding reference genome SNP databases on Bioconductor: > I’m the creator of theMungeSumstatspackage on Bioconductor for the standardisation and processing of GWAS sumstats. I currently use Bioconductor packages derived from dbSNP to infer missing RS IDs. I use SNPlocs.Hsapiens.dbSNP144.GRCh38 and SNPlocs.Hsapiens.dbSNP144.GRCh37 dependent on the genome build. Does anyone know if there are later versions of dbSNP available than 144 on Bioconductor? I know there is SNPlocs.Hsapiens.dbSNP151.GRCh38 for GRCh38 but I can’t seem to find similar for GRCh37? Also how will these different versions compare to other reference genome datasets in Bioconductor (I also use BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38 for different checks)? For example, is BSgenome.Hsapiens.NCBI.GRCh38 up-to-date with SNPlocs.Hsapiens.dbSNP151.GRCh38?
Vince Carey (08:49:15): > @Hervé Pagès^^
2022-04-06
Martin Rodriguez Nuñez (16:24:36): > @Martin Rodriguez Nuñez has joined the channel
2022-04-07
Hervé Pagès (10:26:15) (in thread): > Hi Alan, > I started to look into building new SNPlocs packages for dbSNP155. Unfortunately I can no longer use my scripts for this because they are relying on the ASN.1 files that dbSNP no longer provides. Now they provide JSON and VCF files instead:https://ftp.ncbi.nih.gov/snp/latest_release/(Note that they made that switch about 4 years ago, around dbSNP152, seehttps://www.ncbi.nlm.nih.gov/mailman/pipermail/dbsnp-announce/2018q4/000193.html) > The JSON files are huge and hard to parse. I came up with some naive code that I’ve run on the JSON files for chromosomes MT, Y, and 22. It’s very slow:disappointed:I estimate it would take about 2 weeks to run it on all chromosomes! I should probably try to parse the VCF files instead. > > For example, is BSgenome.Hsapiens.NCBI.GRCh38 up-to-date with SNPlocs.Hsapiens.dbSNP151.GRCh38? > TheSNPlocs.Hsapiens.dbSNP.GRCh38packages only contain SNPs located on the chromosomes (SNPs located on scaffolds or alt/patch/fix sequences are omitted) so are compatible withBSgenome.Hsapiens.NCBI.GRCh38(contains the original GRCh38 assembly) andBSgenome.Hsapiens.UCSC.hg38***(based on the GRCh38.p13 assembly).
Alan Murphy (10:34:12) (in thread): > HeyHervé! Ah okay thanks for the explanation, that’s good to know! Yeah I would guess the VCFs are easier to work with, there are quite a few packages in R read them in, including MungeSumstats. Are you working in R for this? Do you have a sample of a format are you trying to get them to?
Sarath Kumar Murugan (10:41:09): > @Sarath Kumar Murugan has joined the channel
Hervé Pagès (10:46:18) (in thread): > I have a pipeline. The first step and most CPU-intensive is to convert the JSON files into simple tab-delimited files with 6 columns and one RefSNP id per line. Seehttps://github.com/hpages/SNPlocsForge/blob/273c0ecc0bb01984783747e4744d6ad1aa8b538c/man/extract_raw_snps_from_json.Rd#L46-L51The code is written in R. Then I feed these tab-delimited files to the rest of the pipeline. > I’ll try to generate the tab-delimited files from dbSNP’s VCF files instead.
Alan Murphy (10:50:02) (in thread): > That makes sense, thanks! If I get some time I’ll do the same to see if I can come up with something to speed it up. Creating the tab-delimited file is the time intensive step too yeah?
Hervé Pagès (11:18:09) (in thread): > yep, that’s the most time intensive step
2022-04-11
William Rodriguez (15:53:57): > @William Rodriguez has joined the channel
2022-04-12
Vivian Chu (13:31:35): > @Vivian Chu has joined the channel
2022-04-13
Alan Aw (13:16:31): > @Alan Aw has joined the channel
2022-04-15
Rana SU (09:19:25): > @Rana SU has joined the channel
Rümeysa Aksu (09:28:46): > @Rümeysa Aksu has joined the channel
Ceylin Karatepe (10:10:48): > @Ceylin Karatepe has joined the channel
2022-04-16
Hervé Pagès (14:33:01) (in thread): > @Alan MurphySNPlocs.Hsapiens.dbSNP155.GRCh38is ready (BioC 3.15 only).
2022-04-18
Alan Murphy (14:16:05) (in thread): > @Hervé Pagèsthis is amazing, thank you very much! Did you end up using the VCF? Will a version of dbSNP 155 also be made available for GRCh37? Both would be massively useful for MungeSumstats
Hervé Pagès (16:55:37) (in thread): > The JSON files. Using brute force to process the 25 JSON files in parallel on a powerful server took about 2 days. The source tarball of the GRCh38 package is about 6 GB. The package for GRCh37 could be made lighter by reusing the rs id, chrom, and alleles columns from the GRCh38 package, so it would actually only need to contain the positions. This should make it between 3 and 4 times smaller. Or maybe it’s easy enough to use something likertracklayer::liftOver()to translate between GRCh38 and GRCh37 positions, in which case the package for GRCh37 wouldn’t even be needed. I’ll look into this.
2022-04-19
Alan Murphy (02:49:37) (in thread): > Thank you!
2022-04-20
SoniaGR (06:35:42): > @SoniaGR has joined the channel
2022-04-21
Indrik Wijaya (03:10:17): > @Indrik Wijaya has joined the channel
Genoa Polumbo (09:57:06): > @Genoa Polumbo has joined the channel
Ynnez Bestari (15:12:44): > @Ynnez Bestari has joined the channel
2022-04-22
Anna Quaglieri (she/her) (00:17:19): > hey there! What’s the suggested way to, given a list of human proteins/genes map them to the latest protein/Gene Ids? Sometimes names changes or synonims are used.
Lluís Revilla (03:19:25) (in thread): > I think the easiest would be: > > library("Org.Hs.eg.db") > select(Org.Hs.eg.db, keys = my_genes, keytype = "SYMBOL", columns = "GENEID") > > If you want the NCBI gene ID. There are several solutions, using other annotation packages if you want the ENSEMBL ids. I would recommend to look at the select help page, as there are arguments to decide what to do with synonyms (not sure about name changes). You could also use biomaRt to retrieve this kind of information.
Anna Quaglieri (she/her) (05:27:51) (in thread): > Thanks a lot@Lluís Revilla! I will try this option:+1:
Marie Oestreich (09:27:23): > @Marie Oestreich has joined the channel
Arda Keles (17:57:32): > @Arda Keles has joined the channel
2022-04-25
Antoine de Weck (19:51:54): > @Antoine de Weck has joined the channel
2022-04-26
Kevin Rue-Albrecht (06:16:31): > Does anyone know a “console” type of font that is not converted to outline by Illustrator when saving as SVG? > I’m using a console font for some illustrations of the (work in progress) Carpentries lesson here:https://carpentries-incubator.github.io/bioc-project/05-s4/index.html#the-methods-packageand it’s frustrating to have bits of code text converted to individual characters when coming back to edit the file
Janani Ravi (14:12:54) (in thread): > DoesFiracodework? Haven’t tried but worth a shot.
mattin snow (14:48:23): > @mattin snow has joined the channel
2022-04-27
Kevin Rue-Albrecht (06:08:00) (in thread): > Look like it’s working yes! thanks
Lori Shepherd (17:32:18): > Bioconductor 3.15 is released! See full release announcement:https://bioconductor.org/news/bioc_3_15_release/
Lori Shepherd (17:33:03) (in thread): > Thanks to all developers and community members for contributing to the project!
2022-04-29
Leonardo Collado Torres (12:20:17) (in thread): > thanks to you and the BioC Core team for putting it all together:smiley:
2022-05-01
James Ward (17:13:15): > @James Ward has joined the channel
James Ward (17:57:38): > I asked on Twitter, and curious if it’s suitable to post here also.“using SummarizedExperiment: > I want something like assayData() to hold tabular data about each matrix in assays(), one row per assay. > When storing more than one assay matrix, I encode too much into the assay name.Has this idea been discussed?”I see curatedTCGAData uses custom functions as a work-around, their experiment names are things like > “ACC_CNASNP-20160128” > If someone wants to filter experiment name they use a TCGA function. > I basically want an empty DataFrame on slot se@assayData with one row per entry in se@assaysThen I’ll add columns to that DataFrame as needed.
2022-05-02
Fabricio Almeida-Silva (10:58:11): > Hi, everyone! Does anyone know if there’s any PAL2NAL equivalent in R or a package to convert protein alignments to codon alignments?
2022-05-03
Vince Carey (10:45:14) (in thread): > Have you considered using the metadata slot of SummarizedExperiment?
Vince Carey (10:46:09) (in thread): > @Laurent Gatto… perhaps you have worked on this?
James Ward (10:55:59) (in thread): > Thanks for the response! That’s a potential workaround I thought about and may try in the meantime. I could store an assays DataFrame there with info. The step that isn’t ideal is subsetting assays, I was hoping for something that would also subset the assays DataFrame.The metadata slot is useful but is sort of like using S3 object attributes, it doesn’t stay in sync with the main object. At least it isn’t dropped during subsetting as with S3 object attributes!The rowData and colData are useful to keep data in sync with those dimensions. I was thinking of assays as another dimension.As I think it out, a driver of the use cases appears to be the subsetting step. (Also the addition of new assay matrix. Ahhh.) Even if the DataFrame is not subset, the rownames could be used to sync with what assayNames are present.
Vince Carey (10:58:46) (in thread): > I’d suggest filing a feature request on the SummarizedExperiment github issues page. The more details you can give on the strength of the use case the greater the likelihood there will be discussion and code produced in response.
James Ward (11:04:02) (in thread): > Silly question, but is this the URL? It looks active with Hervè Pagès making commits, that’s a good sign.https://github.com/Bioconductor/SummarizedExperiment/issues
Vince Carey (11:05:57) (in thread): > That’s the place.
Laurent Gatto (11:33:44) (in thread): > No, sorry, I can’t help.
Laurent Gatto (11:33:53) (in thread): > (Thanks for tagging me though)
James Ward (11:34:09) (in thread): > https://github.com/Bioconductor/SummarizedExperiment/issues/62
Fabricio Almeida-Silva (15:26:13) (in thread): > Thanks anyway!
2022-05-04
Laura Marcos-Zambrano (11:50:40): > @Laura Marcos-Zambrano has joined the channel
2022-05-05
Alan Murphy (07:14:16) (in thread): > Hey@Hervé Pagès, not to rush/annoy you but is there any update on creating the dbSNP155 for GRCh37? I would like to make these useable for MungeSumstats on bioc devel (3.16).
Lori Shepherd (10:46:19): > :warning:The search onbioconductor.orgis currently unavailable. we are investigating the issue.
Roberto Bullitta (10:52:24): > @Roberto Bullitta has joined the channel
Jixing Zhong (23:56:13): > @Jixing Zhong has joined the channel
2022-05-06
Ziga Sanda (06:51:12): > @Ziga Sanda has joined the channel
Anelda Van der Walt (11:02:07): > @Anelda Van der Walt has joined the channel
2022-05-07
Jeremy Selva (04:19:38): > @Jeremy Selva has joined the channel
Victor Lee (04:23:23): > @Victor Lee has joined the channel
Oluwafemi Oyedele (04:48:36): > @Oluwafemi Oyedele has joined the channel
Hervé Pagès (15:24:33) (in thread): > I took a look at artracklayer::liftOver()-based solution and the one-to-zero-or-many nature of the mapping from GRCh38 to GRCh37 coordinates is problematic. I’ll investigate the possibility of making a lightSNPlocs.Hsapiens.dbSNP155.GRCh37that reuses the rs id, chrom, and alleles columns fromSNPlocs.Hsapiens.dbSNP155.GRCh38.
2022-05-08
Eliana Ibrahimi (02:27:01): > @Eliana Ibrahimi has joined the channel
2022-05-09
Alan Murphy (01:17:25) (in thread): > That makes sense, thanks Hervé I really appreciate your work on this!
Nathan Temple (12:40:30): > @Nathan Temple has joined the channel
Suhas (13:59:42): > @Suhas has joined the channel
Raoul Kamadjeu (17:21:39): > @Raoul Kamadjeu has joined the channel
Paul Villafuerte (22:04:34): > @Paul Villafuerte has joined the channel
2022-05-10
Madelyn Carlson (10:14:19): > @Madelyn Carlson has joined the channel
Aidan Lakshman (12:26:05): > @Aidan Lakshman has joined the channel
2022-05-11
Anusha Nagari (12:35:24): > @Anusha Nagari has joined the channel
Anusha Nagari (14:59:00): > Hi everyone! Are the commits made to the release branches (ex: RELEASE_3_15) are reflected real time or will it take the usual 24-48 hours to propagate the changes like in dev version
Marcel Ramos Pérez (15:00:07): > They should be reflected close to real time athttps://code.bioconductor.org/browse/and expect the changes to propagate via the BBS on M, W, and Fhttps://bioconductor.org/checkResults/
Anusha Nagari (15:03:00) (in thread): > @Marcel Ramos PérezThank you, I am trying to push the changes to RELEASE_3_15 and following the steps fromMerge changes to the current release branch, however having issues with the changes not being pushed to. Could you please let me know if I am missing something?
Marcel Ramos Pérez (15:07:03) (in thread): > I’d recommendhttps://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel
Anusha Nagari (15:08:56) (in thread): > I did not realize that I have to change the release version as well and already made the changes to devel branch. In that case can I follow the above thread?
Marcel Ramos Pérez (15:10:39) (in thread): > If it is a bug fix, you should cherry-pick the commits over to the release branch
Marcel Ramos Pérez (15:10:42) (in thread): > and yes
Anusha Nagari (16:05:12) (in thread): > I followed the steps and merged updates resolving conflicts. But getting the error: ! [remote rejected] master -> master (pre-receive hook declined) > > Attached is the screenshot. git status shows the working tree is clean
Anusha Nagari (16:05:16) (in thread): - File (PNG): image.png
Marcel Ramos Pérez (16:08:26) (in thread): > It looks like the conflicts weren’t fully resolved, committed, and were caught by the git hook
Anusha Nagari (16:19:37) (in thread): > Got it. I am unable to find the conflicts how do i go about this?
Marcel Ramos Pérez (16:33:08) (in thread): > Did you try using grep? e.g., grep -rn ‘===+’
Marcel Ramos Pérez (16:34:30) (in thread): > Also seehttps://contributions.bioconductor.org/git-version-control.html?q=merge%20conflig#resolve-merge-conflicts - Attachment (contributions.bioconductor.org): Chapter 21 Git Version Control | Bioconductor Packages: Development, Maintenance, and Peer Review > The Bioconductor project is maintained in a Git source control system. Package maintainers update their packages by pushing changes to their git repositories. This chapter contains several…
2022-05-12
Anusha Nagari (00:52:22) (in thread): > Thank you, I was able to resolve the conflicts and push the changes to the release branch
Kristen Steenbergen (22:53:54): > @Kristen Steenbergen has joined the channel
2022-05-13
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
Aidan Lakshman (10:31:34): > Have people been notified yet for Bioc2022 in-person attendance? They said we’d hear back by 9am EST today, so just trying to figure out if having heard nothing means they’re delayed or that I didn’t get a spot:sweat_smile:
Erica Feick (11:11:08): > We are working on them now - if we said 9am ET that was an overestimation on our part. Emails will go out today.
Aidan Lakshman (13:11:22): > No worries, thank you!
2022-05-17
Monica Coelho (03:37:49): > @Monica Coelho has joined the channel
Francesco Cecere (10:13:36): > @Francesco Cecere has joined the channel
Kristian Ullrich (16:36:10): > @Kristian Ullrich has joined the channel
2022-05-18
Santiago Thibaud (13:53:51): > @Santiago Thibaud has joined the channel
Anuj Sharma (13:59:00): > @Anuj Sharma has joined the channel
Amanda Poissonnier (14:03:30): > @Amanda Poissonnier has joined the channel
2022-05-19
Tyrone Lee (09:10:54): > @Tyrone Lee has joined the channel
rebecca jaszczak (13:53:51): > @rebecca jaszczak has joined the channel
2022-05-20
Simon Pearce (03:14:47): > @Simon Pearce has joined the channel
Alan Murphy (03:32:02) (in thread): > Hey Herve! Is there any update on this? Sorry to push but I have had numerous people asking about discrepancies in MSS results which all stem back to differences in the dbSNP version. I think it’s vital that I get dbSNP implemented in MSS to ensure it remains useful. Cheers
Michal (09:04:14): > @Michal has joined the channel
Hervé Pagès (14:59:53) (in thread): > Some progress but I got distracted by other things. It’s going to take a few more days.
Alan Murphy (15:05:38) (in thread): > That’s no problem, thanks for the update!!
2022-05-21
Alexandru-Ioan Voda (07:56:29): > Say I want to download a dependency, a baseline-model for a package that needs it to run specific analyses on new datasets. > > How would I download the data to<package_install_path>/extdata/using****BiocFileCache****and****usethis****? I was told to use these but the docs are a bit convoluted for me > > I understand that****usethis****is useful because it can help format Windows-like paths (with\instead of/like we do in Linux or Macs) for system calls, but the docs of****usethis******** and ********BiocFileCache******** ****seem very long and address many use-cases that I don’t need?
Vince Carey (09:13:02): > You should not operate on<package_install_path>… use BiocFileCache. Maybe there are enough hints in > > > get_cached_model > function(path = "/tmp/beta.csv", cache=BiocFileCache::BiocFileCache()) { > chk = BiocFileCache::bfcquery(cache, "beta.csv") > if (nrow(chk)==0) { > tag = names(BiocFileCache::bfcadd(cache, path, action="copy")) > } > else tag = chk$rid > cache[[tag]] > } > > to get you going. This handles caching a file on disk. The man page for bfcadd has indications on ways of handling something on the web. If the value to be cached is small, download it to the cache. Only R itself should be writing into<package_install_path>
Alexandru-Ioan Voda (09:19:30) (in thread): > Thank you for your reply! > > The data is quite large, which is why I don’t put it inextdatadirectly with documentation, and I’d prefer to have it in a non/tmp/-like path, since it should be perma-stored as long as the package is installed/used > > Thanks for the code snippet, I’ll try this out:relaxed:
Alan O’C (10:05:05) (in thread): > The file cache is kept in the users home directory rather than/tmpeg I have~/.cache/R/ExperimentHubetc
2022-05-23
Dora Zvjerković (09:58:07): > @Dora Zvjerković has joined the channel
2022-05-24
Kristian Ullrich (04:42:27) (in thread): > Yes, it is, see here:
Kristian Ullrich (04:42:28) (in thread): > https://gitlab.gwdg.de/mpievolbio-it/crbhits/-/blob/master/R/cds2codonaln.R - Attachment (GitLab): R/cds2codonaln.R · master · mpievolbio-it / CRBHits > CRBHits is a reimplementation of the Conditional Reciprocal Best Hit algorithm crb-blast in R.
Kristian Ullrich (04:53:04) (in thread): > However, I need to say, that my implementation starts directly from CDS. This is because in a lot of times even on “good” resources the CDS and protein sequences do not match perfectly and PAL2NAL will also through an error for this situations. Of course there are cases of post-transcriptional AA changes which will be hard to be back-translated into codon alignments anyway.
Kristian Ullrich (04:55:03) (in thread): > Thehttps://github.com/drostlab/orthologrpackage has a wrapper to PAL2NAL already implemented.
Josh Moore (05:08:38): > @Josh Moore has joined the channel
Sanket Verma (06:39:35): > @Sanket Verma has joined the channel
Jamshaid Ahmad (09:20:04): > @Jamshaid Ahmad has joined the channel
Jiefei Wang (09:34:41): > @Jiefei Wang has joined the channel
Erdal Cosgun (14:52:02): > @Erdal Cosgun has joined the channel
2022-05-25
Fabricio Almeida-Silva (02:35:33) (in thread): > Thanks a million,@Kristian Ullrich!
Brian Hanratty (14:51:20): > @Brian Hanratty has joined the channel
2022-05-26
Cindy Fang (14:50:59): > @Cindy Fang has joined the channel
Michael Lawrence (18:18:54): > Has anyone tried using rhub’s containers to build packages that depend on Bioconductor packages? It seems that they are still usingsource("biocLite.R")to install things, which is obviously obsolete.
Michael Lawrence (18:24:21): > Never mind, looks like the bug is fixed in the GitHub version of rhub. The CRAN version has not been updated in 3 years. Who knows the story behind that.
Sneha Challa (18:56:31): > @Sneha Challa has joined the channel
2022-05-27
이상호 (00:43:13): > @이상호 has joined the channel
2022-05-30
Pablo I. Picazo (03:34:59): > @Pablo I. Picazo has joined the channel
2022-06-01
Andrew Abrams (07:50:34): > @Andrew Abrams has joined the channel
Tara Chari (18:23:38): > @Tara Chari has joined the channel
2022-06-02
Alan Murphy (05:50:16) (in thread): > Apologies Hervé, any update on this? I am finishing up other work in the current dev cycle and would like to include this if at all possible
2022-06-03
Julián Montoto Louzao (05:36:11): > @Julián Montoto Louzao has joined the channel
Jacopo Umberto Verga (09:07:29): > @Jacopo Umberto Verga has joined the channel
Aakanksha Singh (12:41:18): > @Aakanksha Singh has joined the channel
Hervé Pagès (13:22:08) (in thread): > Some progress, but I’m running into some unexpected difficulties when trying to extract the snp placements on GRCh37 from the big JSON files. Will take me a few more days.
2022-06-04
Nitesh Mishra (21:23:11): > @Nitesh Mishra has joined the channel
2022-06-07
Hervé Pagès (15:49:44) (in thread): > Major surprise is that some rs ids have been placed on a different chromosome in GRCh37 vs GRCh38 (e.g. rs183986666 was on chr10 in GRCh37 and is now on chr9 in GRCh38, seehttps://www.ncbi.nlm.nih.gov/snp/rs183986666#variant_details). This breaks the naive assumptions I made when I wrote the scripts to extract SNP placements from the RefSNP json files e.g. snps inrefsnp-chr9.json.bz2are not necessarily on chr9 in GRCh37. Had to refactor things substantially but now extraction is even slower. Will take days before completion…:disappointed:
Alan Murphy (16:20:37) (in thread): > Wow that’s mental! Ah no that’s annoying, sorry to hear that and thank you very much for working on this!
2022-06-08
E Loo (13:19:47): > @E Loo has joined the channel
2022-06-09
James Perkins (06:09:35): > @James Perkins has joined the channel
2022-06-10
Andrew Gromenko (10:48:28): > @Andrew Gromenko has joined the channel
2022-06-12
Karat Sidhu (12:35:14): > @Karat Sidhu has joined the channel
Kartik (18:50:14): > @Kartik has joined the channel
2022-06-15
Zuguang Gu (04:34:12): > @Zuguang Gu has joined the channel
Micheal O Dalaigh (09:58:06): > @Micheal O Dalaigh has joined the channel
2022-06-16
Ariel Hippen (15:35:47): > In a SingleCellExperiment object, is there a way to subset based on gene expression values?
Ariel Hippen (15:35:52): > Say I wanted to filter down to cells that express EPCAM. I could make a subset with just EPCAM and pass it to scater’saddPerCellQCfunction, then subset onsce$subsets_epcam_sumbut it seems like there must be a more direct route
kent riemondy (16:35:52) (in thread): > You can subset more directly by examining the count matrix, e.g.: > > #BiocManager::install("scRNAseq") > library(scRNAseq) > sce <- FletcherOlfactoryData() > > # if you want to select cells positive for 1 gene, e.g. Epcam > epcam_positive <- which(assay(sce, "counts")["Epcam", ] > 0) > epcam_pos_sce <- sce[, epcam_positive] > > assay(epcam_pos_sce, "counts")["Epcam", 1:5] > #> OEP01_N706_S501 OEP01_N701_S501 OEP01_N707_S507 OEP01_N705_S501 OEP01_N702_S505 > #> 80 203 40 736 3 > > # if you want to select cells positive for more than 1 gene > genes_to_check <- c("Msi2", "Epcam", "Trp53") > positive_cells <- which(colSums(assay(sce, "counts")[genes_to_check, ] > 0) == length(genes_to_check)) > triple_pos_sce <- sce[, positive_cells] > > assay(triple_pos_sce, "counts")[genes_to_check, 1:5] > #> OEP01_N706_S501 OEP01_N703_S501 OEP01_N704_S503 OEP01_N704_S506 > #> Msi2 18 22 115 65 > #> Epcam 80 228 317 111 > #> Trp53 741 42 1 1 > #> OEP01_N708_S506 > #> Msi2 3 > #> Epcam 12 > #> Trp53 5584 >
Ariel Hippen (16:42:52) (in thread): > This works, thank you!
2022-06-17
Alyssa Columbus (14:00:37): > @Alyssa Columbus has joined the channel
George Odette (17:23:17): > @George Odette has joined the channel
2022-06-19
Federico Marini (15:18:28) (in thread): > the colData-based approach is good if you want for example to compute “signature scores” or so
2022-06-20
Shruti Shah (06:19:59): > @Shruti Shah has joined the channel
2022-06-21
Alan Murphy (03:03:39) (in thread): > Hey Herve, was there any joy getting the refactored code to complete? I know you mentioned it would take even longer to run now
Will Blevins (05:32:26): > @Will Blevins has joined the channel
2022-06-22
Jenny Drnevich (10:10:36): > Any one else noticed/irritated by RStudio’s recent change to their Help tab? The Usage section for any function’s help page is now in a separate text box that has it’s own scroll bar at the bottom of the Usage section, which often isn’t visible when there are lots of functions in the Usage. Makes it almost impossible to scroll and see a function at the same time, without make the Help pane extreme large!:rage:
Marcel Ramos Pérez (10:24:39) (in thread): > That does sound frustrating. Can you provide an example function that has that? I haven’t encountered one with that feature (I’m running RStudio 2022.02.3 Build 492). If you create an issue athttps://community.rstudio.com/and link back here, we can upvote:slightly_smiling_face:
Jenny Drnevich (11:09:47) (in thread): > I am also running 2022.02.3 Build 492; for Windows, so maybe it’s different on Mac.?limma::goanais one and?gplots::heatmap.2has an egregiously long Usage section, but at least most of that only has one argument per line so scrolling isn’t needed. I’ll try to find some others later to create the RStudio issue.
2022-06-24
stefano mangiola (04:08:15) (in thread): > There are many alternative ways, > > a tidy way is using tidySingleCellExeriment > > data |> join_features(shape=“wide”) |> filter(CD3G > 50)
stefano mangiola (04:09:34) (in thread): > a tidy alternative, using filter() and even gating (FACS style) is herehttps://tidytranscriptomics-workshops.github.io/iscb2022_tidytranscriptomics/articles/tidytranscriptomics_case_study.html - Attachment (tidytranscriptomics-workshops.github.io): Tidy Transcriptomics for Single-cell RNA Sequencing Analyses > iscb2022tidytranscriptomics
Jan Otoničar (09:45:09): > @Jan Otoničar has joined the channel
Anna Šenovská (09:45:12): > @Anna Šenovská has joined the channel
Anže Lovše (09:45:24): > @Anže Lovše has joined the channel
benedek.danko (09:45:58): > @benedek.danko has joined the channel
Albert Fradera-Sola (09:51:02): > @Albert Fradera-Sola has joined the channel
Lasse Myr (10:05:03): > @Lasse Myr has joined the channel
Abdul Saboor Khan (10:05:24): > @Abdul Saboor Khan has joined the channel
João Tiago Aparício (10:09:34): > @João Tiago Aparício has joined the channel
Katharina Bosch (11:10:48): > @Katharina Bosch has joined the channel
Giorgia Bolognesi (11:51:55): > @Giorgia Bolognesi has joined the channel
Victoria Fincke (13:24:48): > @Victoria Fincke has joined the channel
2022-06-25
Yatzu Chiu (01:01:00): > @Yatzu Chiu has joined the channel
Paul Schwerd-Kleine (01:04:33): > @Paul Schwerd-Kleine has joined the channel
Thomas Parigger (09:51:33): > @Thomas Parigger has joined the channel
Antoine Delhaye (13:08:47): > @Antoine Delhaye has joined the channel
2022-06-26
Theresa Mulholland (08:52:58): > @Theresa Mulholland has joined the channel
Daniel Fridljand (10:22:45): > @Daniel Fridljand has joined the channel
2022-06-27
Alice Antonello (03:08:37): > @Alice Antonello has joined the channel
Stephan (05:00:10): > @Stephan has joined the channel
Sebastian Wolf (06:36:49): > @Sebastian Wolf has joined the channel
SFS Worms (08:52:15): > @SFS Worms has joined the channel
SFS Worms (08:56:00): > Having some issue trying to extract specific sequences from NGS set (I have one randomised region that I want to extract from amplicon reads). My code run, but it takes about 1hour for 60*10^6 reads. I’m thinking trying to run things with parallel processing might help, but I can’t figure it out, does anyone got good ressources on using parallel processing with multiple alignments?
Kasper D. Hansen (11:04:13): > Taking advantage of multiple processors efficiently is pretty hard. However, is your problem inherently embarrasingly parallel? Then you should get tons of milage out of additional processors. I am pretty unclear on what you’re trying to do.
SFS Worms (11:41:03): > Sorry, I was pretty unclear, so I have a bunch of sequences from a drift experiment in a fastq file. All the sequences have a conserved sequence followed by a randomized sequence that I am interested in, let’s say ATGGTAGTNNNGTGA or whatever. I want to extract all the NNN sequences. Right now I’m doing it by aligning TAGT to sequence to see where the NNN is and then subsetting it with subseq, but the alignment provedure is extremely slow and I was hoping to parallellize it.
Rob Patro (11:45:32): > So you want to extract all (say 3) nucleotide sequences that occur downstream of aTAGT?
Rob Patro (11:45:44): > and only in the forward or also in the reverse complement?
SFS Worms (11:46:33): > Only in the foward seq would do
SFS Worms (11:47:00): > And I’m reasonably certian thatTAGTonly occurs once in the sequence in my case
Rob Patro (11:55:04): > Have you tried something straightforward like the following? > > gunzip -c <fastq> | grep -oP "TAGT\K([ACGT]{3})" >
Rob Patro (11:55:12): > grep can be super fast
SFS Worms (11:56:04): > Mmmmmmh, no, I’ll try now
SFS Worms (11:56:06): > Thanks!
Rob Patro (12:24:04): > you’re welcome!
Rob Patro (12:24:41): > I’ll note thegunzip -c <fastq> |part is only if your fastq is gzipped, if it’s already uncompressed it’s justgrep -oP "TAGT\K([ACGT]{3})" <fastq>
SFS Worms (13:19:11): > i’m not familiar with regex, but what’s the role of ? Not take the things before?
Martin Morgan (13:19:36): > In R Ithinkthis could be implemented as > > library(Biostrings); library(stringi) > reads = readDNAStringSet("<fastq>") > stri_extract(reads, regex = "(?<=TAGT)[ACGT]{3}") > > This uses ‘lookbehind’(<=TAGT)(?<=says start the match after the string in parentheses). If the fastq file where large one could iterate through in chunks (e.g., of 10’s of millions of reads at a time) as illustrated on the help page?readDNAStringSet.
Rob Patro (13:21:01): > Ingrep,@Martin Morgansuggests,I.e.printoutonlythecapturegroup.
SFS Worms (13:21:19): > Thanks!
SFS Worms (13:32:59) (in thread): > This works fine, but somehow stri extract is even slower than my previous method, Ill look into it tomorrow
Martin Morgan (14:41:38) (in thread): > It will be slow if you run out of memory; in that case you will need to iterate through your files in chunks.
2022-06-28
Lea Seep (03:01:56): > @Lea Seep has joined the channel
Arvid Hutzfeldt (04:54:55): > @Arvid Hutzfeldt has joined the channel
Moni (07:06:04): > @Moni has joined the channel
SFS Worms (09:10:58) (in thread): > So I’m not sure I understand why, but on 100k sequence > > extract.peptide2 = function(dnaSeq, regexPattern = "(?<=TGGCTTCATTGCGAGCAAT)[ACGT]{24}"){ > seq = stri_extract(dnaSeq, regex = regexPattern) %>% DNAStringSet() > return(seq) > } > > runs in 5.7 sec. > > extract.peptide3 = function(dnaSeq, regexPattern = "(?<=TGGCTTCATTGCGAGCAAT)[ACGT]{24}"){ > x <- str_locate(dnaSeq, "(?<=TGGCTTCATTGCGAGCAAT)[ACGT]{24}") > peptideList <- subseq(x = dnaSeq, start = x[,1], end = x[,2]) > return(peptideList) > } >
SFS Worms (09:11:05) (in thread): > Second on in 0.47
SFS Worms (09:11:22) (in thread): > And > > extract.peptide4 = function(dnaSeq, regexPattern = "TGGCTTCATTGCGAGCAAT", pepSize = 24){ > x <- str_locate(dnaSeq, regexPattern) > peptideList <- subseq(x = dnaSeq, start = x[,2]+1, end = x[,2]+pepSize) > return(peptideList) > } >
SFS Worms (09:11:52) (in thread): > In 0.17, so it seems stri_extract is less efficient that subseq() by a lot
SFS Worms (09:12:03) (in thread): > Thanks a ton for the help, really pushed me in the right direction
Martin Morgan (10:36:05) (in thread): > Building on your last example, because theregexPatternis actually fixed, I think you can usevmatchPattern()followed by a little massaging and thensubseq(), maybe something like > > match <- vmatchPattern(regexPattern, dnaSeq, fixed=TRUE) > found <- lengths(match) == 1L > dnaSeq1 <- dnaSeq[found] > subseq( > dnaSeq1, > min(width(dnaSeq1), unlist(end(found)) + 1L), > min(width(dnaSeq1), unlist(end(found)) + pepSize) > ) > > this should be fast because there is no coercion fromDNAStringSettocharacter(), and becausesubseq()actually creates ‘views’ on to the DNA sequence, rather than creating a new DNAStringSet.
SFS Worms (10:44:43) (in thread): > Oh nice, will give it a try!
2022-06-29
Thiago Britto-Borges (10:59:22): > @Thiago Britto-Borges has joined the channel
Uwe (11:18:49): > @Uwe has joined the channel
2022-06-30
Valentina Lorenzi (10:28:58): > @Valentina Lorenzi has joined the channel
2022-07-02
irem Kahveci (08:32:55): > @irem Kahveci has joined the channel
Zachary Kartje (13:04:19): > @Zachary Kartje has joined the channel
Simón(e) Sun (13:40:46): > @Simón(e) Sun has joined the channel
Sarah Pierce (13:42:31): > @Sarah Pierce has joined the channel
Jenn Kim (13:52:58): > @Jenn Kim has joined the channel
Madeline Keenen (13:53:29): > @Madeline Keenen has joined the channel
Mroj Alassaf (16:28:56): > @Mroj Alassaf has joined the channel
2022-07-03
Khanh Nguyen (21:49:29): > @Khanh Nguyen has joined the channel
2022-07-04
Lisa Okamoto (05:51:52): > @Lisa Okamoto has joined the channel
Daniel Lewinsohn (09:07:49): > @Daniel Lewinsohn has joined the channel
Andrew J. Rech (19:44:32): > @Andrew J. Rech has joined the channel
Andrew J. Rech (19:46:10): > @Andrew J. Rech has left the channel
2022-07-05
Ze Chuan Shi (14:53:59): > @Ze Chuan Shi has joined the channel
shuaiwang (15:02:47): > @shuaiwang has joined the channel
2022-07-07
Alan Murphy (07:13:00) (in thread): > Hey@Hervé Pagès, any update on this? Apologies about the constant messages
Clara Pereira (14:23:21): > @Clara Pereira has joined the channel
Amos Schorr (14:44:54): > @Amos Schorr has joined the channel
Xinge Wang (23:05:10): > @Xinge Wang has joined the channel
2022-07-08
Shadie Rezazadeh (00:04:10): > @Shadie Rezazadeh has joined the channel
Athena Chen (11:59:20): > @Athena Chen has joined the channel
2022-07-09
Noorul (08:57:03): > @Noorul has joined the channel
Zhilong Jia (10:15:06): > @Zhilong Jia has joined the channel
Yuan Yin (13:05:16): > @Yuan Yin has joined the channel
2022-07-10
Tríona (12:04:51): > @Tríona has joined the channel
Sajesan Aryal (14:51:20): > @Sajesan Aryal has joined the channel
2022-07-11
Simon (05:16:31): > @Simon has joined the channel
KC Lan (10:52:45): > @KC Lan has joined the channel
2022-07-14
Ashley Robbins (16:51:29): > @Ashley Robbins has joined the channel
Farhan Ameen (23:26:28): > @Farhan Ameen has joined the channel
2022-07-15
Hervé Pagès (02:36:44) (in thread): > I’ve just pushedSNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22.tar.gz(929,496,192 SNPs) andSNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.22.tar.gz(949,021,448 SNPs) to BioC 3.16. The 2 packages should become available viaBiocManager::install()in the next 3 hours or so. > Sorry for the delay, had to completely refactor the pipeline I use to forge these packages. My previous pipeline missed a few SNPs that are included in this new version ofSNPlocs.Hsapiens.dbSNP155.GRCh38.
Alan Murphy (02:37:52) (in thread): > Amazing news, thank you so much for this I really appreciate it!!
Hervé Pagès (02:40:14) (in thread): > You’re welcome. Also FYI I removed the following packages from BioC 3.16 to make room for these 2 new packages: > - SNPlocs.Hsapiens.dbSNP.20101109 > - SNPlocs.Hsapiens.dbSNP.20120608 > - SNPlocs.Hsapiens.dbSNP141.GRCh38 > - XtraSNPlocs.Hsapiens.dbSNP141.GRCh38 > - SNPlocs.Hsapiens.dbSNP142.GRCh37 > - SNPlocs.Hsapiens.dbSNP151.GRCh38 > All of them are currently deprecated in BioC 3.15.
Alan Murphy (02:43:50) (in thread): > That’s all good with me, the only other dbSNP versions I use are: > > SNPlocs.Hsapiens.dbSNP144.GRCh37, > SNPlocs.Hsapiens.dbSNP144.GRCh38 > > which I’d like to keep as users of the package have expressed a need for the older version of dbSNP too
2022-07-18
Filip Stachura (06:39:33): > @Filip Stachura has joined the channel
2022-07-19
Juan Moriano (10:35:14): > @Juan Moriano has joined the channel
Nicholas Cooley (11:07:55): > Hi everyone, does anyone have any suggestions for packages or workflows for creating publication quality figures of alignments? Preferably pairwise alignments?
Seth Shelnutt (14:57:30): > @Seth Shelnutt has joined the channel
Anna Reisetter (17:17:50): > @Anna Reisetter has joined the channel
Zonglin He (19:10:45): > @Zonglin He has joined the channel
Tyrone Chen (22:47:16) (in thread): > http://gosling-lang.org/
2022-07-20
Filip Stachura (08:20:23) (in thread): > We have an experimental support for Gosling for R and Shiny. Let me know if it’s something you would like to check. - File (GIF): output (3).gif - File (GIF): output (2).gif - File (GIF): output (1).gif
GuandongShang (08:52:32) (in thread): > maybe you can try ggmsa?
Nicholas Cooley (10:42:21) (in thread): > thanks for the replies! I think ggmsa will fit into our scripts and things nicely, though Gosling looks really cool!
Jonathan Carroll (17:55:36) (in thread): > @Filip StachuraI’m very interested - I played with the library and managed to get the plots to work in R (and shiny) but my approach felt hacky (shoehorning a templated javascript call into some HTML). Would love to compare notes and take it for a spin.
2022-07-21
Filip Stachura (03:27:41) (in thread): > Hi Jonathan, we do it through React.js through ourshiny.reactpackage. As gosling.js has native support for React this is very clean and elegant. Let’s talk 1-1
Andrzej Białaś (07:18:36): > @Andrzej Białaś has joined the channel
2022-07-22
Mehdi Montazer (03:41:06): > @Mehdi Montazer has joined the channel
Sean Davis (10:37:18) (in thread): > @Filip StachuraFYI: there is further interest in R integration:https://twitter.com/seandavis12/status/1550173910951268352 - Attachment (twitter): Attachment > Check out Gosling, “A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization” > > http://gosling-lang.org/ > > And an editable example! > > https://gosling.js.org/?example=CIRCULAR_OVERVIEW_LINEAR_DETAIL https://pbs.twimg.com/media/FYNSqnSUsAU9uM8.jpg
Gary Sieling (14:40:55): > @Gary Sieling has joined the channel
Claire Rioualen (15:49:25): > @Claire Rioualen has joined the channel
2022-07-25
Filip Stachura (16:32:13) (in thread): > Yes, thank you for sharing. The version from twitter is a wrap up on Python (via reticulate) it will not work in Rmarkdown or Shiny. > > Our version is a wrapper on top of JS and will work everywhere and will be able to act as Shiny input as well (e.g. App will know what range is selected, what was clicked, etc)
2022-07-26
Ryan C. Thompson (23:13:07): > @Ryan C. Thompson has joined the channel
2022-07-27
Ya-Feng Wen (01:09:02): > @Ya-Feng Wen has joined the channel
Rumeysa Fayetörbay (08:59:40): > @Rumeysa Fayetörbay has joined the channel
Alexandre Gouy (10:47:21): > @Alexandre Gouy has joined the channel
Rushika (10:48:41): > @Rushika has joined the channel
Olga (10:50:43): > @Olga has joined the channel
Marouen Ben Guebila (10:55:18): > @Marouen Ben Guebila has joined the channel
Leonardo Collado Torres (11:01:01): > https://twitter.com/rstudio/status/1552285282636120064?s=12&t=ogOujwCMbEM3Krgm-oJzLw - Attachment (twitter): Attachment > We are excited to announce that RStudio, PBC will become Posit, PBC in October! > > More information here: https://www.rstudio.com/blog/rstudio-is-becoming-posit/
Jalees Rehman (11:13:59): > @Jalees Rehman has joined the channel
Ana Ferreira (11:57:04): > @Ana Ferreira has joined the channel
Deena Gendoo (12:21:00): > @Deena Gendoo has joined the channel
Fursham Hamid (13:15:24): > @Fursham Hamid has joined the channel
Garreck Lenz (15:56:51): > @Garreck Lenz has joined the channel
Renuka Potbhare (17:53:49): > @Renuka Potbhare has joined the channel
Ji-Eun Park (18:15:26): > @Ji-Eun Park has joined the channel
Nam Nguyen (18:51:14): > @Nam Nguyen has joined the channel
2022-07-28
Will t (09:39:37): > @Will t has joined the channel
Michael Love (10:03:52) (in thread): > I’ve been building a workshop for BioC on my M1 mac using Rosetta and had a speed quoted for one step at 40 seconds. I was testing on the conference machines and the same version of code runs in ~2 seconds on Linux. I just reproduced this on my cluster as well.. i’m pretty surprised…
SILVIA GIULIA GALFRE’ (12:01:57): > @SILVIA GIULIA GALFRE’ has joined the channel
Anirban Shaw (13:15:07): > @Anirban Shaw has joined the channel
Mervin Fansler (17:14:48): > @Mervin Fansler has joined the channel
Snehal Wani (17:45:55): > @Snehal Wani has joined the channel
Anvesh Dasari (19:37:20): > @Anvesh Dasari has joined the channel
2022-07-29
Mark Bartlett (07:33:23): > @Mark Bartlett has joined the channel
Alexandra Emmons (12:04:43): > @Alexandra Emmons has joined the channel
Aimee Keel (14:11:18): > @Aimee Keel has joined the channel
Paulina Rzasa (14:17:29): > @Paulina Rzasa has joined the channel
Euphy Wu (16:30:38): > @Euphy Wu has joined the channel
Etienne Danis (20:11:15): > @Etienne Danis has joined the channel
Margaret Turner (20:16:39): > @Margaret Turner has joined the channel
Chenchen Zhu (21:51:26): > @Chenchen Zhu has joined the channel
2022-07-30
Afrooz Razi (01:15:07): > @Afrooz Razi has joined the channel
Wenpin Hou (08:11:48): > @Wenpin Hou has joined the channel
2022-07-31
Amos Schorr (05:51:50): > Not related to bio, but hopefully y’all might know some ppl you can share this with. A super awesome org that teaches ppl data science and software engineering in places that don’t offer many opportunities is hiring a couple ppl (IT Dev, Director of Technology) and they really need help getting the word out. They’re fully remote, high impact jobs with explicit salary ranges in the JD. > > 1. IT dev. You need to be able to work with Docker, Redis, PostgreSQL, AWS, jQuery, bootstrap, select2, Linux, Docker, AWS. > > 2. Dir. of Technology. You need some leadership experience, experience developing tech and data products, managing infrastructure on AWS, open source experience, etc.https://carpentries.org/jobs/ - Attachment (The Carpentries): Job Opportunities with 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.
2022-08-01
Sreekala (12:58:37): > @Sreekala has joined the channel
Sriya Malladi (20:45:33): > @Sriya Malladi has joined the channel
Mae Woods (20:45:55): > @Mae Woods has joined the channel
2022-08-02
Kevin Rue-Albrecht (07:04:06): > Open call for a better package name:slightly_smiling_face:https://github.com/kevinrue/iSEEExperimentHub/issues/5
Alan O’C (07:12:42) (in thread): > iSEEEHub seems like a decent option but I can 100% guarantee people will forget how many Es to use
Kevin Rue-Albrecht (07:21:08) (in thread): > yeah, the E’s are definitely a problem here
Kevin Rue-Albrecht (07:22:20) (in thread): > Though hold on “interactive SummarizedExperiment Explorer ExperimentHub” doesn’t make grammatical sense anyway. I think the “iSEE” prefix can be scrapped/replaced
Kevin Rue-Albrecht (07:22:42) (in thread): > “interactive ExperimentHub Explorer” would already make more sense
Alan O’C (07:23:08) (in thread): > I think it’s considered bad form to win your own contest:smile:
Kevin Rue-Albrecht (07:23:09) (in thread): > Though … iEHE.. meh!:neutral_face:
Kevin Rue-Albrecht (07:23:32) (in thread): > (definitely not a winner to me that one:stuck_out_tongue:)
Kevin Rue-Albrecht (07:24:07) (in thread): > if anything i just gave contestants a better starting point:wink:
Kevin Rue-Albrecht (08:10:26) (in thread): > Also, I kinda wanted to keep a mention of iSEE somewhere in there, as there are other interactive Ehub explorers out there, independent from iSEE
Alan O’C (08:17:43) (in thread): > interactive summarised experimenthub explorer? Or “iSEE” for short:stuck_out_tongue:
Simone Montalbano (10:04:33): > @Simone Montalbano has left the channel
Nicholas Cooley (11:21:27): > i have a question that this might be the right crowd for: > > using the SRAToolkit to grab reads,prefetchhas, at least a few times preferentially grabbed the.sralitefile as opposed to the.srafile which is not the behavior i would prefer. Has anyone else encountered this?
2022-08-03
Hans-Ulrich Klein (13:38:34): > @Hans-Ulrich Klein has joined the channel
2022-08-04
Josué Curto Navarro (10:37:45): > @Josué Curto Navarro has joined the channel
László Kupcsik (21:51:21): > @László Kupcsik has joined the channel
2022-08-08
Denis Bienroth (22:05:02): > @Denis Bienroth has joined the channel
Hieu Nim (23:33:11): > @Hieu Nim has joined the channel
2022-08-09
Fabricio Almeida-Silva (02:25:06) (in thread): > Hi, Nicholas. I highly recommend downloading .fastq.gz files directly from ENA, if you can. It is way faster than using SRAToolkit and will lead to less stress. ;)
Ananya Saha (11:06:52): > @Ananya Saha has joined the channel
Moritz E. Beber (11:48:50) (in thread): > If you’ve been wanting to try nextflow, there’s a pipeline for thishttps://nf-co.re/fetchngs - Attachment (nf-co.re): fetchngs » nf-core > Pipeline to fetch metadata and raw FastQ files from public and private databases
Nicholas Cooley (12:30:17) (in thread): > We would i use pull a nextflow docker container for what i’m doing in a few lines already?
Moritz E. Beber (12:31:17) (in thread): > Sorry, I don’t fully get what you’re saying. Can you rephrase please?
Thao Tang (18:02:30): > @Thao Tang has joined the channel
Education Extended (20:02:07): > @Education Extended has joined the channel
2022-08-10
Lukas Gamp (05:50:30): > @Lukas Gamp has joined the channel
2022-08-11
Susanna Downing (11:19:17): > @Susanna Downing has joined the channel
Jacob Steele (11:25:07): > @Jacob Steele has joined the channel
2022-08-15
Michael Kaufman (13:11:51): > @Michael Kaufman has joined the channel
Spencer Siddons (18:27:45): > @Spencer Siddons has joined the channel
2022-08-22
rodrigo arcoverde (07:32:42): > @rodrigo arcoverde has joined the channel
Erin Kelley (14:47:06): > @Erin Kelley has joined the channel
Simone Procaccia (16:29:10): > @Simone Procaccia has joined the channel
2022-08-24
Edward Tettevi (19:32:17): > @Edward Tettevi has joined the channel
2022-08-26
Tyrone Lee (16:16:07): - File (PNG): image.png
Connor Higgins (21:00:18): > @Connor Higgins has joined the channel
2022-08-29
funda ipekten (12:49:03): > Hi all, Is there applying Bhattacharya analysis in R? Is Anyone using it? (düzenlendi)
Yu Zhang (13:41:59): > @Yu Zhang has joined the channel
2022-08-30
Lisa Breckels (07:06:39): > @Lisa Breckels has joined the channel
Ali Quidwai (16:01:36): > @Ali Quidwai has joined the channel
2022-09-01
Matt Ritchie (02:08:20): > Here’s one for those who love a good Venn diagramhttps://twitter.com/PollyLegend/status/1563491876174323712 - Attachment (twitter): Attachment > Today I learned that the Venn diagram was invented by John Venn from Kingston Upon Hull and this is the commemorative plaque in his honour. This makes me very happy!
Moritz E. Beber (03:13:20) (in thread): > Shouldn’t that require four circles?:thinking_face:
2022-09-02
Jiansi Gao (17:42:58): > @Jiansi Gao has joined the channel
2022-09-06
Greg Fragin (21:26:47): > @Greg Fragin has joined the channel
2022-09-07
Laura Marcos-Zambrano (04:55:35): > Hi all:grinning:I will need your advice > I’m preparing a teaching course about R and Bioconductor basics for undergrad students. Everyone is going to bring their own laptop. What will be the best way to prepare everything for solving installation, and dependencies issues in each different computer?
Luke Zappia (05:55:51) (in thread): > From experience teaching Software Carpentry workshops the biggest issue was institutional laptop where things were locked down (stuff like the default home directory being on a shared drive you can’t access). Hopefully that should be ok if people are using personal laptops. > > I would send out a super detailed set of instructions for what to download and install including Windows/MacOS/Linux differences (preferably with pictures). It can seem obvious but just saying “install from this website” is often hard for people to follow. People also often struggle with the difference between R and RStudio and that they need to install both. Check if any of the packages you want to use have extra system dependencies but if you are sticking to common packages the normal install system should be able to handle things. It can also be helpful to get people to install packages in advance to avoid waiting for things to compile and to find any major issues. > > I’m sure people with have other suggestions I have forgotten. > > Good luck with the course!
Laura Marcos-Zambrano (07:15:43) (in thread): > Thank you Luke:slightly_smiling_face:I will go with the “super detailed” set of instructions:stuck_out_tongue:and hope everyone can follow it.
Laurent Gatto (08:04:54) (in thread): > Here’s what we have for the workshop we are going to run next week:https://carpentries-incubator.github.io/bioc-intro/setup.html
Laura Marcos-Zambrano (09:38:58) (in thread): > Thanks!!:slightly_smiling_face:
Kasper D. Hansen (10:22:52) (in thread): > In my experience, a very useful thing to do is to make a script thatcheckswhether the dependencies are installed and tell them to screenshot the output and send it. That way you know it “works” and you know how many people you will need to help.
Federico Marini (12:05:55) (in thread): > On a similar line to@Kasper D. Hansen- for a summer school we recently ran, I specified the requirements in a page, telling them what to do to check if all runs, and then if problems arise, we offered some kind of troubleshooting on day 0. Can be (if not too much going on) on starting time -1 hour:wink:
Ana Beatriz Villaseñor Altamirano (17:50:08) (in thread): > If you have time (and or TAs), you can schedule 1 hr for solving setup issues before starting classes. > Also you could use Rstudio Cloudhttps://www.rstudio.com/resources/webinars/rstudio-cloud-in-the-classroom/as far as I remember it was free for teaching, maybe I’m wrong - Attachment (rstudio.com): RStudio Cloud in the Classroom > Much has been written in the statistics and data science education literature about pedagogical tools and approaches to provide a practical computational foundation for students.
Sean Davis (21:15:57) (in thread): > @Laura Marcos-ZambranoI’m happy to host on Orchestra (http://orchestra.cancerdatasci.org) if you’d like (it’s free). The one caveat is that there is no persistent storage between 8-hour sessions, so students need to download their work. > > If you are teaching a semester course, go through the challenges of getting software installed on their personal laptops. If just a few limited sessions, then Orchestra might be a good fit. I will often do both under the assumption that someone will have problems during coding sessions; it is good to have a backup like Orchestra just in case that you can launch in a couple of minutes for a student.
Sean Davis (21:17:35) (in thread): > Orchestra has the advantage of being able to preinstall software and to include course materials inside the environment.
2022-09-08
Laura Marcos-Zambrano (03:53:30) (in thread): > Thank you everybody:slightly_smiling_face:… It’s a semester course@Sean Davis, so I think I will go trough installation in their laptops. I’m taking a look at Orchestra and I think it’s pretty nice also
Laura Marcos-Zambrano (03:55:52) (in thread): > @Ana Beatriz Villaseñor AltamiranoI was looking Rcloud, but I’m not sure if the free account will be enough for all the classes:thinking_face:
Tom Dean (05:40:23): > @Tom Dean has joined the channel
Abdul Saboor Khan (17:52:17): > Hello everyone, can anyone tell me how to resolve this issue ” Error in eigen(input) : infinite or missing values in ‘x’” , yes I have NAs in my matrix file, I am making the phenotype network using this code “cormat2 <- cor(network_nem[1:16], method =”spearman”, use = “na.or.complete”) ” , and then this qgraph(cormat2,graph = “cor”, layout = “circle”, sampleSize = nrow(network_nem), alpha = 0.3, cut = 5, bonf = T, title = “Phenotype Network of A. nemorensis”, title.cex = 2, vsize = 7, usePCH = T, details = T, threshold=“sig”, height = 30, width = 40, label.scale = T, theme =‘TeamFortress’) . I have one column as a character and I have to keep it in the network but it doesn’t accept other than numeric. If you have the solution please tell me.
Hervé Pagès (18:48:28) (in thread): > Please ask your question again on our support site:https://support.bioconductor.org/Also please make sure to read the posting guide before you post. In particular the code you show should illustrate the problem and others should be able to run it. Format your post by putting code between triple backticks. This helps with readability and it makes it easier for others to copy/paste it. Also please provide yoursessionInfo(). Thanks!
2022-09-11
Janani Ravi (18:15:46): > R@IISAR Workshops by Ayush Patel and @Heather Turner**** in Bengaluru, India, Dec 30, 2022** > > This is the second in the series of R-related conferences and workshops offered as part of the biannualInternational Indian Statistical Association meeting. The first was held inMumbai in 2019. The 2022 day-long workshop will take place at theIndian Institute of Science, Bangaloreon December 30, 2022. This workshop has been endorsed by theR Foundation. This is a call for participants throughout India. Apply to participant using the form on the website: > More info:https://r-iisa2022.rbind.io/| Register here:https://bit.ly/Riisa2022More on Twitter:https://twitter.com/AsiaR_comm/status/1569085556734435328
2022-09-12
Jan Stanstrup (03:35:41) (in thread): > I did a script that checks the R version, installs packages and checks if they installed OK. then writes in the console “good to go!” or “XX is missing”. Also might be good to give them some material to prepare on. It is a mouthful to start R from zero. I collected some videos here:https://nexs-metabolomics.gitlab.io/INM/inm-booklet/0203-R_intro.html - Attachment (nexs-metabolomics.gitlab.io): 2.3 Introduction to R (self-study) | Multivariate analysis with PLSDA > 2.3 Introduction to R (self-study) | Multivariate analysis with PLSDA
Jan Stanstrup (03:36:18) (in thread): > they generally request more info on ggplots since it is used so much. so make sure to find the time for that
Ana Cristina Guerra de Souza (16:52:10): > @Ana Cristina Guerra de Souza has joined the channel
ALAKANSE OLUWASEUN (17:35:55): > @ALAKANSE OLUWASEUN has joined the channel
2022-09-13
Alex Schrader (17:15:02): > @Alex Schrader has joined the channel
2022-09-15
Xiuwen Zheng (00:40:16): > @Xiuwen Zheng has joined the channel
Alan Murphy (05:29:29): > Hey everyone! I’m looking for a database containing the hapmap3 snps set. Has any work been done to put this on Bioconductor?
Zuguang Gu (12:28:01): > @Zuguang Gu has joined the channel
Laura Marcos-Zambrano (12:41:32) (in thread): > Thank you Jan:slightly_smiling_face:very nice course
2022-09-16
verakorenblik (04:24:30): > @verakorenblik has joined the channel
Ida Holopainen (06:07:56): > @Ida Holopainen has joined the channel
Andrea Sottosanti (06:08:29): > @Andrea Sottosanti has joined the channel
Silvia Barbiero (08:18:12): > @Silvia Barbiero has joined the channel
Paul Shannon (11:57:59): > @Paul Shannon has joined the channel
Ivo Kwee (19:18:05): > @Ivo Kwee has joined the channel
2022-09-18
Adam Stevens (17:33:26): > @Adam Stevens has joined the channel
2022-09-19
Vandenbulcke Stijn (06:21:26): > @Vandenbulcke Stijn has joined the channel
Nina Demeulemeester (12:45:31): > @Nina Demeulemeester has joined the channel
Sam Dahlke (13:19:21): > @Sam Dahlke has joined the channel
Ryan Williams (16:49:23): > @Ryan Williams has joined the channel
Chi-Li Chiu (16:50:00): > @Chi-Li Chiu has joined the channel
John Kirkham US (16:50:47): > @John Kirkham US has joined the channel
Mengbo Li (16:53:15): > @Mengbo Li has joined the channel
2022-09-20
Philippe Hauchamps (08:48:05): > @Philippe Hauchamps has joined the channel
2022-09-21
Manon Martin (08:05:52): > @Manon Martin has joined the channel
2022-09-22
Michał Świrski (10:24:41): > @Michał Świrski has joined the channel
E Ra (12:50:59): > @E Ra has joined the channel
Sheryl Rothmuller (20:33:31): > @Sheryl Rothmuller has joined the channel
2022-09-23
Iivari (08:36:43): > @Iivari has joined the channel
2022-09-26
Rehana Rasul (13:31:57): > @Rehana Rasul has joined the channel
2022-09-27
Jennifer Holmes (16:08:32): > @Jennifer Holmes has joined the channel
vin (22:08:51): > @vin has joined the channel
2022-09-28
Barron Chu (00:48:09): > @Barron Chu has joined the channel
Haleema Sadia (15:51:53): > @Haleema Sadia has joined the channel
2022-10-02
Priya (04:40:08): > @Priya has joined the channel
James Dhaliwal (18:07:07): > @James Dhaliwal has joined the channel
2022-10-03
Ana Beatriz Villaseñor Altamirano (01:34:22): > I had the great idea of updating R 4.2.1 (arm64) but now I remember why I shouldn’t:smiling_face_with_tear:. Are there any steps on how to work with Bioc under arm64 or should I go back to 4.1 intel? Thank you BioC community.
Vince Carey (09:31:24): > we are now producing binaries for arm for bioc 3.16 so use devel branch! give it a try@Andres Wokaty
Ana Beatriz Villaseñor Altamirano (09:47:22) (in thread): > That’s wonderful!! Thank you:saluting_face:
Devika Agarwal (12:42:01): > @Devika Agarwal has joined the channel
Leonardo Collado Torres (19:54:59): > Tryhttps://twitter.com/lcolladotor/status/1519665235652579328?s=46&t=cKsEhETNVYQqUewZG9z99Q - Attachment (twitter): Attachment > Do you want to use @Bioconductor 3.15? That means that you’ll need to install R 4.2 on your computer from CRAN https://cran.r-project.org/ > > For macOS users, you might want to use to install :package: deps for compiling > > sudo R > source(“https://mac.R-project.org/bin/install.R”) > install.libs(“all”) > > #rstats https://twitter.com/Bioconductor/status/1519428806150443014 - Attachment (twitter): Attachment > Bioconductor 3.15 is released! See full release announcement: https://bioconductor.org/news/bioc_3_15_release/ #rstats @Bioconductor #Bioc315
2022-10-04
Charlotte Dawson (05:49:16): > @Charlotte Dawson has joined the channel
2022-10-05
Anand Ruban Agarvas (12:30:20): > @Anand Ruban Agarvas has joined the channel
2022-10-06
Charlotte Hutchings (05:00:41): > @Charlotte Hutchings has joined the channel
2022-10-07
John Nyhuis (12:36:19): > @John Nyhuis has joined the channel
2022-10-08
Taku Iwaki (08:07:33): > @Taku Iwaki has joined the channel
Phylis Atieno (12:59:34): > @Phylis Atieno has joined the channel
Mariam Fayena (13:49:42): > @Mariam Fayena has joined the channel
Chizi E (13:54:04): > @Chizi E has joined the channel
Kiki Shuxteau (16:18:59): > @Kiki Shuxteau has joined the channel
2022-10-09
Dike Victoria Chiemela (03:45:33): > @Dike Victoria Chiemela has joined the channel
Karsten Rinas (10:41:05): > @Karsten Rinas has joined the channel
darmimessele seyoum (18:49:45): > @darmimessele seyoum has joined the channel
YuNan Guan (22:47:57): > @YuNan Guan has joined the channel
2022-10-10
Elendu Emmanuel (02:12:21): > @Elendu Emmanuel has joined the channel
Halimat Chisom (03:16:41): > @Halimat Chisom has joined the channel
Ani Chibuike Damian (10:02:34): > @Ani Chibuike Damian has joined the channel
chihurumnanya ikevude (10:23:42): > @chihurumnanya ikevude has joined the channel
Mercilena Benjamin (13:47:49): > @Mercilena Benjamin has joined the channel
Atuhurira Kirabo Kakopo (16:02:34): > @Atuhurira Kirabo Kakopo has joined the channel
2022-10-11
Chinwe (00:28:50): > @Chinwe has joined the channel
Alejandro Pereira-Santana (13:23:20): > @Alejandro Pereira-Santana has joined the channel
Zelal Özgür Durmuş (21:34:15): > @Zelal Özgür Durmuş has joined the channel
2022-10-12
krunal gamit (03:07:35): > @krunal gamit has joined the channel
Akwamfon Eventus (06:36:34): > @Akwamfon Eventus has joined the channel
Michael Milton (18:07:51): > @Michael Milton has joined the channel
Sanyaolu Motunrayo (18:58:37): > @Sanyaolu Motunrayo has joined the channel
Nick Robertson (20:10:55): > @Nick Robertson has joined the channel
Yue Cao (23:15:05): > @Yue Cao has joined the channel
2022-10-13
Prisca Chidimma Maduka (07:53:02): > @Prisca Chidimma Maduka has joined the channel
Imad Abugessaisa (09:30:23): > @Imad Abugessaisa has joined the channel
Delphine (15:17:33): > @Delphine has joined the channel
2022-10-14
Ji Hye Choi (04:19:26): > @Ji Hye Choi has joined the channel
2022-10-17
Julie Iskander (04:28:33): > @Julie Iskander has joined the channel
Iman Linje (11:49:34): > @Iman Linje has joined the channel
Maria Fiorio (12:34:35): > @Maria Fiorio has joined the channel
Nishika Kapuruge (17:36:40): > @Nishika Kapuruge has joined the channel
2022-10-18
gunjan agarwal (00:29:47): > @gunjan agarwal has joined the channel
Tony Papenfuss (01:22:20): > @Tony Papenfuss has joined the channel
2022-10-19
USLACKBOT (10:20:10): > This message was deleted.
Varsha Verma (17:26:17): > @Varsha Verma has joined the channel
Peter Hickey (19:18:40) (in thread): > I doubt Gordon is on here, probably best to email him:thumbsup:
2022-10-20
Adeoye Beatrice (09:42:42): > @Adeoye Beatrice has joined the channel
Samantha Gallaher (11:53:02): > @Samantha Gallaher has joined the channel
2022-10-21
Guerrino Macori (05:28:52): > @Guerrino Macori has joined the channel
John Ogata (16:03:59): > @John Ogata has joined the channel
Ying Wu (17:48:30): > @Ying Wu has joined the channel
2022-10-23
Maria Mironova (21:40:54): > @Maria Mironova has joined the channel
2022-10-24
Marja Heiskanen (08:02:57): > @Marja Heiskanen has joined the channel
2022-10-26
Nicholas Cooley (09:24:29): > Hi everyone, I have a sort of under the hood question aboutmclapply, which to my understanding, works by forking. How do the forks inmclapplyget assigned their memory limits? i.e. do they inheritR_MAX_VSIZEfrom the parent session? Do they initialize their own limits from what’s available? Thanks!
Martin Morgan (11:12:33) (in thread): > I’d guess yes, they inherit from the parent session (because the environment variable is assigned to in C to global variable, and the global variable is inherited by the forked process. But you’d get a more definitive answer on theR-devel mailing list.@Henrik Bengtssonmight also have something to say…
Henrik Bengtsson (13:14:56) (in thread): > Like Martin, I’d also guess forked child processes inherit this from the parent process, but that’s just my best guess. > > BTW, if you’re running into memory issues withmclapply(), please know that forked processing is tricky in R (and sometimes unstable). Although it might spare some memory because of how forking works, eventually child processes might start updating the memory so that the OS eventually end up with make copies. I haven’t formally investigated it, but I can see how this could happen “at random” as R’s garbage collection starts running in the different forked processes.
Nicholas Cooley (14:25:46) (in thread): > Thanks both of you! It’s mostly a curiosity question, because i was running into some instability when the forks were consuming large amounts of memory. I just ended up asking for less cores and things turned out ok.
David S Burton (19:55:36): > @David S Burton has joined the channel
2022-10-27
Beryl Kanali (16:17:44): > @Beryl Kanali has joined the channel
2022-10-28
Brian Schilder (08:26:47): > @Brian Schilder has joined the channel
2022-10-31
Chenyue Lu (10:02:58): > @Chenyue Lu has joined the channel
Huong Le (11:33:27): > @Huong Le has joined the channel
2022-11-01
Jacques SERIZAY (10:23:11): > @Jacques SERIZAY has joined the channel
W ZH (11:05:16): > @W ZH has joined the channel
2022-11-02
Lori Shepherd (14:14:44): > Bioconductor 3.16 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_16_release/
2022-11-03
James MacDonald (09:53:48) (in thread): > Is there a timeline for the Docker containers?
Lori Shepherd (09:55:59) (in thread): > in the future yes – currently no (I would guess no more than by next week) – we are redistributing that task and should have a better idea in the next day or two
James MacDonald (09:57:03) (in thread): > OK, thanks.
Kris Alavattam (12:01:04): > @Kris Alavattam has joined the channel
Pablo Yamild Rosiles Loeza (23:26:37): > @Pablo Yamild Rosiles Loeza has joined the channel
2022-11-04
Benjamin McMichael (15:03:17): > @Benjamin McMichael has joined the channel
2022-11-06
Yihun Zeleke (02:40:27): > @Yihun Zeleke has joined the channel
Sherine Khalafalla Saber (11:18:44): > @Sherine Khalafalla Saber has joined the channel
2022-11-08
Nicolas (20:10:03): > @Nicolas has joined the channel
2022-11-09
Selin Jessa (21:45:53): > @Selin Jessa has joined the channel
2022-11-10
Roger Giné Bertomeu (08:31:07): > @Roger Giné Bertomeu has joined the channel
2022-11-11
Oriol Senan (06:13:47): > @Oriol Senan has joined the channel
2022-11-16
Marie HIDJO (02:56:46): > @Marie HIDJO has joined the channel
2022-11-17
Gerry Tonkin-Hill (17:17:07): > @Gerry Tonkin-Hill has joined the channel
2022-11-18
Martin Davila (05:23:14): > @Martin Davila has joined the channel
Laura Häkkinen (11:32:38): > @Laura Häkkinen has joined the channel
2022-11-19
Federica Gazzelloni (04:23:21): > @Federica Gazzelloni has joined the channel
Mikaila Chetty (21:28:27): > @Mikaila Chetty has joined the channel
2022-11-20
Pageneck Chikondowa (03:50:26): > @Pageneck Chikondowa has joined the channel
2022-11-22
Michael Lee (00:13:21): > @Michael Lee has joined the channel
Wossen Mengesha (00:39:46): > @Wossen Mengesha has joined the channel
2022-11-23
ashish tp53 (01:06:15): > @ashish tp53 has joined the channel
2022-11-24
Heidelinde Sammallahti (06:28:35): > @Heidelinde Sammallahti has joined the channel
2022-11-25
Olly Crook (10:17:04): > @Olly Crook has joined the channel
2022-11-27
Robert Shear (04:48:25): > @Robert Shear has joined the channel
Carolyn de Graaf (20:17:47): > @Carolyn de Graaf has joined the channel
2022-11-28
Yi-Wen Hsiao (06:55:35): > @Yi-Wen Hsiao has joined the channel
Kasidech Aewsrisakul (07:43:53): > @Kasidech Aewsrisakul has joined the channel
2022-11-29
Javier Carpinteyro Ponce (12:55:15): > @Javier Carpinteyro Ponce has joined the channel
Sinan Durmuş (13:00:43): > @Sinan Durmuş has joined the channel
Chunlei Liu (16:55:43): > @Chunlei Liu has joined the channel
2022-11-30
David Shih (09:03:31): > @David Shih has joined the channel
Givanna Putri (18:02:01): > @Givanna Putri has joined the channel
Jean-Philippe Fortin (21:09:56): > @Jean-Philippe Fortin has joined the channel
Bhavika Kumar (21:10:19): > @Bhavika Kumar has joined the channel
Calandra Grima (21:11:25): > @Calandra Grima has joined the channel
Nora Liu (21:11:25): > @Nora Liu has joined the channel
Melody Jin (21:11:37): > @Melody Jin has joined the channel
Mark Ziemann (21:16:36): > @Mark Ziemann has joined the channel
Chiachun Chiu (22:15:00): > @Chiachun Chiu has joined the channel
Ruqian Lyu (22:31:53): > @Ruqian Lyu has joined the channel
Chao WANG (22:35:45): > @Chao WANG has joined the channel
Alex Wong (23:37:18): > @Alex Wong has joined the channel
2022-12-01
chunman zuo (22:40:13): > @chunman zuo has joined the channel
2022-12-02
George Howitt (00:07:05): > @George Howitt has joined the channel
Terence Speed (00:42:22): > @Terence Speed has joined the channel
Lachlan Dryburgh (01:21:25): > @Lachlan Dryburgh has joined the channel
Hsiao-Chi Liao (01:42:59): > @Hsiao-Chi Liao has joined the channel
Sam Godwin (22:13:37): > @Sam Godwin has joined the channel
Jinming Cheng (23:04:04): > @Jinming Cheng has joined the channel
2022-12-04
Pooja Venkat (18:49:59): > @Pooja Venkat has joined the channel
2022-12-05
HESBORN OMWANDHO (06:09:44): > @HESBORN OMWANDHO has joined the channel
Joseph (13:17:31): > @Joseph has joined the channel
Lizhong Chen (17:48:03): > @Lizhong Chen has joined the channel
2022-12-06
Alan O’C (10:30:47): > Any clues as to why I see ggplot2 deprecation warnings (sigh,aes_string…) when running tests locally, but not on the build machines? Both running ggplot2 3.4.0 apparently
Marcel Ramos Pérez (11:00:04) (in thread): > Have you tried to reproduce inside the Bioc container? My guess is that the deprecation warning shows up once per session and gets triggered in another package first?:thinking_face:
Alan O’C (11:57:12) (in thread): > Ah!This warning is displayed once every 8 hours.
Hervé Pagès (13:34:45) (in thread): > Is this a case of over engineering? I understand that they don’t want to make too much noise but OTOH this is not great for reproducibility.
Alan O’C (13:37:19) (in thread): > It’s kind of antisocial imo. two of my packages had a tonne of warnings that don’t show up on the BBS, and these functions are deprecated since 3.0 apparently. Not sure if CRAN has the same issue, but it does probably mean when they make them defunct then half of Bioc will be in the red
Hervé Pagès (13:43:08) (in thread): > Maybe they could mitigate the problem by turning this into a hard warning ifIS_BIOC_BUILD_MACHINE=true?
Hervé Pagès (13:43:52) (in thread): > and something similar whenR CMD checkruns on a CRAN machine
Mike Smith (14:09:10) (in thread): > Switching around the effort, I think they provide the option for setting the frequency as a global option i.e.https://rlang.r-lib.org/reference/abort.html#muffling-and-silencing-conditionsPerhaps that could be set on the build machines? - Attachment (rlang.r-lib.org): Signal an error, warning, or message — abort > These functions are equivalent to base functions base::stop(), > base::warning(), and base::message(). They signal a condition > (an error, warning, or message respectively) and make it easy to > supply condition metadata: > Supply class to create a classed condition that can be caught > or handled selectively, allowing for finer-grained error > handling. > Supply metadata with named … arguments. This data is stored > in the condition object and can be examined by handlers. > Supply call to inform users about which function the error > occurred in. > Supply another condition as parent to create a chained condition. > > Certain components of condition messages are formatted with unicode > symbols and terminal colours by default. These aspects can be > customised, see Customising condition messages.
Hervé Pagès (14:47:28) (in thread): > Maybe. But if the goal is reproducibility, an environment variable that we can add tohttps://master.bioconductor.org/checkResults/3.17/bioc-LATEST/Renviron.biocwould be nice.
Hervé Pagès (15:50:39) (in thread): > Issue opened forlifecycle:https://github.com/r-lib/lifecycle/issues/150
2022-12-07
Hamdi Furkan Kepenek (02:35:42): > @Hamdi Furkan Kepenek has joined the channel
2022-12-08
Dario Rocha (05:33:09): > @Dario Rocha has joined the channel
Jenna (16:39:54): > @Jenna has joined the channel
2022-12-12
Zainab Ashimiyu-Abdusalam (04:41:00): > @Zainab Ashimiyu-Abdusalam has joined the channel
Amos Schorr (10:52:08): > Hey folks! I work for Norn Group, a nonprofit in the bio of aging research field (we’re best known for our Impetus Grants program). Because this is such a new field, it’s fragmented and hard for everyone to navigate. So we’re building out an opt-in database for ppl who have or want careers in aging. It will NOT be a community you need to participate in. We’ll just be using this to make connections and help people build out labs, companies, and careers. > > We’re launching today and as of now have ~70 signups of people at all levels and in all kinds of roles. If this intrigues you, get more info and sign up if you likehere! It’s free and could be useful for you. > > Additionally, if you’d be so kind as toretweet/share our postson LinkedInannouncing it, that would be just darling of you:heart:My linkedin profile picture is of me moderating a panel with a dog on my lap. Or, more accurately, an adorable dog that’s sitting on my lap not giving a damn about the awesome conversation we were having. So it’s worth sharing my post if only for that.
Sue McClatchy (10:55:07): > @Sue McClatchy has joined the channel
Melysssa Minto (16:54:00): > @Melysssa Minto has joined the channel
Umran (17:55:00): > @Umran has joined the channel
Deanne Nixie Miao (17:55:20): > @Deanne Nixie Miao has joined the channel
Kendall H. Burks (17:55:38): > @Kendall H. Burks has joined the channel
Jennifer Foltz (17:55:42): > @Jennifer Foltz has joined the channel
Jenea Adams (17:55:59): > @Jenea Adams has joined the channel
Lexi Bounds (17:56:41): > @Lexi Bounds has joined the channel
Eugenia Radulescu (17:57:31): > @Eugenia Radulescu has joined the channel
Sarah Djeddi (17:58:25): > @Sarah Djeddi has joined the channel
José Basílio (17:58:44): > @José Basílio has joined the channel
Manqi Cai (17:59:11): > @Manqi Cai has joined the channel
Nicolaj Hackert (18:00:58): > @Nicolaj Hackert has joined the channel
Sofya Marchenko (18:03:01): > @Sofya Marchenko has joined the channel
Yalda Zare (18:08:21): > @Yalda Zare has joined the channel
Carlos José Ferreira da Silva (18:47:12): > @Carlos José Ferreira da Silva has joined the channel
2022-12-13
Niko Fleischer (03:04:12): > @Niko Fleischer has joined the channel
Shizhong (10:47:48): > @Shizhong has joined the channel
Geo Pertea (11:05:15): > @Geo Pertea has joined the channel
Apua Paquola (12:24:22): > @Apua Paquola has joined the channel
Carissa Chen (17:42:55): > @Carissa Chen has joined the channel
Yunwei Zhang (17:43:01): > @Yunwei Zhang has joined the channel
Helen Fu (18:00:17): > @Helen Fu has joined the channel
Xiangnan Xu (18:30:58): > @Xiangnan Xu has joined the channel
Daniel Kim (18:56:05): > @Daniel Kim has joined the channel
2022-12-14
GCARa (08:45:40): > @GCARa has joined the channel
Kangjin Kim (11:47:04): > @Kangjin Kim has joined the channel
Bárbara Zita Peters Couto (14:08:32): > @Bárbara Zita Peters Couto has joined the channel
Giulio Pergola (18:30:34): > @Giulio Pergola has joined the channel
Lijia Yu (19:36:51): > @Lijia Yu has joined the channel
2022-12-19
JP Courneya (00:15:39): > @JP Courneya has joined the channel
David Henderson (14:00:03): > @David Henderson has joined the channel
Matti Ruuskanen (14:14:38): > @Matti Ruuskanen has joined the channel
2022-12-20
Camille Santistevan (09:36:24): > @Camille Santistevan has joined the channel
2022-12-23
Nicholas Cooley (09:38:31): > Hi folks, I’ve got a question that I’ve been unable to find a satisfying answer to: > Given a fasta file, and a gff, can I generate a gbk file for region subsets? I haven’t been able to find any tools that will do this.
Spencer Nystrom (11:05:11) (in thread): > I think something in theembosstoolkit can do this.https://emboss.sourceforge.net/docs/
Spencer Nystrom (11:05:57) (in thread): > seqretI think can do what you want.
Spencer Nystrom (11:06:36) (in thread): > I’m not familiar with Bioc support for gbk files though.
Nicholas Cooley (11:15:51) (in thread): > Thanks! I found a github repo for a package calledbiofilesthat seems to almost work, but it doesn’t appear to be currently supported.
Spencer Nystrom (11:30:43) (in thread): > Yeah, it doesn’t help that genbank is notorious for being the worst to parse.
2022-12-30
Hervé Pagès (11:30:38): > One million distinct IPs in 2022:https://bioconductor.org/packages/stats/bioc/Great milestone!
2023-01-02
Virginie Stanislas (04:26:59): > @Virginie Stanislas has joined the channel
Sara (15:58:17): > @Sara has joined the channel
2023-01-05
Olivier Kirsh (03:28:08): > @Olivier Kirsh has joined the channel
Martin Grigorov (07:09:19): > @Martin Grigorov has joined the channel
Will Russell (19:12:13): > @Will Russell has joined the channel
2023-01-09
Giovanni Palla (06:20:56): > @Giovanni Palla has joined the channel
Emalie Clement (20:50:51): > @Emalie Clement has joined the channel
2023-01-10
Tim Treis (05:44:24): > @Tim Treis has joined the channel
Andrzej Oleś (06:23:56): > @Andrzej Oleś has joined the channel
Nick R. (18:38:40): > @Nick R. has joined the channel
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 (05:51:22): > @Zedias Chikwambi has joined the channel
Katariina Pärnänen (05:53:01): > @Katariina Pärnänen has left the channel
2023-01-20
Yikun Jiang (03:00:36): > @Yikun Jiang has joined the channel
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
Idowu Festus (10:28:23): > @Idowu Festus has joined the channel
Hien (15:58:48): > @Hien has joined the channel
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
2023-01-24
Jennifer Gerbracht (08:30:21): > @Jennifer Gerbracht has joined the channel
Levi Waldron (11:06:35): > I asked theopenai.comAPI playground some questions about Bioconductor using their Q&A endpoint: > > Human: What do you know about the Bioconductor project for open-source bioinformatics? > AI: I understand that the Bioconductor project is an open-source software platform for analyzing and visualizing biological data. It provides a comprehensive suite of software for basic and advanced analyses of high-throughput data in genomics and proteomics. It also provides tools for common data-mining tasks. > Human: What is the Bioconductor project good for? > AI: The Bioconductor project is best known for its ability to facilitate a wide range of genomic data analysis tasks. It offers tools for gene expression, proteomics, high-throughput screening, sequence analysis, and many more. It is also used to integrate data from diverse sources and visualize it in meaningful ways. > Human: What are the weaknesses of the Bioconductor project? > AI: The main weakness of the Bioconductor project is that it can take a lot of time and effort for users to learn how to use all the tools available. Additionally, the project does not provide a unified user interface, so users must be familiar with different programming languages and learn the commands associated with each tool. > Human: How do you get involved in the Bioconductor project? > AI: To get involved in the Bioconductor project, you can join their community and take part in discussions. You can contribute to the open-source software by developing new features or fixing bugs. Additionally, you can also participate in workshops and educational events related to the project. > Human: How has Bioconductor changed over the years? > AI: Bioconductor has evolved significantly over the years, incorporating more user-friendly features, offering an updated suite of tools, and providing better support for different platforms. It has become an indispensable resource for bioinformatics researchers and is now used in many different fields. > Human: Why is the Bioconductor project important to science? > AI: The Bioconductor project is important to science because it provides a comprehensive suite of tools for analyzing and visualizing biological data. It allows researchers to make sense of large amounts of genomic or proteomic data, enabling them to uncover novel insights. It also helps to bridge the gap between wet lab studies and computational research. > Human: How does the Bioconductor build system work? > AI: The Bioconductor build system is based on a dependency graph of the various packages. It builds each package by downloading source code, compiling it, and running tests. If the build is successful, it will then generate binaries which can be used to install the package. The system also allows developers to manage the dependencies of their packages. > Human: What are the most important Bioconductor libraries? > AI: The most important Bioconductor libraries are the Biobase, BiocGenerics, and BiocParallel packages. These libraries provide essential functions for data analysis, such as importing and manipulating the data, selecting the appropriate statistical tests to use, and running multiple analyses in parallel. Additionally, they also provide essential support for creating visualizations, developing new packages, and managing dependencies. >
Krithika Bhuvanesh (11:09:57) (in thread): > Interesting . I didn’t think it would be so verbose. Thanks for sharing !
Sean Davis (11:29:29) (in thread): > There is no question the world changed with the introduction of ChatGPT.
Nitesh Turaga (11:37:31) (in thread): > I wonder how it generated this ?? > > Human: What are the weaknesses of the Bioconductor project? > AI: The main weakness of the Bioconductor project is that it can take a lot of time and effort for users to learn how to use all the tools available. Additionally, the project does not provide a unified user interface, so users must be familiar with different programming languages and learn the commands associated with each tool. >
Janani Ravi (13:15:05) (in thread): > Very cool — and mind blownagain!:shocked_face_with_exploding_head:
Hervé Pagès (17:58:21) (in thread): > Big fail on the last question though
2023-01-27
Hannes Oberreiter (08:46:09): > @Hannes Oberreiter has left the channel
Jenny Drnevich (10:30:58): > From the microbiome slack space (in their R channel): I’m on team %>%. What should our colors be?? - File (PNG): image (3).png
Samuel Gamboa (11:21:06) (in thread): > Team |>
Jenny Drnevich (11:24:43) (in thread): > |> was too late to the party! I’ve got %>% ingrained in my finger muscle memory.:grin:
David Puerta Martos (15:25:02): > @David Puerta Martos has joined the channel
2023-01-28
Moritz E. Beber (03:58:15) (in thread): > You can change the Rstudio keyboard shortcut ‘ctrl + shift + m’ to insert the native pipe. Haven’t looked back since.
Sean Maden (23:22:54): > @Sean Maden has joined the channel
2023-01-30
mahamtariq58 (09:34:04): > @mahamtariq58 has joined the channel
Ibra Lujumba (13:28:20): > I came across thishttps://picoportal.org/2023/01/29/chatgpt/ - Attachment (PICO Portal): Systematic Reviewing and ChatGPT – Live Demo - PICO Portal > Don’t miss PICO Portal’s free webinar that will explore several uses of ChatGPT for systematic review and other literature review. This featured presentation will pose tasks and questions and explore the AI response. We will discuss the limitations and strengths of each example including how it might be useful and how the technology would need […]
2023-01-31
Ahmad Al Ajami (08:14:37): > @Ahmad Al Ajami has joined the channel
Francesc Català-Moll (14:31:51): > @Francesc Català-Moll has joined the channel
Rebecca Butler (15:05:31): > @Rebecca Butler has joined the channel
2023-02-01
Alex Pan (16:40:45): > @Alex Pan has joined the channel
2023-02-02
Yogesh Lakhotia (01:56:04): > @Yogesh Lakhotia has joined the channel
2023-02-03
Deborah (08:32:38): > @Deborah has joined the channel
A.s. (08:57:46): > @A.s. has joined the channel
2023-02-05
Stephen Guest (20:29:09): > @Stephen Guest has joined the channel
2023-02-06
Rishi (08:53:37): > @Rishi has joined the channel
Doug Joubert (14:20:03): > @Doug Joubert has joined the channel
2023-02-07
Iris van ’t Erve (14:07:21): > @Iris van ’t Erve has joined the channel
Monalika Patnaik (14:30:06): > @Monalika Patnaik has joined the channel
Eirini Moysi (14:54:51): > @Eirini Moysi has joined the channel
2023-02-08
Anandhakumar (05:07:28): > @Anandhakumar has joined the channel
赵玉 (05:08:12): > @赵玉 has joined the channel
Dan Cotton (08:23:12): > @Dan Cotton has joined the channel
Sean Jacobson (15:49:46): > @Sean Jacobson has joined the channel
2023-02-10
Renee Garcia Flores (15:21:35): > @Renee Garcia Flores has joined the channel
2023-02-13
Anushka Jain (00:45:06): > @Anushka Jain has joined the channel
2023-02-14
Dr Nay (02:14:18): > @Dr Nay has joined the channel
2023-02-15
Tom Lin (22:05:06): > @Tom Lin has joined the channel
2023-02-16
Min Zhang (14:30:17): > @Min Zhang has joined the channel
Rui Fu (17:43:22): > @Rui Fu has joined the channel
2023-02-17
Xiaolong Cheng (12:59:27): > @Xiaolong Cheng has joined the channel
2023-02-18
KritikaVerma (00:07:40): > @KritikaVerma has joined the channel
2023-02-21
Fatima Zohra (15:30:28): > @Fatima Zohra has joined the channel
Wes Horton (19:57:30): > @Wes Horton has joined the channel
2023-02-22
Junxia Lin (00:04:53): > @Junxia Lin has joined the channel
2023-02-23
Jędrzej Świeżewski (05:26:37): > @Jędrzej Świeżewski has joined the channel
Zarmena Khan (13:06:20): > @Zarmena Khan has joined the channel
Anson (13:14:36): > @Anson has joined the channel
Claire Seibold (15:48:19): > @Claire Seibold has joined the channel
Lambda Moses (17:55:19): > Just wondering, I know that Bioconductor counts the number of downloads and number of distinct IP addresses downloading each package each month. Does that include downloads by CIs like GitHub Actions, say used by the package authors themselves or by authors of other packages that depend on those packages?
Sean Davis (19:58:21): > It includes all downloads but not git checkouts and does include instances where the package is a dependency and not a direct install.
Hervé Pagès (20:19:45): > Yes, to be precise, we only count downloads fromhttps://bioconductor.org/packages/, which is where the standard installation method (BiocManager::install()) picks Bioconductor packages from. Whether the package was explicitely requested or got downloaded to satisfy a dependency is counted the same way, as 1 download (or 1 hit).
Lambda Moses (20:21:03): > Thanks!
Lambda Moses (20:22:36): > I don’t think anyone is actually doing it. I’m just wondering what if someone artificially increases the package download ranking by automatically downloading the packages by CIs run several times a day.:zany_face:
Hervé Pagès (20:28:23): > That will only increase the “Nb of downloads” but not the “Nb of distinct IPs” (unless they manage to automatically download each time from a distinct IP). We’ve seen something like this in the past where some package would suddendly get repeatedly downloaded thousands of times per month by some script running somewhere on a cluster (some sys admin probably left a rogue script running unintentionally). This is why we’ve switched to only consider the “Nb of distinct IPs” for the package ranking. This is a more meaningful/more reliable metrics.
Lambda Moses (20:35:29): > Right, almost forgot. I heard about that happening from a blog post analyzing CRAN package download data. GitHub Actions runners don’t have a fixed IP address and there’re ranges of IP addresses. Hence it’s possible to artificially increase the number of distinct IP addresses downloading a package by repeatedly running a GitHub Action, but that’s limited by the number of IP addresses Microsoft’s data centers have. OK, thanks! Won’t waste more of your time.
2023-02-26
Aleksey Chepovoi (04:34:49): > @Aleksey Chepovoi has joined the channel
Arup Ghosh (14:47:38): > @Arup Ghosh has joined the channel
2023-02-28
jj (00:57:27): > @jj has joined the channel
Ramin (15:26:57): > @Ramin has joined the channel
Krithika Bhuvanesh (16:46:26): > @Krithika Bhuvanesh has joined the channel
2023-03-01
jeremymchacón (12:09:38): > @jeremymchacón has joined the channel
Rodney R (21:45:01): > @Rodney R has joined the channel
2023-03-02
Monica Valecha (10:34:20): > @Monica Valecha has joined the channel
Brad Presson (16:51:46): > @Brad Presson has joined the channel
2023-03-03
Richard White (04:30:27): > @Richard White has joined the channel
2023-03-05
CesarBC (15:05:02): > @CesarBC has joined the channel
2023-03-06
Anna Šenovská (04:58:04): > Hello, any tips for a bioinformatics workshop in Europe this year? Preferably with focus on R, seq data, data visualization and statistics. I attended bioconductor CSAMA last year and the line-up this year seems to be quite similar. Cheers!
Thomas Klammsteiner (06:32:45): > @Thomas Klammsteiner has joined the channel
Brian Schilder (07:12:16) (in thread): > EurBioc2023 is in Ghent this year. Havent been to these confs myself yet but looking forward to it:https://eurobioc2023.bioconductor.org/
Anna Šenovská (09:26:58) (in thread): > Thank you Brian. I can see there are also some workshops and demos. Anyway, I will keep looking for a more “hands-on” event
Anthony Ramnauth (10:40:20): > @Anthony Ramnauth has joined the channel
Busayo Ojo (11:18:35): > @Busayo Ojo has joined the channel
Kayla Okereke (11:27:37): > @Kayla Okereke has joined the channel
Caroline Shi (11:47:52): > @Caroline Shi has joined the channel
Riya Sharma (12:08:30): > @Riya Sharma has joined the channel
Dinithi Wickramaratne (12:55:46): > @Dinithi Wickramaratne has joined the channel
khadijah (12:59:11): > @khadijah has joined the channel
Emmanuel Taiwo devbird007 (13:39:31): > @Emmanuel Taiwo devbird007 has joined the channel
Anushka Sharma (15:04:42): > @Anushka Sharma has joined the channel
Eunice Miriti (15:32:47): > @Eunice Miriti has joined the channel
Reece (16:06:07): > @Reece has joined the channel
Ludwig Geistlinger (16:35:19) (in thread): > Maybe this one is relevant for you:https://www.physalia-courses.org/courses-workshops/course19/
Barakat Dindi (18:03:53): > @Barakat Dindi has joined the channel
Maryam Gbemisola (22:27:41): > @Maryam Gbemisola has joined the channel
Vivian Ginikachukwu Ikeh (23:12:39): > @Vivian Ginikachukwu Ikeh has joined the channel
2023-03-07
Violet Akpeh (00:56:44): > @Violet Akpeh has joined the channel
Aayushi Chauhan (01:39:08): > @Aayushi Chauhan has joined the channel
Ameerah Kabir (02:31:24): > @Ameerah Kabir has joined the channel
Sonali Kumari (02:34:28): > @Sonali Kumari has joined the channel
Esther (02:48:31): > @Esther has joined the channel
Patricia Brianna (02:55:24): > @Patricia Brianna has joined the channel
Maryam Gbemisola (04:12:26): > @Maryam Gbemisola has joined the channel
Aayushi Singh (04:12:49): > @Aayushi Singh has joined the channel
Diana Ofodu (04:36:30): > @Diana Ofodu has joined the channel
Ozomma Linda (04:55:08): > @Ozomma Linda has joined the channel
Petrah (05:50:20): > @Petrah has joined the channel
Anna Šenovská (06:46:26) (in thread): > yes! Thank you Ludwig, the topic is exactly what I was looking for. However, the downside is that the workshop is held online
Laurent Gatto (07:01:51) (in thread): > The EMBL in Heidelberg and EBI in Hinxton do organise workshops, some probably related to R and sequencing.
Sreeyusha Vajinapally (08:00:20): > @Sreeyusha Vajinapally has joined the channel
Blessing Obafemi (08:13:21): > @Blessing Obafemi has joined the channel
Richard Dushime (08:37:29): > @Richard Dushime has joined the channel
Sweta Kumari (08:52:32): > @Sweta Kumari has joined the channel
Aliyu Atiku Mustapha (09:02:26): > @Aliyu Atiku Mustapha has joined the channel
Ufuoma Ejite (10:41:32): > @Ufuoma Ejite has joined the channel
Evan Chinny (11:02:31): > @Evan Chinny has joined the channel
Shravani Nag (11:21:33): > @Shravani Nag has joined the channel
Ibizugbe Merit (15:11:52): > @Ibizugbe Merit has joined the channel
Rukky (15:30:00): > @Rukky has joined the channel
Arby Abood (16:26:34): > @Arby Abood has joined the channel
Kelvin Joseph (17:09:53): > @Kelvin Joseph has joined the channel
anshika bhatt (23:29:11): > @anshika bhatt has joined the channel
2023-03-08
Unyime William (01:07:34): > @Unyime William has joined the channel
MaryJones (01:23:59): > @MaryJones has joined the channel
Ayantika Sen (01:34:27): > @Ayantika Sen has joined the channel
Atrayee Samanta (02:10:53): > @Atrayee Samanta has joined the channel
Anna Šenovská (02:58:19) (in thread): > Thank you Laurent, that looks promising!
Palak Tahlyani (03:23:43): > @Palak Tahlyani has joined the channel
kashish ramani (03:37:55): > @kashish ramani has joined the channel
Indraneel (04:16:39): > @Indraneel has joined the channel
Treasure Okafor (05:28:26): > @Treasure Okafor has joined the channel
Pragya Jha (06:16:28): > @Pragya Jha has joined the channel
Namusisi Sharon (09:06:26): > @Namusisi Sharon has joined the channel
Desire Oluwarotimi (10:29:55): > @Desire Oluwarotimi has joined the channel
Shallie (10:32:54): > @Shallie has joined the channel
Job David (11:10:05): > @Job David has joined the channel
Aditi Singh (13:02:00): > @Aditi Singh has joined the channel
Swazi (13:46:38): > @Swazi has joined the channel
Fortune Nnamdi (14:58:33): > @Fortune Nnamdi has joined the channel
OLADIRAN OLUWASHOLA (17:59:03): > @OLADIRAN OLUWASHOLA has joined the channel
sophy (23:34:29): > @sophy has joined the channel
Tsoure (23:57:11): > @Tsoure has joined the channel
2023-03-09
Ukpai Bishop (02:20:46): > @Ukpai Bishop has joined the channel
Hannah Honda (03:03:04): > @Hannah Honda has joined the channel
Chioma Grace (03:59:17): > @Chioma Grace has joined the channel
K Nodia (04:19:24): > @K Nodia has joined the channel
Bazgha Razi (08:29:34): > @Bazgha Razi has joined the channel
Yogita Tufchi (10:15:08): > @Yogita Tufchi has joined the channel
Aiysha shahid (10:52:57): > @Aiysha shahid has joined the channel
maliha Mohammed (21:42:27): > @maliha Mohammed has joined the channel
Aguobi Amara (22:52:18): > @Aguobi Amara has joined the channel
Advit Mittal (23:41:53): > @Advit Mittal has joined the channel
2023-03-10
Busayo Samuel (she/her) (00:30:50): > @Busayo Samuel (she/her) has joined the channel
jnsereko (00:33:29): > @jnsereko has joined the channel
Dilara (03:43:42): > @Dilara has joined the channel
Dennis Ndubi (04:05:55): > @Dennis Ndubi has joined the channel
Dennis Ndubi (04:24:45): > 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 connections
Chioma Nnadi (08:11:54): > @Chioma Nnadi has joined the channel
Roseline (13:15:21): > @Roseline has joined the channel
Maximilian Mattessich (15:01:22): > @Maximilian Mattessich has joined the channel
Joaquin Reyna (15:09:16): > @Joaquin Reyna has joined the channel
Edel Aron (15:18:35): > @Edel Aron has joined the channel
Anna Konstorum (16:30:21): > @Anna Konstorum has joined the channel
Daianna Gonzalez-Padilla (17:09:46): > @Daianna Gonzalez-Padilla has joined the channel
2023-03-11
Muluh (01:54:21): > @Muluh has joined the channel
Harrydas Ombati (04:51:39): > @Harrydas Ombati has joined the channel
ezinne (04:55:46): > @ezinne has joined the channel
Jeffery Orazulike (07:16:07): > @Jeffery Orazulike has joined the channel
Prudence Levison (08:34:56): > @Prudence Levison has joined the channel
Cindy Apiyo (10:53:13): > @Cindy Apiyo has joined the channel
2023-03-12
Taofeekat Olorunkosebi (20:51:24): > @Taofeekat Olorunkosebi has joined the channel
2023-03-13
Suwaibat Suleiman (03:58:35): > @Suwaibat Suleiman has joined the channel
Emile-Daisy (04:50:53): > @Emile-Daisy has joined the channel
Parul Chaddha (08:48:25): > @Parul Chaddha has joined the channel
dherahrose (21:30:20): > @dherahrose has joined the channel
2023-03-14
Joanna Mocko (04:27:18): > @Joanna Mocko has joined the channel
Joanna Mocko (04:33:26): > :wave:Hey everyone, are there any R Shiny enthusiasts here? Annual ShinyConf starts tomorrow! You can still join us for 3 days of a Shiny extravaganza, with amazing speakers, expert tips, community case studies, and enterprise solutions. > The conference is all virtual and you can register for free here:https://shinyconf.appsilon.com:raised_hands: - Attachment (ShinyConf2023): ShinyConf 2023 - Shiny – Loved by Users, Powered by Community > ShinyConf is an annual, virtual conference hosted by Appsilon with support from Posit.
Martin Grigorov (05:39:29): > @Martin Grigorov has left the channel
Mugdha Pendse (07:57:57): > @Mugdha Pendse has joined the channel
Elisheba Asiimwe Joanita (09:55:54): > @Elisheba Asiimwe Joanita has joined the channel
Juanjuan Song (11:02:10): > @Juanjuan Song has joined the channel
JP Flores (20:29:34): > @JP Flores has joined the channel
2023-03-15
Rishi Singh (08:42:49): > @Rishi Singh has joined the channel
Grace Wangui (10:51:57): > @Grace Wangui has joined the channel
Jiefei Wang (11:14:40): > @Jiefei Wang has joined the channel
Enis Afgan (13:44:32): > @Enis Afgan has joined the channel
idubor itohan (18:31:30): > @idubor itohan has joined the channel
2023-03-16
pande.erawijantari (05:04:33): > @pande.erawijantari has joined the channel
Anju Maurya (09:16:24): > @Anju Maurya has joined the channel
Crestable Ayesiga (11:52:26): > @Crestable Ayesiga has joined the channel
Stefania Pirrotta (12:27:39): > @Stefania Pirrotta has joined the channel
Queen Anthony (16:15:16): > @Queen Anthony has joined the channel
Beekaz (17:02:04): > @Beekaz has joined the channel
Afolabi Owoloye (17:07:49): > @Afolabi Owoloye has joined the channel
Natalie Ohaneje (19:55:16): > @Natalie Ohaneje has joined the channel
2023-03-17
Wendy Ondigo (05:24:09): > @Wendy Ondigo has joined the channel
2023-03-18
Y-h. Taguchi (12:02:43): > @Y-h. Taguchi has joined the channel
Y-h. Taguchi (12:16:04): > There seems to be some problem in Bioconductor Single Package builder,http://bioconductor.org/spb_reports/TDbasedUFEadv_buildreport_20230318114618.html > > Error in library(testthat) : there is no package called 'testthat' > there is no package called Biobase > > I believe that these should not happen, Actually, Mac in Bioconductor Single Package builder does not report these errors. Is it possible for you to fix? Or have I done something wrong?
Suhana (12:24:22): > @Suhana has joined the channel
Andres Wokaty (23:40:55) (in thread): > We updated R on the devel builders Thursday and Friday, so it usually takes a two runs to get back to normal, but this might be due to a change on our linux builder on Friday to help identify missing dependencies:https://github.com/Bioconductor/BBS/issues/248. - Attachment: #248 WISH: Check with *R_CHECK_SUGGESTS_ONLY*=true to identify missing package dependencies > (This replaces invalid feature requests #242, #243, and #244.) > > Background > > Using *R_CHECK_SUGGESTS_ONLY*=true will run R CMD check with sandboxed an R library, where on declared package dependencies in DESCRIPTION + recursive hard dependencies are included. If an example, package test, or a vignette needs a package that is not in this set of dependencies, it will not be available to be loaded and result in an error. > > Wish > > Add *R_CHECK_SUGGESTS_ONLY*=true to Renviron.bioc to detect missing package dependencies. > > R CMD check sets up a sandboxed R library for it’s life span. It <https://github.com/wch/r-source/blob/8bf881e5da4da60f3aaad1b1812924817906bb29/src/library/tools/R/check.R#L138-L277|uses symbolic file links to do this>, so the performance overhead for doing this is really small. I could not detect a performance penalty (see below for details). > > Examples > > I ran the following examples using Renviron.bioc for Bioconductor 3.17: > > > wget [https://raw.githubusercontent.com/Bioconductor/BBS/master/3.17/Renviron.bioc](https://raw.githubusercontent.com/Bioconductor/BBS/master/3.17/Renviron.bioc) > > > I also ran with: > > > export *R_CHECK_TESTS_NLINES*=17 > > > to make it clear what one of the ERRORs is about. > > Example 1: Package bnem (missing RUnit for tests and BiocStyle for vignettes) > > Downloading bnem package source tarball: > > > $ wget [https://bioconductor.org/packages/devel/bioc/src/contrib/bnem_1.7.0.tar.gz](https://bioconductor.org/packages/devel/bioc/src/contrib/bnem_1.7.0.tar.gz) > > > Current Bioconductor 3.17 checks > > When checking with: > > > $ R_CHECK_ENVIRON=Renviron.bioc R --vanilla CMD check bnem_1.7.0.tar.gz > > > package passes with a single NOTE. > > * using log directory ‘/tmp/bioc/bnem.Rcheck’ > * using R Under development (unstable) (2022-11-30 r83391) > * using platform: x86_64-pc-linux-gnu (64-bit) > * using session charset: UTF-8 > * checking for file ‘bnem/DESCRIPTION’ … OK > * checking extension type … Package > * this is package ‘bnem’ version ‘1.7.0’ > * package encoding: UTF-8 > * checking package namespace information … OK > * checking package dependencies … OK > * checking if this is a source package … OK > * checking if there is a namespace … OK > * checking for hidden files and directories … OK > * checking for portable file names … OK > * checking for sufficient/correct file permissions … OK > * checking whether package ‘bnem’ can be installed … OK > * checking installed package size … OK > * checking package directory … OK > * checking ‘build’ directory … OK > * checking DESCRIPTION meta-information … OK > * checking top-level files … OK > * checking for left-over files … OK > * checking index information … OK > * checking package subdirectories … OK > * checking R files for non-ASCII characters … OK > * checking R files for syntax errors … OK > * checking whether the package can be loaded … OK > * checking whether the package can be loaded with stated dependencies … OK > * checking whether the package can be unloaded cleanly … OK > * checking whether the namespace can be loaded with stated dependencies … OK > * checking whether the namespace can be unloaded cleanly … OK > * checking loading without being on the library search path … OK > * checking dependencies in R code … NOTE > Namespace in Imports field not imported from: ‘rmarkdown’ > All declared Imports should be used. > * checking S3 generic/method consistency … OK > * checking replacement functions … OK > * checking foreign function calls … OK > * checking R code for possible problems … OK > * checking Rd files … OK > * checking Rd metadata … OK > * checking Rd cross-references … OK > * checking for missing documentation entries … OK > * checking for code/documentation mismatches … OK > * checking Rd sections … OK > * checking Rd contents … OK > * checking for unstated dependencies in examples … OK > * checking contents of ‘data’ directory … OK > * checking data for non-ASCII characters … OK > * checking data for ASCII and uncompressed saves … OK > * checking installed files from ‘inst/doc’ … OK > * checking files in ‘vignettes’ … OK > * checking examples … OK > * checking for unstated dependencies in ‘tests’ … OK > * checking tests … > Running ‘runTests.R’ > OK > * checking for unstated dependencies in vignettes … OK > * checking package vignettes in ‘inst/doc’ … OK > * checking running R code from vignettes … > ‘bnem.rmd’ using ‘UTF-8’… OK > NONE > * checking re-building of vignette outputs … OK > * checking PDF version of manual … OK > * DONE > > Status: 1 NOTE
> See
> ‘/tmp/bioc/bnem.Rcheck/00check.log’
> for details. > With also *R_CHECK_SUGGESTS_ONLY*=true > > When checking with: > > > $ *R_CHECK_SUGGESTS_ONLY*=true R_CHECK_ENVIRON=Renviron.bioc R --vanilla CMD check bnem_1.7.0.tar.gz > > > the package fails with two ERRORs: > > > * checking tests ... > Running ‘runTests.R’ > ERROR > Running the tests in ‘tests/runTests.R’ failed. > Complete output: > > BiocGenerics:::testPackage("bnem") > Error in library("RUnit", quietly = TRUE) : > there is no package called 'RUnit' > > > and > > > * checking re-building of vignette outputs ... ERROR > Error(s) in re-building vignettes: > ... > --- re-building ‘bnem.rmd’ using rmarkdown > Error: processing vignette 'bnem.rmd' failed with diagnostics: > there is no package called ‘BiocStyle’ > > > * using log directory ‘/tmp/bioc2/bnem.Rcheck’ > * using R Under development (unstable) (2022-11-30 r83391) > * using platform: x86_64-pc-linux-gnu (64-bit) > * using session charset: UTF-8 > * checking for file ‘bnem/DESCRIPTION’ … OK > * checking extension type … Package > * this is package ‘bnem’ version ‘1.7.0’ > * package encoding: UTF-8 > * checking package namespace information … OK > * checking package dependencies … OK > * checking if this is a source package … OK > * checking if there is a namespace … OK > * checking for executable files … OK > * checking for hidden files and directories … OK > * checking for portable file names … OK > * checking for sufficient/correct file permissions … OK > * checking whether package ‘bnem’ can be installed … OK > * checking installed package size … OK > * checking package directory … OK > * checking ‘build’ directory … OK > * checking DESCRIPTION meta-information … OK > * checking top-level files … OK > * checking for left-over files … OK > * checking index information … OK > * checking package subdirectories … OK > * checking R files for non-ASCII characters … OK > * checking R files for syntax errors … OK > * checking whether the package can be loaded … OK > * checking whether the package can be loaded with stated dependencies … OK > * checking whether the package can be unloaded cleanly … OK > * checking whether the namespace can be loaded with stated dependencies … OK > * checking whether the namespace can be unloaded cleanly … OK > * checking loading without being on the library search path … OK > * checking dependencies in R code … NOTE > Namespace in Imports field not imported from: ‘rmarkdown’ > All declared Imports should be used. > * checking S3 generic/method consistency … OK > * checking replacement functions … OK > * checking foreign function calls … OK > * checking R code for possible problems … OK > * checking Rd files … OK > * checking Rd metadata … OK > * checking Rd cross-references … OK > * checking for missing documentation entries … OK > * checking for code/documentation mismatches … OK > * checking Rd sections … OK > * checking Rd contents … OK > * checking for unstated dependencies in examples … OK > * checking contents of ‘data’ directory … OK > * checking data for non-ASCII characters … OK > * checking data for ASCII and uncompressed saves … OK > * checking installed files from ‘inst/doc’ … OK > * checking files in ‘vignettes’ … OK > * checking examples … OK > * checking for unstated dependencies in ‘tests’ … OK > * checking tests … > Running ‘runTests.R’ > ERROR > Running the tests in ‘tests/runTests.R’ fa…
Y-h. Taguchi (23:58:03) (in thread): > @Andres WokatyThank you very much for your information. In that case, may I expect that this problem will be solved in a few days?
2023-03-19
Sagar Arya (11:18:08): > @Sagar Arya has joined the channel
Reece11 (12:12:44): > @Reece11 has joined the channel
2023-03-20
Edward Yang (00:30:08): > @Edward Yang has joined the channel
Vince Carey (08:51:04): > curated thread on chatbot assistance for bioinformatics:https://twitter.com/simocristea/status/1599834929751547905?lang=en - Attachment (twitter): Attachment > Can’t keep up with all the interesting #ChatGPT prompts? > > Nothing to worry about! I curated a :thread:for you with key messages & relevant tweets on where our new academic companion #ChatGPT excels or fails in writing #Bioinformatics code, academic grants & tutorials:point_down:
Y-h. Taguchi (18:19:06) (in thread): > The errors seem not to be fixed yet.http://bioconductor.org/spb_reports/TDbasedUFEadv_buildreport_20230320100447.html#nebbiolo1_check_anchorWhen are they expected to be fixed?
2023-03-21
Harshita (04:47:53): > @Harshita has joined the channel
Eineje Ameh (05:06:41): > @Eineje Ameh has joined the channel
victory lelekumo (05:37:31): > @victory lelekumo has joined the channel
Oluwabukola Bamigbade (05:53:27): > @Oluwabukola Bamigbade has joined the channel
Lori Shepherd (08:52:21) (in thread): > @Andres Wokatycan you put in the PR to updatehttp://contributions.bioconductor.org/troubleshooting-build-report.html#how-do-i-reproduce-the-build-system-error - 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…
Tim Reznicek (11:49:56): > @Tim Reznicek has joined the channel
Augustine (11:52:36): > @Augustine has joined the channel
Hyacinthe TUYUBAHE (11:56:54): > @Hyacinthe TUYUBAHE has joined the channel
Hervé Pagès (17:05:54) (in thread): > @Y-h. TaguchiThis should be fixed now. See Lori’s announcement on the bioc-devel list:https://stat.ethz.ch/pipermail/bioc-devel/2023-March/019536.htmlYou should be able to trigger a new build for your package by bumping its version.
Y-h. Taguchi (19:21:07): > I know that Core team work hard and it is unrealistic to ask them something more. But I wonder if we can access single package builder during development before we start issue at github of bioconductor. I have foundherethatCheckTimeis doubled in Mac compared with other platforms. Since I do not have mac box, only opportunity for me to check how long CheckTime in Mac is only after the submission. Then I was forced to struggle with shortening CheckTime with including rewriting application completely. It might not be very efficient.
Vince Carey (19:38:19): > @Y-h. Taguchithis is a good question. I think you would be able to get a handle on performance in the mac domain using github actions. It is not straightforward to perfectly emulate the bioconductor build system but it would be possible to get a reasonable approximation. We have a group working on github actions recommendations for bioconductor packages and the slack channel#github-actions. In the long run we would not want to have individual developers using SPB but would prefer to have valid SPB emulators available. Have a look at the actions channel and consider using biocthis or rworkflows to build a .github/workflows entry for you. Let us know how it works out.
2023-03-22
Jeannie Mounger (03:19:03): > @Jeannie Mounger has joined the channel
Keerthana (08:00:27): > @Keerthana has joined the channel
Y-h. Taguchi (12:10:55) (in thread): > I am not sure what has happened butthis timeCheckTime is quite common between Mac and Ubuntu (both are short). Can anyone inform me what has happened?
Emmanuel Adamolekun (18:37:45): > @Emmanuel Adamolekun has joined the channel
2023-03-23
Simone Montalbano (04:46:01): > @Simone Montalbano has joined the channel
Trishna Patel (13:56:27): > @Trishna Patel has joined the channel
Sarah Parker (15:00:54): > @Sarah Parker has joined the channel
Biola Adeyemi (17:03:51): > @Biola Adeyemi has joined the channel
Jenny Drnevich (21:32:37) (in thread): > @Laurent Gatto@Charlotte SonesonLook what ChatGPT could do for a couple of the exercises in our bioc-intro! - File (PNG): image.png - File (PNG): image.png
2023-03-24
Luyi Tian (02:54:07): > @Luyi Tian has joined the channel
Simone Montalbano (05:55:26): > Hi, I’m looking forward to register for**** CSAMA 2023.****However my PhD school strictly require that any external course I follow provides ECT or at least some certificate of participation with an hours count. From the website is not super clear and I would need some kind of official confirmation before registering. I sent an email to the contact person (info@bioconductor.eu) but got no answer, so I’m trying here
Laurent Gatto (06:23:43) (in thread): > You get a certificate of participation, but I don’t think it has a details hours count.@Simone Bellwill be able to help.
H. Emre (07:22:26): > @H. Emre has joined the channel
Davide Risso (08:19:03) (in thread): > Can we have AI generated pictures of the squishy cat please?:smile:
Jenny Drnevich (08:51:24) (in thread): > It can’t get everything right - there is still the need for us humans!
Boyi Guo (11:06:35): > @Boyi Guo has joined the channel
2023-03-25
Anne-Maud Ferreira (00:24:32): > Hello, is there a place that describes the process to change the email address of a package author or who to contact? The current email address associated with my package will be deleted so I would like to change it to be able to continue maintaining my package. Thank you so much for your help:slightly_smiling_face:Best.
Lori Shepherd (09:12:07): > The important one will be to update your email in the package description and push that up. You should deleting the old and add the new to the bioc-devel mailing list. I think you should be able to update the bioccredentials account itself but let me know if you have issue and the same with the support site.
Lydia Edogiawerie (09:26:05): > @Lydia Edogiawerie has joined the channel
Joy Akinyi (16:25:34): > @Joy Akinyi has joined the channel
2023-03-27
Simone Montalbano (03:26:36) (in thread): > Solved thank you!
2023-03-28
Susan (09:05:30): > @Susan has joined the channel
Matt Montierth (14:34:25): > @Matt Montierth has joined the channel
Austin Richardson (14:52:37): > @Austin Richardson has joined the channel
Anne-Maud Ferreira (23:12:58) (in thread): > Thank you for your answer. I will try this!
2023-03-30
Huang Frederick Lin (21:03:44): > @Huang Frederick Lin has joined the channel
2023-03-31
Saksham Gupta (06:31:53): > @Saksham Gupta has joined the channel
Laura Masatti (06:44:53): > @Laura Masatti has joined the channel
Vince Carey (19:30:18): > This is a question for jupyter enthusiasts. Is it clear why jupyter does not respect print or show methods defined on the fly? In the standard repl, mentioningwinvokes the print.z method. - File (JPEG): jup.jpg
Vince Carey (19:36:36): > If the method is defined in a package, it does get used.
2023-04-01
Chengyang Ji (03:50:04) (in thread): > My guess is the jupyter repl is actually not running on the lowest R environment(since jupyter is a python web app). The S3 class print function defined on the fly is not registered in the lowestenvironment.When using implicit print, it only calls the print function in the lowest environment and won’t look up. > I could be totally wrong here.
2023-04-03
Zuguang Gu (10:04:11): > I tried this: - File (PNG): image.png
Vince Carey (13:34:03): > thanks for checking. maybe my kernel version or some other feature is inconsistent with yours. what platform did you use@Zuguang Gu
Zuguang Gu (15:13:53): > I found ifclass(w) = c("z", "numeric"), printingwgives 5, and ifclass(w) = "z", it gives the message output. > > I used the one from Jupyter website:https://jupyter.org/try - Attachment (jupyter.org): Project Jupyter > The Jupyter Notebook is a web-based interactive computing platform. The notebook combines live code, equations, narrative text, visualizations, interactive dashboards and other media.
2023-04-04
David Rach (22:44:05): > @David Rach has joined the channel
2023-04-05
Simone Riva (09:54:10): > @Simone Riva has joined the channel
stefano mangiola (19:30:32): > @stefano mangiola has left the channel
2023-04-08
Wangchen Tsering (15:45:42): > @Wangchen Tsering has joined the channel
2023-04-09
mgunady (17:01:11): > @mgunady has joined the channel
2023-04-12
aaronwolen (14:59:42): > @aaronwolen has joined the channel
Monica Padilla (21:07:52): > @Monica Padilla has joined the channel
2023-04-13
Ismael Rodriguez (05:11:01): > @Ismael Rodriguez has joined the channel
Jiefei Wang (15:22:34): > @Jiefei Wang has joined the channel
2023-04-17
Alex Mahmoud (13:32:52): > Repost from CZI Open Sci slack in case it is interesting to people::loud_sound:Maybe of interest to folks here, and anyone from the R community! > At *******10am UTC+1 this Thursday ,*The Turing Way will be hosting Julia Silge from Posit (formerly RStudio) and Ella Kaye (Warwick University) to hear about their experience developing open source tools and communities with the R project. > Please sign up via theEventbrite pageif you are interested. - Attachment (Eventbrite): The Turing Way hosts: Julia Silge and Ella Kaye > The Turing Way welcomes Julia Silge and Ella Kaye to exchange insights from community building with R/Python and Open Source tools.
Lori Shepherd (14:14:23): > 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 (14:18:27) (in thread): > The webpage for the awards will be updated within the hour to reflect 2023 information.
2023-04-18
Matthew Broerman (13:50:17): > @Matthew Broerman has joined the channel
Dr. Amanda Martin (14:35:03): > @Dr. Amanda Martin has joined the channel
Jermiah Joseph (16:36:55): > @Jermiah Joseph has joined the channel
2023-04-19
Kozo Nishida (01:54:41): > Hi all, > Is there a way to enumerate the Bioconductor packages that have Shiny app within it?
Lluís Revilla (05:44:23) (in thread): > I don’t think there is a direct way. One could check how many packages depend or suggest Shiny.
Mike Smith (07:14:50) (in thread): > 190 packages mention the word “shiny” in their DESCRIPTION files (https://code.bioconductor.org/search/search?q=shiny+f%3ADESCRIPTION) - Attachment (code.bioconductor.org): Bioconductor Code: Search > Search source code across all Bioconductor packages
Hervé Pagès (12:49:02) (in thread): > Looks like we have a Bioc view for that, but only 9 packages there:disappointed::https://bioconductor.org/packages/release/BiocViews.html#___ShinyApps
Federico Marini (15:50:24) (in thread): > happy to populate it a bit more by adding a couple I maintain:slightly_smiling_face:
2023-04-20
Estella Dong (08:07:13): > @Estella Dong has joined the channel
Sam Chou (15:59:04): > @Sam Chou has joined the channel
2023-04-21
Kozo Nishida (03:45:13) (in thread): > Thanks everyone for the replies. > (Sorry for the delay in my reply…) > > I will try to write a community blog post about this thread!
Kozo Nishida (03:46:25) (in thread): > By the way, how can we contribute to the BiocViews [update]?
Yuanhua Huang (10:07:08): > @Yuanhua Huang has joined the channel
Sarah Kaspar (10:33:19): > @Sarah Kaspar has joined the channel
Hervé Pagès (13:41:05) (in thread): > PR?https://github.com/Bioconductor/biocViews
Kozo Nishida (13:59:37) (in thread): > @Hervé PagèsThanks for the information! > I think that should also be written in a community blog post!
Kozo Nishida (14:21:49) (in thread): > By the way, now I found there is#shiny, Sorry!
Hervé Pagès (14:22:40) (in thread): > good to know.. didn’t know about that either
Maria Doyle (14:29:52) (in thread): > maybe we need a blog post about the Bioc Slack channels too:slightly_smiling_face:
2023-04-22
Luca (08:32:28): > @Luca has joined the channel
2023-04-24
Joshua Ho (13:16:15): > @Joshua Ho has joined the channel
2023-04-26
Lori Shepherd (15:40:50): > Thanks to all developers and community members for contributing to the project! Bioconductor 3.17 is now available! > Please see the full release announcement:https://bioconductor.org/news/bioc_3_17_release/
2023-05-01
Said Salehe (15:00:57): > @Said Salehe has joined the channel
Ning Liu (21:34:14): > @Ning Liu has joined the channel
Krithika Bhuvanesh (22:10:32): > I’m looking to use the Hilbert curve algorithm to map a 3D space (a variable with X, Y and Z coordinatte) to a single dimension. I think “HilbertCurve” is the right Bioc package to use. Can anyone tell me how I can do this ? The vignette does not have what I am looking for. Thanks
2023-05-03
Ahmad Alkhan (07:46:16): > @Ahmad Alkhan has joined the channel
Kozo Nishida (11:58:09): > Hi all, > I am interested in [re]implementing some Bioconductor packages in Python, would that be considered a different idea thanhttps://github.com/BiocPy? > (I would like to contribute to BiocPy if the idea is not different.)
Jayaram Kancherla (12:12:21) (in thread): > I would love to have more contributions from the community (need to work on advertising this effort more). > > what packages are you planning on implementing?
Kozo Nishida (12:33:06) (in thread): > There are two that have already been implemented, not planned. > * https://github.com/cytoscape/py4cytoscape(that is Python equivalent ofhttps://www.bioconductor.org/packages/release/bioc/html/RCy3.html > * https://github.com/kozo2/pywikipathways(that is Python equivalent ofhttps://bioconductor.org/packages/release/bioc/html/rWikiPathways.html) > (However, py4cytoscape was implemented by a Cytoscape community member who is not me.) - Attachment (Bioconductor): RCy3 > Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function. - Attachment (Bioconductor): rWikiPathways > Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.
Kozo Nishida (12:34:57) (in thread): > In addition to the above, I would also like to implement all Cytoscape-related Bioconductor packages in Python as well.
Kozo Nishida (12:36:33) (in thread): > I am very interested in a Python implementation of AnnotationHub in case of non-Cytoscape related packages.
Kozo Nishida (12:40:09): > I wonder if this is related to the above, but how should we understand the difference between rOpenSci and Bioconductor package review? > I am asking this because I have recently started working with the pyOpenSci community (I am also active in the PyData community). > I’m wondering if the Python implementation of Bioconductor would now go to pyOpenSci if the BiocPy management policy is not well known.
Leopoldo Valiente (12:48:19): > @Leopoldo Valiente has joined the channel
Martin Morgan (12:58:14) (in thread): > This might be interesting with respect to AnnotationHub –https://github.com/scverse/genomic-features– a (very much in ‘beta’) Python package to make EnsemblDb objects from AnnotationHub available to Python users.
Jayaram Kancherla (12:58:47) (in thread): > AnnotationHubwould be an awesome contribution to the BiocPy org, taking advantage of the data representations already in biocpy. > > In addition, I was considering how to make Bioconductor-[like, ish] packages more discoverable on PyPI. One way of improving the search is by addingBioconductoras a custom classifiers (https://pypi.org/classifiers/) in PyPI. Haven’t gotten around to submitting this yet, but I will
Martin Morgan (13:20:46) (in thread): > One maybe mistaken reservation I have about BiocPy is that it seems to capture the ‘implementation’ details, rather than the ‘interface’ to the object, e.g., for GenomicRanges one only needs two of three of start / end / width, with the specific choice an implementation detail. If all that is available is the implementation, then the Python community has to understand the internal representations and then re-implement the user interface (including all the edge cases accumulated over the years in Bioconductor!)
Isaac Virshup (16:39:04) (in thread): > Hey Kozo, I haven’t found the python ecosystem to be anywhere near as centralized to the R one. > > For the cytoscape stuff, I would suggest asking the biocypher people? They’re interested in bio knowledge graphs generally and could point you in the right direction. > > I’d really like to see more reuse of annotation hub in the python ecosystem (I’m working on thegenomic-featurespackage Martin mentioned, and am involved in scverse), so could be interested in collaborating there.
Franck RICHARD (17:10:11): > @Franck RICHARD has joined the channel
2023-05-04
Hassan Kehinde Ajulo (11:38:03): > @Hassan Kehinde Ajulo has joined the channel
sophy (13:02:58): > @sophy has left the channel
Vince Carey (15:28:16) (in thread): > @Isaac Virshupthanks for chiming in. I am very interested in helping to ensure that scientists can use the language of their choice to do the analyses they want to do. How to synchronize efforts in Bioc and scverse is a basic concern. I started trying to understand some of the issues involved by writing scviR which is in Bioc 3.17. I am sure I am behind the development cycle of scvi-tools, and catching up will take nontrivial effort. We are also discussing how to enhance AnnotationHub and we wouldn’t want to break things that you might be working with in genomic-features. (I think the risk is quite low but you never know). I think Bioconductor has benefited greatly by a) having the clearly identified, ~6 month parallel release (no API changes) and devel (can break with deprecation process) cycles, and b) limiting dependencies to bioc and CRAN packages. These approaches have their costs but I think they have been outweighed by benefits. Do you see any tendencies towards this kind of centralization/periodicity in scverse?
Vince Carey (15:33:29) (in thread): > @Kozo NishidaI don’t know how we should proceed as BiocPy matures. I will note that we can have vignettes for R packages that use python chunks; in BiocHail I get python/spark via basilisk. One way to think of Bioc for python is that we think of PyPi as a kind of CRAN, and anyone wanting to provide python capabilities for Bioconductor users would just have to write a basilisk-based package that pins the desired versions of exported python functionality. A thorough review might require python expertise – but if there is a review/credentialing/regular testing process underlying the PyPi component, maybe we would only be concerned with the R code defining the interface.
Vince Carey (15:49:51) (in thread): > And maybe we need to start a new channel? “BiocPython”?
Vince Carey (15:52:51) (in thread): > Just one more point. Wanted to mention the alabaster.* packages as tools for converting Bioc data structures like SingleCellExperiment to JSON+HDF5 (e.g.) for ingestion in other languages/systems. Getting experience with the metadata and construction of nicely usable instances in other languages will be worthwhile. alabaster.ranges for GRanges, for example.
Theary Chhim (19:03:50): > @Theary Chhim has joined the channel
2023-05-05
Kozo Nishida (00:34:05) (in thread): > Thanks for the info.@Vince CareyI understand your thoughts on BiocPy. > Thanks for the info on BiocHail. I am a hail user but did not know BiocHail. > I will try to use basilisk.
Kozo Nishida (00:35:18) (in thread): > I started a new channel#biocpython.
Isaac Virshup (07:47:57) (in thread): > @Vince Carey > > We are also discussing how to enhance AnnotationHub and we wouldn’t want to break things that you might be working with in genomic-features. > Would be happy to be a part of this conversation! I talked about this a little bit with@Martin Morganat the recentscverse hackathon. It could be useful to include people fromopen2cin this as well depending on which area of annotationhub. - Attachment (Twitter): scverse on Twitter > Many exciting things – and intense coding – at the scverse hackathon this week hosted by @OliverStegle and @saezlab in Heidelberg! >
> Our focus was on interoperability across languages and knowledgebases. Read on to see what we made! 1/n
Isaac Virshup (07:49:28) (in thread): > > I think Bioconductor has benefited greatly by a) having the clearly identified, ~6 month parallel release (no API changes) and devel (can break with deprecation process) cycles > This has been a thing we’ve discussed a bunch, which I’ll try to summarize here. It’s also something that we touched on in the scverse announcement publication (rdcu.be/c9Bx6) and during the review process with Wolfgang. > > I don’t think we’ll go for big parallel releases. We definitely don’t have the resources to arrange this for the whole community at the moment. > > What we are doing/ going to do is: > * Make release candidates for packages with many dependents (e.g. scverse core) > * Make it easy for downstream packages to have a CI job that tests against these (e.g.this CI job(which needs better documentation)). We would like to monitor these for failure after making a release candidate, but are still figuring that out. > > * We may add this as requirement to be listed as a “scverse ecosystem package” (https://scverse.org/packages/#ecosystem) > The core packages also follow semantic versioning w.r.t. API changes. I’d encourage downstream packages to do the same, but we’re not taking steps to enforce that. > > b) limiting dependencies to bioc and CRAN packages. > Does this essentially mean: “no installing dependencies from github”? Or is it more than that? > > Do you see any tendencies towards this kind of centralization/periodicity in scverse? > Periodicity: Not on the same scale. We would like to have more regular releases of tools, but are still figuring out greater development resources first. Even then, it’d be a goal, not necessarily a requirement. > > Centralization: Yes, but with a lighter touch. Essentially, we have restrictions on packages that we’ll advertise/ give a badge to. But we don’t want to go so far as having our own package distribution.
Vince Carey (08:07:25) (in thread): > Right – we do not permit dependence on github-only packages, and if a package is removed from CRAN the dependent package needs to adjust or motivate the CRAN contributor to fix to get it back into CRAN. Since your ecosystem requirements include PyPi availability, it may not be such a stretch to enlarge the scope of Bioconductor software contributions to explicitly support interop with scverse via basilisk. But further discussion will be needed.
Vince Carey (08:10:42) (in thread): > @Alex Mahmoud@Brian Schilderthere is a link above to agithub actionfor CI in scverse. Seems like it connects with the concerns we have in the cloud working group/rworkflows…
Brian Schilder (08:53:48) (in thread): > will give some thoughts on the new#biocpythonchannel
Gregor Sturm (09:36:54): > @Gregor Sturm has joined the channel
Danila (09:49:25): > @Danila has joined the channel
2023-05-07
William Ryan (19:28:02): > @William Ryan has joined the channel
2023-05-08
Louise (04:27:17): > @Louise has joined the channel
Sebastian Lobentanzer (08:50:22): > @Sebastian Lobentanzer has joined the channel
2023-05-09
Ben Parks (05:15:04): > @Ben Parks has joined the channel
esther jordana Muwanguzi (23:44:10): > @esther jordana Muwanguzi has joined the channel
2023-05-10
Aliyu Atiku Mustapha (11:55:02): > @Aliyu Atiku Mustapha has left the channel
2023-05-11
Gamal Akabani (01:14:37): > @Gamal Akabani has joined the channel
Sonia Barasa (02:54:05): > @Sonia Barasa has joined the channel
Joost Groot (14:09:55): > @Joost Groot has joined the channel
2023-05-12
Aljes Binkevich (07:28:55): > @Aljes Binkevich has joined the channel
Sebastien Lelong (20:36:53): > @Sebastien Lelong has joined the channel
2023-05-15
Shixiang Wang (23:12:07): > May I ask if there are any Ph.D. positions in tumor bioinformatics that are suitable for my junior colleague currently available? He recently completed his master’s degree and is looking for opportunities to pursue a Ph.D. His skills and capabilities are impressive, so any recommendations or assistance would be greatly appreciated.:pray:
Shixiang Wang (23:12:49) (in thread): > I have attached his CV here for someone interested in. - File (PDF): wanggsh_CV_en.pdf
2023-05-16
Laurent Gatto (05:58:19) (in thread): > Here are two open position for proteomics/bioinformatics PhD students in my group [https://lgatto.github.io/spatprot-job-2023/,https://lgatto.github.io/scp-job-2023/]. Even though not explicit in the advertisement, application to tumour biology are possible (especially given the focus of many labs in the institute). He’s welcome to contact me directly. - Attachment (~/): Open position in the CBIO lab: spatial proteomics and PTMs > A position for a PhD student (4 years) or a research assistant (1 yearcontracts, renewable) is open in the CBIO lab focusing on proteinsub-cellular localisation (spatial) proteomics, post-translationalmodification and machine learning. - Attachment (~/): Open position in the CBIO lab: single-cell proteomics > A fully-funded position for a PhD student (4 years) or a post-doctoralresearcher (2 - 3 years, depending on experience) is open in theComputational Biology and Bioinformatics lab (CBIO) at the de DuveInstitute, UCLouvain in Brussels, Belgium.
Shixiang Wang (06:18:43) (in thread): > @Laurent GattoThank you Laurent. I will transfer the good message to him :).
Sarvesh Nikumbh (07:26:42) (in thread): > Searching on Twitter with keywords “tumor bioinformatics phd positions”, some of the links on this webpage came up. May be some of these are interesting:http://www.begenomics.com/phdscholarship/ - Attachment (BeGenomics): PhD scholarship in Bioinformatics and Genomics > PhD scholarship in Bioinformatics, Genomics, Life Sciences and Machine learning
2023-05-17
Artur Sannikov (02:57:01): > @Artur Sannikov has joined the channel
2023-05-19
Ajda Pristavec (11:07:58): > @Ajda Pristavec has joined the channel
Michael Kesling (14:04:51): > @Michael Kesling has joined the channel
Yuka Takemon (14:26:55): > @Yuka Takemon has joined the channel
2023-05-20
PN (18:58:11): > @PN has joined the channel
2023-05-22
Anna Powell (06:37:22): > @Anna Powell has joined the channel
2023-05-23
Jennifer Foltz (17:20:01): > Hi! I am new to the Bioconductor conference and planning to register this year! Does anyone know what talks will be there and/or when a schedule will be posted?:grinning:
Kasper D. Hansen (17:31:06): > Have you looked at the schedule:https://bioc2023.bioconductor.org/schedule/ - Attachment (bioc2023.bioconductor.org): Schedule > Schedule
Kasper D. Hansen (17:31:35): > It seems that the keynotes have no names attached but they will be from the speakers onhttps://bioc2023.bioconductor.org
Kasper D. Hansen (17:31:55): > I am assuming that the organizers are still working on finalizing who talks when
Kasper D. Hansen (17:33:14): > although confusingly I count 6 speakers and 5 keynote slots
Maria Doyle (17:36:21): > It looks like Keynote 4 is there twice
Jennifer Foltz (17:38:32) (in thread): > Thank you! For some reason when I looked just a couple hours ago, I saw the 2022 schedule. This is helpful!
Samuel Gamboa (17:38:52): > Fixed. It was a typo. Thanks.
2023-05-24
Katie Roberts (11:58:56): > @Katie Roberts has joined the channel
James Malone (11:58:59): > @James Malone has joined the channel
Nick Zafiropoulos (12:05:23): > @Nick Zafiropoulos has joined the channel
Matt Obee (13:51:29): > @Matt Obee has joined the channel
William Hutchison (20:48:48): > @William Hutchison has joined the channel
2023-05-25
Kate Hertweck (11:37:13): > @Kate Hertweck has joined the channel
Jacob Krol (17:11:55): > @Jacob Krol has joined the channel
Will (23:02:48): > @Will has joined the channel
2023-05-27
nezar (15:46:00): > @nezar has joined the channel
2023-05-30
Jianhai Zhang (12:22:24): > @Jianhai Zhang has joined the channel
Haowen Zhou (13:21:55): > @Haowen Zhou has joined the channel
2023-05-31
Alyssa Obermayer (13:25:50): > @Alyssa Obermayer has joined the channel
2023-06-01
Louis Le Nézet (03:17:34): > @Louis Le Nézet has joined the channel
Steve Goode (09:10:38): > @Steve Goode has joined the channel
Asiye (09:20:17): > @Asiye has joined the channel
Megha Lal (13:45:31): > @Megha Lal has joined the channel
2023-06-03
Alyssa Obermayer (19:06:09): > @Alyssa Obermayer has joined the channel
2023-06-04
taigaaoki (04:25:20): > @taigaaoki has joined the channel
2023-06-05
Stefanie Peschel (07:23:12): > @Stefanie Peschel has joined the channel
Marisa (18:58:35): > @Marisa has joined the channel
2023-06-06
Gil Poiares-Oliveira (06:12:39): > @Gil Poiares-Oliveira has joined the channel
Lisanna Paladin (06:22:21): > @Lisanna Paladin has joined the channel
Tomi Suomi (06:53:19): > @Tomi Suomi has joined the channel
Isabel Fernandez Escapa (14:24:45): > @Isabel Fernandez Escapa has joined the channel
Jonas Fischer (15:11:31): > @Jonas Fischer has joined the channel
2023-06-07
Andre Nana (10:27:18): > @Andre Nana has joined the channel
Kevin Yamauchi (13:34:27): > @Kevin Yamauchi has joined the channel
Laura Luebbert (13:34:42): > @Laura Luebbert has joined the channel
Kayla Jackson (13:49:03): > @Kayla Jackson has joined the channel
Jen Crainic (16:45:38): > @Jen Crainic has joined the channel
2023-06-08
Jacquelyn Shevin (11:31:42): > @Jacquelyn Shevin has joined the channel
2023-06-09
Daphne Babirye (11:41:52): > @Daphne Babirye has joined the channel
Anam Akhtar (14:58:35): > @Anam Akhtar has joined the channel
2023-06-10
Jenea Adams (10:16:34): > Hello, the Black Women in Computational Biology Network is about 2 hours away from this public networking event for the broader compbio community. If you work or recruit in the field, we’d love to have you join us for a program of community-buildinghttps://www.blackwomencompbio.org/event-details/q2-compbio-community-mixer - Attachment (BlackWomenCompBio): CompBio Community Mixer | BlackWomenCompBio > BWCB members and supporters are invited to our Q2 mixer! Join the BWCB community and other computational biologists, share research, and make new connections.
2023-06-12
Carmen Navarron (02:55:22): > @Carmen Navarron has joined the channel
Natasha (10:48:56): > @Natasha has joined the channel
Bulut Hamali (19:26:38): > @Bulut Hamali has joined the channel
2023-06-14
Lucy Farrimond (08:55:22): > @Lucy Farrimond has joined the channel
Edoardo Bertolini (11:15:19): > @Edoardo Bertolini has joined the channel
Aedin Culhane (21:12:10) (in thread): > @Kozo Nishidawant to write the post?
Kozo Nishida (21:40:05) (in thread): > @Aedin CulhaneYes, but I have other posts I need to write, and if someone else wants to write it, I would like to leave it to them. > We have the blog post ideas here.https://github.com/Bioconductor/biocblog/issuesI welcome anyone to write biocblog post ! > (Either fromhttps://github.com/Bioconductor/biocblog/issuesor from outside of the GitHub Issues!)
2023-06-15
Clara Tejido (11:52:38): > @Clara Tejido has joined the channel
Catherine Quinn (she/her) (12:35:29): > @Catherine Quinn (she/her) has joined the channel
2023-06-16
Souhaila (05:20:10): > @Souhaila has joined the channel
Jennifer Wischhusen (08:05:00): > @Jennifer Wischhusen has joined the channel
Shivang Bhanushali (08:12:27): > @Shivang Bhanushali has joined the channel
Miquéias Fernandes (08:18:09): > @Miquéias Fernandes has joined the channel
Jacob T. Mitchell (12:12:20): > @Jacob T. Mitchell has joined the channel
Gouri Rajaram (18:40:52): > @Gouri Rajaram has joined the channel
2023-06-19
Pierre-Paul Axisa (05:07:38): > @Pierre-Paul Axisa has joined the channel
2023-06-20
Michelle Luk (07:31:24): > @Michelle Luk has joined the channel
Nicholas Cooley (08:31:44): > Hi, does anyone know if there’s a quick way to get the list of all IPG identifiers from the NCBI?
Janani Ravi (09:14:06) (in thread): > Edirect/eutils—did you happen to try that?
Nicholas Cooley (10:08:43) (in thread): > I know how to get the records once I have the identifiers with edirect, I don’t know how to get the whole list beforehand.
2023-06-21
Linyi Zhu (04:43:16): > @Linyi Zhu has joined the channel
Lena (04:43:46): > @Lena has joined the channel
Jennifer Southcombe (04:43:51): > @Jennifer Southcombe has joined the channel
Chunhao Gu (08:51:49): > @Chunhao Gu has joined the channel
2023-06-22
Zahida Sheikh (14:39:44): > @Zahida Sheikh has joined the channel
2023-06-26
Ali (06:44:03): > @Ali has joined the channel
John Scanlan (08:53:39): > @John Scanlan has joined the channel
2023-06-27
Louis Le Nézet (04:52:55): > Hi everyone, > i don’t really know where to post this question, so feel free to redirect me to the correct channel:slightly_smiling_face:I was wondering how is the S3 and S4 methods supported in bioconductor and how to nicely write them. > In my case, I’m writing different functions that either take a dataframe and a list of columns names or a list of vector. > The aim would be to do the same as withboxplot. > Should I write something like the following: > > test <- function(x, ...){ > UseMethod("test") > } > > test.default <- function(x, x1, x2, ...){ > print("Is default with multiple vector") > } > > test.data.frame <- function(x, colnames, ...){ > print("Is data.frame") > print(colnames) > } >
Lluís Revilla (05:23:20) (in thread): > Bioconductor doesn’t have a special support for S3 and S4 methods than R. You can use other books likehttps://adv-r.hadley.nz/s4.htmlto learn how to write them. The special case for Bioconductor is that whenever possible you should reuse classes to benefit from their methods. But this is a nice question for the Bioconductor working grouphttps://github.com/Bioconductor/BiocClassesWorkingGroup(I’ll log it so that we can answer them in future materials)
Asier Ortega (06:16:21): > @Asier Ortega has joined the channel
Yoon Ji Jung (06:58:02): > @Yoon Ji Jung has joined the channel
Louis Le Nézet (07:13:37) (in thread): > Thanks for the answer:slightly_smiling_face:
Marjani Hall (11:09:28): > @Marjani Hall has joined the channel
Laurent Gatto (11:52:20) (in thread): > And following up from Lluís comment, most of the methods are S4, because the Bioconductor classes are exclusively S4. The important point is thus the data that you are handling and want to write a method for.
Hervé Pagès (13:59:17) (in thread): > Yes, Bioconductor recommends defining an S4 generic and methods for this. No need for an S3 generic and methods. So: > > setGeneric("foo", function(x, ...) standardGeneric("foo")) > > setMethod("foo", "ANY", > function(x, ...) { > all_vectors <- list(x, ...) > stopifnot(all(sapply(all_vectors, is.vector))) > ... > ... > } > ) > > setMethod("foo", "data.frame", > function(x, colnames) { > ... > ... > } > ) >
2023-06-28
Andrew Ghazi (10:52:35): > @Andrew Ghazi has joined the channel
2023-06-29
Basil Courbayre (13:59:02): > @Basil Courbayre has joined the channel
2023-07-01
Castro Mbithi (16:51:56): > @Castro Mbithi has joined the channel
2023-07-02
Leslie Smith (13:04:56): > @Leslie Smith has joined the channel
2023-07-03
Taleb Ahsan (16:42:25): > @Taleb Ahsan has joined the channel
2023-07-04
akurut evelyn (01:39:48): > @akurut evelyn has joined the channel
Pageneck Chikondowa (04:39:06): > @Pageneck Chikondowa has joined the channel
Alexander Bender (09:36:15): > @Alexander Bender has left the channel
VicHB (21:07:14): > @VicHB has joined the channel
2023-07-05
Gerardo Mirizio (21:29:17): > @Gerardo Mirizio has joined the channel
2023-07-06
Joy Lee (00:25:27): > @Joy Lee has joined the channel
Vikash Sharma (14:46:31): > @Vikash Sharma has joined the channel
atongsa miyamoto (23:23:09): > @atongsa miyamoto has joined the channel
2023-07-10
Lluís Revilla (10:01:29): > I’m interested in theFEM packageremoved in 3.12. According togit.bioconductor.orgI see it listedR packages/FEMbut when I try to clone it or see it via thecode browserit doesn’t appear. I could download the source code, but while checking the package I was surprised to see that it still hasdownloadsas of this year. Are the downloads numbers across all versions (Bioconductor & package) but without the mirrors?
Helge Hecht (22:41:18): > There will be a mass spectrometry BoF at the Galaxy Community Conference - meeting details are in the following document:https://docs.google.com/document/d/1G_k4xtvaNkXkVOFiN22vahx_iryNeRaBj5JaeZuclmI/editIf you’d like to learn about the state of MS tools in Galaxy or would like to learn more about the activities this meeting is open for everyone to join and express their interest!
2023-07-11
Akewak Jeba (02:19:37): > @Akewak Jeba has joined the channel
Harvinder Singh (02:26:13): > @Harvinder Singh has joined the channel
Mike Smith (10:56:11) (in thread): > Don’t take this as gospel, but I’ll try to answer the bits I know. > > AFAIK a deprecated package is never actually removed from the git server. In fact, if you try this command you can still cloneFEM: > > git clone[https://git.bioconductor.org/packages/FEM.git](https://git.bioconductor.org/packages/FEM.git) > > When a package is removed from Bioconductor, it’s actually removed from the “Manifest”, the master list(s) of all packages in the current devel branch. (I think) these drive the build system, package propagation, landing package creation etc. You can actually download and look at the manifest files yourself, they’re also in a git repository: > > git clone[https://git.bioconductor.org/admin/manifest.git](https://git.bioconductor.org/admin/manifest.git) > > I use the software package list to determine what’s available in the code browser. If a package get’s deprecated and removed from the manifest, it disappears from the code browser. That’s probably not ideal, but when I was developing the site the manifest seemed a good way to easily obtain a comprehensive list of packages and to know when a new package was added to Bioc that I needed to add to the browser. > > I presume the list of packages in a particular release is just whatever is in the Manifest on the date of the release freeze - but I don’t actually know that for sure. There’s not anyRELEASE_X_Ybranches in the manifest repo that pinpoint those moments, but there are commits where multiple packages are removed around past release times. > > I don’t know much about the download counts, but I suspect you’re correct that the download counts are across all versions of the packages, andFEMstill gets a small number of download for the old versions. Maybe@Robert Shearknows more, I believe he’s spent some time looking at the download statistics and might know how the counts are aggregated.
Lluís Revilla (12:13:19) (in thread): > Thanks Mike, I am not sure what happened, because when I tried git clone ... yesterday it didn’t clone the repo. Many thanks for maintaining thecode.bioconductor.orgsite and a glimpse behind the curtains on how it works.
Robert Shear (12:13:41) (in thread): > It appears as though FEM was removed in the 3.12 release, so the last published release is 3.11. You can access it athttp://www.bioconductor.org/packages/3.11/bioc/html/FEM.html. If you want to see all the packages in 3.12, you can visithttp://bioconductor.org/packages/3.12/. - Attachment (Bioconductor): FEM > The FEM package performs a systems-level integrative analysis of DNA methylation and gene expression data. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed. For full details, see Jiao et al Bioinformatics 2014.
Lluís Revilla (12:14:18) (in thread): > I was surprised because it is removed and it has almost the same amount of downloads as one of my packages (I was thinking this could be used to control for “background”/automatic downloads of Bioconductor). Thanks!
Lluís Revilla (12:15:31) (in thread): > That’s what I did@Robert Shear! A publication used FEM and I wanted to avoid rewriting it from scratch. Thanks!
Robert Shear (12:16:26) (in thread): > All of the packages accessed viawww.bioconductor.orgorbioconductor.orgare in the download count. As you suspect, nothing from the mirrors is counted. Access viagit.bioconductor.orgis not counted.
Caterina (15:34:49): > @Caterina has joined the channel
Amos Schorr (17:13:09): > Hey folks! If you’re curious about what the near future of bio looks like in the wetlab, boy do I have a treat for you! We’ve got 4 leaders talking IN A REALLY GROUNDED WAY about what these changes might be and what you might want to think about to best equip yourself to do goddamn brilliant work on July 12th. Free for student & academics. Pay what you wish for everyone else.https://www.eventbrite.com/e/near-future-skills-gaps-14-the-wetlab-tickets-639557713337 - Attachment (Eventbrite): Near Future Skills Gaps (1/4): The Wetlab > A virtual panel of leaders in aging biology discussing neglected topics central to doing good work & building a career.
2023-07-12
Samuel Ortion (02:06:44): > @Samuel Ortion has joined the channel
Guillaume Devailly (02:50:13): > @Guillaume Devailly has joined the channel
Ahmed Hassan (11:37:33): > @Ahmed Hassan has joined the channel
Vivek Sharma (16:00:41): > @Vivek Sharma has joined the channel
Jesse Raab (17:21:41): > @Jesse Raab has joined the channel
Kishori (18:57:42): > @Kishori has joined the channel
2023-07-13
Brian Schilder (07:00:02): > @Brian Schilder has joined the channel
Tetiana Salamovska (07:05:06): > @Tetiana Salamovska has joined the channel
Lev Kravchuk (07:07:03): > @Lev Kravchuk has joined the channel
Ogechi Ogoke (08:43:39): > @Ogechi Ogoke has joined the channel
2023-07-14
Lluís Revilla (05:35:21): > https://fosstodon.org/@R_Foundation/110711709044056935: > > Save the date! > > We are pleased to announce that useR! 2024 will be a hybrid conference, taking place 8-11 July in Salzburg, Austria. > > We will share the conference website and social media accounts in due course. - Attachment (Fosstodon): The R Foundation :rstats: (@R_Foundation@fosstodon.org) > :date: Save the date! > > We are pleased to announce that useR! 2024 will be a hybrid conference, taking place 8-11 July in Salzburg, Austria. > > We will share the conference website and social media accounts in due course. > > #RStats
elena giorgi (23:56:21): > @elena giorgi has joined the channel
2023-07-17
Physalia-courses (06:13:21): > @Physalia-courses has joined the channel
Ellis Hughes (11:09:43): > @Ellis Hughes has joined the channel
2023-07-18
Smriti Chawla (12:31:22): > @Smriti Chawla has joined the channel
Thomas Tam (18:09:40): > @Thomas Tam has joined the channel
2023-07-19
Pratibha Panwar (22:38:11): > @Pratibha Panwar has joined the channel
2023-07-20
Almog Angel (08:22:21): > @Almog Angel has joined the channel
2023-07-21
Amos Schorr (05:04:41): > Hi! We’ve got 2 virtual events coming up that I’d love you to join and share with good folks you know. They’re focused on near-future skill gaps in aging biology research. On July 26th, we’ll be discussing CompBio with Jacob Kimmel (co-founder @ NewLimit), Ravi Pandya (Sr. Director, ML & Computational Platform @ Altos Labs), and Jarod Rutledge (co-founder @ Teal Omics, a Wyss-Coray lab spinout). And on August 9th, we’ll be discussing software & ML with Joe Betts-LaCroix (CEO @ Retro Bio), Luca Naef (CTO, VantAI), and our very own @Andy Lee (CTO, Vincere Biosciences).https://www.eventbrite.com/e/near-future-skill-gaps-24-computational-biology-tickets-665910445067https://www.eventbrite.com/e/near-future-skill-gaps-34-software-ml-tickets-677946495217 - Attachment (Eventbrite): Near Future Skill Gaps (2/4): Computational Biology > A virtual panel of leaders in aging biology discussing neglected topics central to doing good work & building a career. - Attachment (Eventbrite): Near Future Skill Gaps (3/4): Software & ML > A virtual panel of leaders in aging biology discussing neglected topics central to doing good work & building a career.
Cirilla (07:00:46): > @Cirilla has joined the channel
2023-07-22
Aziz Khan (20:44:01): > @Aziz Khan has joined the channel
2023-07-24
Lluís Revilla (07:47:59): > :mega:Registration for the Spanish R conference is now open! If you want to come to sunny Barcelona you have now a good reason to come:https://bit.ly/CongresoRBCN2023We welcome any presentation/posters from Bioconductor or any other field, we will also have workshops (if you want to train people about your package/tools do not hesitate). > If your institution might be interested to sponsor the event let me know and I will send you more details.:speaking_head_in_silhouette:Languages: English or Spanish:calendar:The conference will be between 15th to 17th November!:female-teacher:We will have some local people and international speakers!
Samuel Bharti (17:25:30): > @Samuel Bharti has joined the channel
2023-07-25
Aartik Sarma (15:53:16): > @Aartik Sarma has joined the channel
Deeksha Shetty (16:20:14): > @Deeksha Shetty has joined the channel
Roque Palacios (22:33:46): > @Roque Palacios has joined the channel
2023-07-26
Hechen Li (03:22:24): > @Hechen Li has joined the channel
Aia Oz (08:30:39): > @Aia Oz has joined the channel
Abdullah Al Nahid (09:04:37): > @Abdullah Al Nahid has joined the channel
2023-07-27
Geert van Geest (04:15:45): > @Geert van Geest has joined the channel
Clemens Kohl (07:29:21): > @Clemens Kohl has joined the channel
Clemens Kohl (07:31:35): > @Clemens Kohl has joined the channel
Louise Morlot (07:32:46): > @Louise Morlot has joined the channel
2023-07-28
Andrea Komljenovic (01:08:28): > @Andrea Komljenovic has joined the channel
Jiaji George Chen (10:33:40): > @Jiaji George Chen has joined the channel
Paul Kwong Yu (11:31:09): > @Paul Kwong Yu has joined the channel
Kinnary Shah (12:23:20): > @Kinnary Shah has joined the channel
Konstantinos Daniilidis (13:45:36): > @Konstantinos Daniilidis has joined the channel
Yeji Bae (14:25:28): > @Yeji Bae has joined the channel
Ingo (14:59:54): > @Ingo has joined the channel
Greg Stacey (15:06:26): > @Greg Stacey has joined the channel
Benjamin Yang (15:55:29): > @Benjamin Yang has joined the channel
2023-07-29
Rochelle Yap (12:58:46): > @Rochelle Yap has joined the channel
John Thomas (23:33:15): > @John Thomas has joined the channel
2023-07-31
Shashank (06:05:47): > @Shashank has joined the channel
Dongweon Shin (06:11:32): > @Dongweon Shin has joined the channel
Nikhil Mane (17:13:36): > @Nikhil Mane has joined the channel
Jamin Liu (22:44:07): > @Jamin Liu has joined the channel
2023-08-01
Andrés Arredondo Cruz (00:36:29): > @Andrés Arredondo Cruz has joined the channel
Esther Camacho (01:46:09): > @Esther Camacho has joined the channel
Madan Mohan (02:29:37): > @Madan Mohan has joined the channel
Kacper Żukowski (08:04:50): > @Kacper Żukowski has joined the channel
Mohamed S.AboHoussien (11:02:49): > @Mohamed S.AboHoussien has joined the channel
Yeji Bae (18:05:00): > @Yeji Bae has joined the channel
Kwangwoon (Jon) Lee (18:39:27): > @Kwangwoon (Jon) Lee has joined the channel
2023-08-02
Harkirat Sohi (00:58:31): > @Harkirat Sohi has joined the channel
Greg Bedwell (05:39:01): > @Greg Bedwell has joined the channel
Mehak Chopra (07:59:48): > @Mehak Chopra has joined the channel
Kaelyn Long (08:10:57): > @Kaelyn Long has joined the channel
Beth Cimini (08:19:03): > @Beth Cimini has joined the channel
Erinn Dady (08:24:55): > @Erinn Dady has joined the channel
Trisha Timpug (09:24:32): > @Trisha Timpug has joined the channel
Brian Gural (10:23:32): > @Brian Gural has joined the channel
Abiud Cantu (15:31:14): > @Abiud Cantu has joined the channel
2023-08-03
Nithya Rangasamy (02:09:25): > @Nithya Rangasamy has joined the channel
Scott Norton (11:02:05): > @Scott Norton has joined the channel
Flávia E. Rius (11:11:01): > @Flávia E. Rius has joined the channel
Kirt Hanks (11:12:11): > @Kirt Hanks has joined the channel
Ken Saville (11:19:00): > @Ken Saville has joined the channel
Ed Lauzier (15:32:11): > @Ed Lauzier has joined the channel
Ritika Giri (15:55:20): > @Ritika Giri has joined the channel
Frans Cuevas (21:28:40): > @Frans Cuevas has joined the channel
tho nguyen (23:54:19): > @tho nguyen has joined the channel
2023-08-04
Maximilian (04:28:50): > @Maximilian has joined the channel
goodnews sandy (06:32:07): > @goodnews sandy has joined the channel
Simran Chhabria (11:03:05): > @Simran Chhabria has joined the channel
Loveth Omokaro (12:41:06): > @Loveth Omokaro has joined the channel
Dror Perk (13:01:14): > @Dror Perk has joined the channel
Sophia Chaudhry (14:03:14): > @Sophia Chaudhry has joined the channel
Lucio Queiroz (14:17:20): > @Lucio Queiroz has joined the channel
Ember Tokarski (15:11:58): > @Ember Tokarski has joined the channel
Shiheng Huang (17:08:52): > @Shiheng Huang has joined the channel
Kudakwashe (19:05:55): > @Kudakwashe has joined the channel
2023-08-05
Abdullah Al Nahid (10:49:31): > Hi everyone, I created a simple chrome extension to access PDF files directly, to avoid waiting for this screen (screenshot attached) to load. > It will inject a floating PDF icon in the bottom right corner of your screen when you visit such a paper with epdf like in ASM, Willey. > > Here’s the downloadable zip file and the source code of the extension that you can unzip and load into your browser:https://github.com/nahid18/journal-epdf-downloaderFeel free to star the repo if you like it - File (PNG): image.png
2023-08-07
Emily Chima (03:59:17): > @Emily Chima has joined the channel
Adam Rosen (10:59:11): > @Adam Rosen has joined the channel
1Njeru (13:13:16): > @1Njeru has joined the channel
Alexandra Kern (13:48:28): > @Alexandra Kern has joined the channel
Erio Crucecia (16:29:37): > @Erio Crucecia has joined the channel
2023-08-08
Yumi K (00:34:43): > @Yumi K has joined the channel
jamie_park (13:03:04): > @jamie_park has joined the channel
2023-08-10
Dirk Eddelbuettel (14:06:25): > My google-fu is failing me. I had glanced at, and quite enjoyed, JJ’s keynote at this year’s BioC Conf about quarto, manuscripts and all that jazz and have now tried twice to share them but … can no longer find it. Is there a public repo with his slides including the short embedded screen capture videos at the end?
Hervé Pagès (15:12:04) (in thread): > Don’t know about the slides but the video of his presentation is available for replay on Hopin athttps://app.hopin.com/events/bioc2023/replay
2023-08-11
Sarah Parker (12:36:23) (in thread): > Here are the slides! He used a quarto presentation–https://jjallaire.quarto.pub/reproducible-manuscripts-with-quarto/#/title-slideYou can find all his quarto pubs athttps://jjallaire.quarto.pub/
Dirk Eddelbuettel (12:37:55) (in thread): > My google-fu and memory are clearly bad because I once knew that too, of course. Silly me looked for his GH repos and found nuttin and was perplexed. Quarto domain it is, of course. Thanks a million!
2023-08-12
Sara Carioscia (00:39:00): > @Sara Carioscia has joined the channel
Tiago (10:05:57): > @Tiago has joined the channel
2023-08-14
Guido Putignano (03:13:08): > @Guido Putignano has joined the channel
Tu Hu (07:14:32): > @Tu Hu has joined the channel
ndacyayisenga noah (08:19:46): > @ndacyayisenga noah has joined the channel
David Gonilski (18:11:09): > @David Gonilski has joined the channel
2023-08-15
Tamnjong Larry Tabeh (16:09:28): > @Tamnjong Larry Tabeh has joined the channel
2023-08-17
Rachel Queen (05:54:29): > @Rachel Queen has joined the channel
2023-08-18
Victor Yuan (12:34:37): > @Victor Yuan has joined the channel
2023-08-21
Nikhita Damaraju (15:29:11): > @Nikhita Damaraju has joined the channel
Mustafa Sevim (17:53:29): > @Mustafa Sevim has joined the channel
2023-08-22
Katie Roberts (07:00:25): > @Katie Roberts has left the channel
Juan Ignacio Eizaguirre (07:40:44): > @Juan Ignacio Eizaguirre has joined the channel
Ezinne Anne Emilia (10:33:26): > @Ezinne Anne Emilia has joined the channel
Mary Bearkland (14:52:01): > @Mary Bearkland has joined the channel
2023-08-24
Lachlan Baer (01:11:23): > @Lachlan Baer has joined the channel
2023-08-26
chilam (11:46:52): > @chilam has joined the channel
2023-08-28
Thurman Lincoln (17:48:59): > @Thurman Lincoln has joined the channel
2023-08-30
Julia Lohr (08:02:29): > @Julia Lohr has joined the channel
Oluwafemi Oyedele (12:53:34): > 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
2023-08-31
Ebru Kocakaya (15:01:19): > @Ebru Kocakaya has joined the channel
2023-09-01
Eddie Ruiz (09:31:34): > @Eddie Ruiz has joined the channel
2023-09-04
Anna Lewkowicz (16:49:50): > @Anna Lewkowicz has joined the channel
2023-09-05
Pooja Shah (11:09:45): > @Pooja Shah has joined the channel
Dima Lvovs (13:08:49): > @Dima Lvovs has joined the channel
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
Lambda Moses (18:43:28): > Having been using R for so long, I somehow never thought that there’s the original paper for R itself, which I just stumbled upon on Mastodon:https://www.stat.auckland.ac.nz/~ihaka/downloads/R-paper.pdf
2023-09-07
Sonali Tamhankar (13:01:42): > @Sonali Tamhankar has joined the channel
2023-09-08
Jaclyn Mallard (13:51:42): > @Jaclyn Mallard has joined the channel
2023-09-10
Jane Zhang (17:56:45): > @Jane Zhang has joined the channel
2023-09-12
Christopher Mason (07:17:45): > @Christopher Mason has joined the channel
Jiwoon Park (09:02:24): > @Jiwoon Park has joined the channel
Laura Symul (10:30:20): > @Laura Symul has joined the channel
Eliah Overbey (12:29:11): > @Eliah Overbey has joined the channel
Cem Meydan (15:19:15): > @Cem Meydan has joined the channel
Christopher Chin (15:21:06): > @Christopher Chin has joined the channel
Robert Phillips (15:32:55): > @Robert Phillips has joined the channel
2023-09-13
shaimaa Elsafoury (09:48:02): > @shaimaa Elsafoury has joined the channel
Ruben Dries (10:53:14): > @Ruben Dries has joined the channel
Shane Sanders (19:47:22): > @Shane Sanders has joined the channel
2023-09-14
Daniela Corbetta (12:00:39): > @Daniela Corbetta has joined the channel
Valentyna_Tararina (12:01:15): > @Valentyna_Tararina has joined the channel
Mariia (12:02:32): > @Mariia has joined the channel
Anna (12:03:42): > @Anna has joined the channel
Helena Crowell (12:07:29): > @Helena Crowell has joined the channel
Monica Della Rosa (12:41:55): > @Monica Della Rosa has joined the channel
Yile (12:44:09): > @Yile has joined the channel
Alexander Botzki (12:58:44): > @Alexander Botzki has joined the channel
Matthias Meyer-Bender (14:07:15): > @Matthias Meyer-Bender has joined the channel
David Novak (14:18:36): > @David Novak has joined the channel
Taylor Reiter (15:30:23): > @Taylor Reiter has joined the channel
Mayank Murali (20:16:20): > @Mayank Murali has joined the channel
2023-09-15
Kerry (01:36:05): > @Kerry has joined the channel
Marco Geigges (02:51:45): > @Marco Geigges has joined the channel
Pablo (02:58:18): > @Pablo has joined the channel
Maryna Chepeleva (03:36:26): > @Maryna Chepeleva has joined the channel
Maryna Chepeleva (03:39:02): > @Maryna Chepeleva has joined the channel
Fiona Ross (04:00:56): > @Fiona Ross has joined the channel
Philippe (04:03:07): > @Philippe has joined the channel
Benjamin Rombaut (04:05:42): > @Benjamin Rombaut has joined the channel
Celine Everaert (04:10:08): > @Celine Everaert has joined the channel
Philippine Louail (04:15:06): > @Philippine Louail has joined the channel
Lydia King (04:15:41): > @Lydia King has joined the channel
Taras Lukashiv (04:19:46): > @Taras Lukashiv has joined the channel
Andrea Vicini (04:21:16): > @Andrea Vicini has joined the channel
Alexandre Segers (04:36:26): > @Alexandre Segers has joined the channel
Leo Lahti (04:40:50): > @Leo Lahti has joined the channel
Cyril de Bodt (06:47:40): > @Cyril de Bodt has joined the channel
Wassim Gabriel (09:13:44): > @Wassim Gabriel has joined the channel
Angelo Velle (09:38:06): > @Angelo Velle has joined the channel
Louise Deconinck (09:47:25): > @Louise Deconinck has joined the channel
Laurent (10:03:27): > @Laurent has joined the channel
Blessy Boby (13:04:23): > @Blessy Boby has joined the channel
2023-09-17
Hyeongseok Lim (11:09:49): > @Hyeongseok Lim has joined the channel
2023-09-18
Julie Devis (04:01:55): > @Julie Devis has joined the channel
Ruth Seurinck (05:29:13): > @Ruth Seurinck has joined the channel
Samuel Grégoire (06:32:58): > @Samuel Grégoire has joined the channel
Raj Karan Pandey (08:24:08): > @Raj Karan Pandey has joined the channel
Trushar (08:38:37): > @Trushar has joined the channel
Sebastian Lobentanzer (09:12:38): > @Sebastian Lobentanzer has joined the channel
Daria Fijalkowska (13:43:42): > @Daria Fijalkowska has joined the channel
Ahmed K Saad (13:45:12): > @Ahmed K Saad has joined the channel
Ahmed K Saad (13:48:30): > @Ahmed K Saad has joined the channel
2023-09-19
Katharina Imkeller (04:05:49): > @Katharina Imkeller has joined the channel
louisc (04:36:03): > @louisc has joined the channel
Thomas Naake (07:33:03): > @Thomas Naake has joined the channel
Biancamaria Florenzi (12:24:46): > @Biancamaria Florenzi has joined the channel
Richard Heery (12:52:21): > @Richard Heery has joined the channel
Francesco Dossena (14:46:41): > @Francesco Dossena has joined the channel
Roberto Albanese (18:19:59): > @Roberto Albanese has joined the channel
Megan Othus (22:45:48): > @Megan Othus has joined the channel
2023-09-20
Laure Cougnaud (03:20:19): > @Laure Cougnaud has joined the channel
Franka Voigt (03:31:11): > @Franka Voigt has joined the channel
Alik Huseynov (04:21:04): > @Alik Huseynov has joined the channel
Jaykishan (04:58:51): > @Jaykishan has joined the channel
Erin (06:02:43): > @Erin has joined the channel
Teresa Maia (06:17:26): > @Teresa Maia has joined the channel
Sandra Garcia (06:33:35): > @Sandra Garcia has joined the channel
Maria Maia (07:27:19): > @Maria Maia has joined the channel
Adrienne Unsworth (08:07:42): > @Adrienne Unsworth has joined the channel
Mauro Masiero (09:14:37): > @Mauro Masiero has joined the channel
Timothy Keyes (18:10:55): > @Timothy Keyes has joined the channel
Samuel Njikan (19:02:05): > @Samuel Njikan has joined the channel
Eliot Finch (23:29:41): > @Eliot Finch has joined the channel
2023-09-21
Teresa (10:31:01): > @Teresa has joined the channel
2023-09-22
Donnacha Fitzgerald (04:09:22): > @Donnacha Fitzgerald has joined the channel
Tümay (04:09:46): > @Tümay has joined the channel
Brad Hall (05:37:50): > @Brad Hall has joined the channel
Svetlana Ugarcina Perovic (05:45:55): > @Svetlana Ugarcina Perovic has joined the channel
Amanda Hiser (13:52:36): > @Amanda Hiser has joined the channel
Dabao Zhang (14:50:37): > @Dabao Zhang has joined the channel
Min Zhang (14:52:30): > @Min Zhang has joined the channel
Igor (15:21:32): > @Igor has joined the channel
Abu Zar (23:33:35): > @Abu Zar has joined the channel
2023-09-24
Teemu Daniel Laajala (04:31:55): > @Teemu Daniel Laajala has joined the channel
Rotilho (09:37:38): > @Rotilho has joined the channel
2023-09-25
Kerim Secener (09:12:15): > @Kerim Secener has joined the channel
Nikhita (18:40:07): > @Nikhita has joined the channel
2023-09-30
Victoria Nduka (12:16:48): > @Victoria Nduka has joined the channel
2023-10-02
myles (12:26:43): > @myles has joined the channel
Onalo Deborah (12:26:47): > @Onalo Deborah has joined the channel
Peace Sandy (12:37:21): > @Peace Sandy has joined the channel
Kabirat Adeniyi (12:43:12): > @Kabirat Adeniyi has joined the channel
Chinwendu Enyinna (12:45:34): > @Chinwendu Enyinna has joined the channel
Faizah Salami (13:24:35): > @Faizah Salami has joined the channel
Aleru Divine (13:30:34): > @Aleru Divine has joined the channel
Ikeh Chukwuka (13:49:22): > @Ikeh Chukwuka has joined the channel
Joan C. Chukwuemeka (14:34:30): > @Joan C. Chukwuemeka has joined the channel
Ayesha Younas (14:48:29): > @Ayesha Younas has joined the channel
Sabastine Iroka (17:20:52): > @Sabastine Iroka has joined the channel
Kehinde Adebisi (17:55:56): > @Kehinde Adebisi has joined the channel
Earl-Millen Toh Akwe (18:26:07): > @Earl-Millen Toh Akwe has joined the channel
Mary Ikott (19:44:53): > @Mary Ikott has joined the channel
2023-10-03
Maktuma Alam (01:00:06): > @Maktuma Alam has joined the channel
Komuhangi Tumuhairwe (01:01:41): > @Komuhangi Tumuhairwe has joined the channel
Sinmi Adesanya (01:17:29): > @Sinmi Adesanya has joined the channel
Chinecherem Joy (02:34:21): > @Chinecherem Joy has joined the channel
Grace Ogundaini (02:59:33): > @Grace Ogundaini has joined the channel
Thara Ehizogie (03:10:43): > @Thara Ehizogie has joined the channel
Paulina Boadiwaa Mensah (04:46:01): > @Paulina Boadiwaa Mensah has joined the channel
Scholastica Urua (04:51:34): > @Scholastica Urua has joined the channel
cynthia (05:04:01): > @cynthia has joined the channel
Chioma Onyido (06:06:04): > @Chioma Onyido has joined the channel
kan (09:42:32): > @kan has joined the channel
Esther Afuape (09:58:10): > @Esther Afuape has joined the channel
Olumide Micheal (10:24:55): > @Olumide Micheal has joined the channel
Nwajei Edgar (10:51:47): > @Nwajei Edgar has joined the channel
Temabo Omame (11:03:36): > @Temabo Omame has joined the channel
Chloe (11:36:29): > @Chloe has joined the channel
Ugoo-Okonkwo Stella Ozioma (12:04:33): > @Ugoo-Okonkwo Stella Ozioma has joined the channel
Cynthia (12:15:06): > @Cynthia has joined the channel
Chidimma Blessing Onuora (12:25:00): > @Chidimma Blessing Onuora has joined the channel
Ayowale Ojo (13:20:03): > @Ayowale Ojo has joined the channel
Aminat Odedeyi (13:52:54): > @Aminat Odedeyi has joined the channel
Karen254. Kingecha (14:14:51): > @Karen254. Kingecha has joined the channel
Isoken Ibizugbe (16:18:32): > @Isoken Ibizugbe has joined the channel
Ayomide Solarin (17:14:05): > @Ayomide Solarin has joined the channel
Odigiri Great Alume (18:04:52): > @Odigiri Great Alume has joined the channel
Shakira Ndagire (18:50:10): > @Shakira Ndagire has joined the channel
Albert Han (21:10:47): > @Albert Han has joined the channel
Quinuel Ndip-Agbor (21:38:15): > @Quinuel Ndip-Agbor has joined the channel
2023-10-04
Eric Kyalo (03:53:21): > @Eric Kyalo has joined the channel
Wangui Thuo (04:01:44): > @Wangui Thuo has joined the channel
edilawit (04:06:53): > @edilawit has joined the channel
Chiagoziem David (04:10:22): > @Chiagoziem David has joined the channel
Omoyeme Sim-Okoduwa (05:32:29): > @Omoyeme Sim-Okoduwa has joined the channel
Iram Jamshed (07:13:23): > @Iram Jamshed has joined the channel
Ajoke Yusuf (07:26:13): > @Ajoke Yusuf has joined the channel
Yigakpoa Ikpae (08:40:08): > @Yigakpoa Ikpae has joined the channel
Romane Libouban (08:40:43): > @Romane Libouban has joined the channel
Khalidat Ola-Dauda (08:50:35): > @Khalidat Ola-Dauda has joined the channel
Olajumoke Adeoyo (09:05:06): > @Olajumoke Adeoyo has joined the channel
Zaha (09:21:22): > @Zaha has joined the channel
Heran Ephraim (10:02:35): > @Heran Ephraim has joined the channel
Greatman Ugorji (10:18:30): > @Greatman Ugorji has joined the channel
Khadija (10:24:16): > @Khadija has joined the channel
Dimitri Meistermann (11:26:22): > @Dimitri Meistermann has joined the channel
Tolulope Ogunleye (14:03:33): > @Tolulope Ogunleye has joined the channel
Onyewuchi Esther Chikamso (15:16:35): > @Onyewuchi Esther Chikamso has joined the channel
Shashank RM (20:10:56): > @Shashank RM has joined the channel
2023-10-05
Umjovial (02:27:24): > @Umjovial has joined the channel
Bonheur (07:24:26): > @Bonheur has joined the channel
Spyke Lionel (08:15:03): > @Spyke Lionel has joined the channel
Jonathan Nutsugah (08:33:24): > @Jonathan Nutsugah has joined the channel
Aishat Adebayo (11:20:59): > @Aishat Adebayo has joined the channel
James Hennessy (11:25:03): > @James Hennessy has joined the channel
Chika Nwachukwu (11:54:57): > @Chika Nwachukwu has joined the channel
Mildred Anashie (14:11:15): > @Mildred Anashie has joined the channel
Nana Fidausi Mohammed (14:13:38): > @Nana Fidausi Mohammed has joined the channel
Anirudh (18:21:51): > @Anirudh has joined the channel
2023-10-06
Taiwo Adeyombo (03:17:28): > @Taiwo Adeyombo has joined the channel
Hodan Abdirisak (04:11:59): > @Hodan Abdirisak has joined the channel
Chioma Obioha (06:20:13): > @Chioma Obioha has joined the channel
Chisom Obidike (06:40:27): > @Chisom Obidike has joined the channel
Sara Mohammed (08:02:09): > @Sara Mohammed has joined the channel
Jul (12:46:51): > @Jul has joined the channel
Jake Fanale (15:03:44): > @Jake Fanale has joined the channel
Liliana Garmendia (15:56:04): > @Liliana Garmendia has joined the channel
Sophie Sorenson (16:02:42): > @Sophie Sorenson has joined the channel
Shriya Kamat Tarcar (17:52:52): > @Shriya Kamat Tarcar has joined the channel
2023-10-07
Adefolake Durosinmi (08:12:53): > @Adefolake Durosinmi has joined the channel
Precious Adedeji (11:15:53): > @Precious Adedeji has joined the channel
Erika Villa (11:39:58): > @Erika Villa has joined the channel
Ukaoha Chizoba (18:58:43): > @Ukaoha Chizoba has joined the channel
Clarissa Abidog (22:27:50): > @Clarissa Abidog has joined the channel
Raji Azeez (23:39:19): > @Raji Azeez has joined the channel
2023-10-08
Osaruese Faluyi (17:21:33): > @Osaruese Faluyi has joined the channel
Gloria Kaduru (19:01:29): > @Gloria Kaduru has joined the channel
Nana (19:36:23): > @Nana has joined the channel
2023-10-09
Zoran Lee (03:46:26): > @Zoran Lee has joined the channel
nyong godwill (05:40:00): > @nyong godwill has joined the channel
Israel Anguiano (06:00:06): > @Israel Anguiano has joined the channel
winnie (06:25:57): > @winnie has joined the channel
Sumbal (07:48:22): > @Sumbal has joined the channel
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 (07:54:13): > @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
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
Nokuthula (07:52:44): > @Nokuthula has joined the channel
Julian (08:36:49): > @Julian has joined the channel
Francisca_Eze (13:34:10): > @Francisca_Eze has joined the channel
2023-10-12
Shruti Pal (04:22:09): > @Shruti Pal has joined the channel
Uchechukwu Favour Ojunta (11:20:09): > @Uchechukwu Favour Ojunta has joined the channel
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
Nancy Wairimu Nyambura (09:45:05): > @Nancy Wairimu Nyambura has joined the channel
2023-10-14
Manka Velda Manjong (05:15:19): > @Manka Velda Manjong has joined the channel
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 (05:17:32): > @Boyd Tarlinton has joined the channel
Karthik Desingu (23:47:07): > @Karthik Desingu has joined the channel
2023-10-16
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
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
Kunal Bagga (04:09:58): > @Kunal Bagga has joined the channel
Chahat Bhatia (05:08:17): > @Chahat Bhatia has joined the channel
rohitsatyam102 (15:45:36): > Hi Every. Can anyone here tell if there is an R package for calculating dN/dS or pN/pS based on SNPEff annotated VCF and reference FASTA and GTF file. I am aware that there is a package called dNdScv but it is highly biased toward using annotation from Ensembl and idk how to calculate CDS start and End per transcript from GTF file.
Amanda Hiser (16:41:24): > @Amanda Hiser has left the channel
Abdullah Al Nahid (21:27:43): > @Abdullah Al Nahid has left the channel
Hervé Pagès (22:53:09) (in thread): > > idk how to calculate CDS start and End per transcript from GTF file. > Import the file as a TxDb object withGenomicFeatures::makeTxDbFromGFF(), then do (assumingtxdbis your TxDb object): > > tx <- transcripts(txdb) > > ## Add 'cds_start' and 'cds_end' metadata columns: > > tx_lens <- transcriptLengths(txdb, with.cds_len=TRUE, > with.utr5_len=TRUE, > with.utr3_len=TRUE) > # sanity check > stopifnot(identical(tx_lens$tx_id, mcols(tx)$tx_id)) > > cds_start <- start(tx) + > ifelse(strand(tx) == "+", tx_lens$utr5_len, tx_lens$utr3_len) > cds_end <- end(tx) - > ifelse(strand(tx) == "+", tx_lens$utr3_len, tx_lens$utr5_len) > > no_cds_idx <- which(tx_lens$cds_len == 0L) > cds_start[no_cds_idx] <- NA > cds_end[no_cds_idx] <- NA > > mcols(tx)$cds_start <- cds_start > mcols(tx)$cds_end <- cds_end > > This is whattxlooks like with the 2 additional metadata cols: > > > tx > GRanges object with 29173 ranges and 4 metadata columns: > seqnames ranges strand | tx_id tx_name cds_start > <Rle> <IRanges> <Rle> | <integer> <character> <integer> > [1] chr2L 7529-9484 + | 1 FBtr0300689 7680 > [2] chr2L 7529-9484 + | 2 FBtr0300690 7680 > [3] chr2L 7529-9484 + | 3 FBtr0330654 7680 > [4] chr2L 21952-24237 + | 4 FBtr0309810 <NA> > [5] chr2L 66584-71390 + | 5 FBtr0306539 67116 > ... ... ... ... . ... ... ... > [29169] chrYHet 319739-320997 - | 29169 FBtr0114244 <NA> > [29170] chrYHet 327052-328489 - | 29170 FBtr0114245 <NA> > [29171] chrUextra 523024-523048 - | 29171 FBtr0330363 <NA> > [29172] chrUextra 523024-523086 - | 29172 FBtr0330361 <NA> > [29173] chrUextra 523060-523086 - | 29173 FBtr0330362 <NA> > cds_end > <integer> > [1] 8610 > [2] 9276 > [3] 8610 > [4] <NA> > [5] 70895 > ... ... > [29169] <NA> > [29170] <NA> > [29171] <NA> > > I wish there was a simpler way though. I’ll think about adding something toGenomicFeatures. > Note that this is the kind of question you would typically ask on our support site.
2023-10-18
rohitsatyam102 (03:35:05) (in thread): > I will open and close it as an issue on TxDb by tagging you. I will test what you have recommended. I am surprised that there is no straightforward tool/R package that ingests VCFs/GVCFs, reference and GTF and provides gene level dN/dS or pN/pS ratio.
PATIENCE ONAH (11:54:07): > @PATIENCE ONAH has joined the channel
Hervé Pagès (12:41:48) (in thread): > Maybe worth asking on the support site about that. The question will get a lot more visibility.
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
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
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
Jenea Adams (09:39:43): > Hi there! We’re (BWCB) on a mission to capture >= 100 responses from computational biologists in our first CompBio Perspectives Survey. We’d like to understand perceptions of resources and opportunity from computational biologists globally. It takes just ~2 minutes to complete and you can find ithere. Feel free to also pass along to others in your network. - Attachment (Google Docs): CompBio Perspectives Survey > WHAT IS THIS SURVEY? > We’re on a mission to learn from at least 100 computational biologists’ professional experiences. > > This is a brief survey The Black Women in Computational Biology Network (BWCB) is deploying to understand the distribution of resources and support across our diverse scientist community. > > This survey should take about 2 minutes. > > WHO SHOULD TAKE THIS SURVEY? > All computational biologists are welcome to complete this survey! If you’re not already registered as a BWCB supporter, you’ll be directed to do so at the end of this survey if you wish. However, prior BWCB affiliation or knowledge is not a prerequisite for this survey. > > WHO SHOULD NOT TAKE THIS SURVEY? > :exclamation:If you’re an active BWCB member (Black women in compbio) do NOT complete this survey! Please check your email inbox for the link to your personalized survey or email mailto:info@blackowmencompbio.org|info@blackowmencompbio.org if you can’t find it :exclamation: > > HOW WILL THIS INFORMATION BE USED? > Your answers to the experience and demographic sections will be anonymized and analyzed in aggregate. This information will provide valuable insights into the challenges and opportunities faced by individuals in the computational biology field. The data will be used to inform strategies for improving inclusivity, diversity, and support within the computational biology field. > Rest assured, your responses are completely anonymous. No personally identifiable information will be linked to your survey data. > As we strive to capture the richness of experiences, we may include individual quotes in the final report. However, these quotes will be anonymized, and any identifying details will be removed to ensure confidentiality. > Your participation is instrumental in shaping the future of computational biology, and we appreciate your candid and thoughtful responses. > Feel free to share with other computational biologists in your network. > > Questions? email us mailto:info@blackwomencompbio.org|info@blackwomencompbio.org
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
Yusuf Mabel (10:27:41): > @Yusuf Mabel has joined the channel
Sunil Poudel (12:52:49): > @Sunil Poudel has joined the channel
2023-10-26
Janetta Top (10:26:37): > @Janetta Top has joined the channel
2023-10-27
Jagadeesh Puvvula (10:42:02): > @Jagadeesh Puvvula has joined the channel
Christopher Carpenter (14:47:41): > @Christopher Carpenter has joined the channel
rohitsatyam102 (18:55:49) (in thread): > @Hervé PagèsPosted this as a query to Bioconductor:https://support.bioconductor.org/p/9154904/#9154905. I haven’t tested the code you suggested as I am distracted with another project this month. But if it works I will reply to it.
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
Zoyander Street (09:46:50): > @Zoyander Street has joined the channel
2023-11-06
Andrew (18:59:00): > @Andrew has joined the channel
Sean Davis (19:22:09): - File (PNG): image.png
2023-11-07
LAR (13:28:09): > @LAR has joined the channel
Khuat Tuan Anh (20:44:38): > @Khuat Tuan Anh has joined the channel
2023-11-09
Melanie (08:02:36): > @Melanie has joined the channel
2023-11-13
Manvi Yaduvanshi (03:26:33): > @Manvi Yaduvanshi has joined the channel
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
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
Priyanka (15:22:02): > @Priyanka has joined the channel
2023-11-17
Mauricio Roza (05:16:40): > @Mauricio Roza has joined the channel
Camila Ribeiro (07:40:40): > @Camila Ribeiro has joined the channel
Eszter Ari (09:11:20): > @Eszter Ari has joined the channel
Yi Gu (09:12:23): > @Yi Gu has joined the channel
Farnoosh Babazadeh (09:16:57): > @Farnoosh Babazadeh has joined the channel
Kalle Tunström (09:32:08): > @Kalle Tunström has joined the channel
Frank Hause (09:41:49): > @Frank Hause has joined the channel
Anurag Daware (09:51:24): > @Anurag Daware has joined the channel
Pourya Naderi (BIDMC/HMS) (10:29:49): > @Pourya Naderi (BIDMC/HMS) has joined the channel
Aurelien (10:50:06): > @Aurelien has joined the channel
Isabelle Leo (12:14:54): > @Isabelle Leo has joined the channel
Juluis Foyet (12:54:51): > @Juluis Foyet has joined the channel
Nur-Taz Rahman (17:25:29): > @Nur-Taz Rahman has joined the channel
2023-11-18
Andrea Mariani (08:41:40): > @Andrea Mariani has joined the channel
Juan Henao (08:52:37): > @Juan Henao has joined the channel
Théotime Pralas (09:29:13): > @Théotime Pralas has joined the channel
karisssq (22:30:33): > @karisssq has joined the channel
2023-11-19
Thao Nguyen-Tran (01:41:18): > @Thao Nguyen-Tran has joined the channel
Emily Holland (15:32:11): > @Emily Holland has joined the channel
2023-11-20
Najla Abassi (07:49:50): > @Najla Abassi has joined the channel
2023-11-22
John Logue (09:52:53): > @John Logue has joined the channel
2023-11-23
Mohammad Omran (05:58:01): > @Mohammad Omran has joined the channel
Magda Kopczynska (09:05:05): > @Magda Kopczynska has joined the channel
2023-11-24
Jonathan Gottlieb (00:34:57): > @Jonathan Gottlieb has joined the channel
2023-11-26
Felipe (21:01:18): > @Felipe has joined the channel
2023-11-28
Daniel Aldea (07:21:40): > @Daniel Aldea has joined the channel
2023-11-29
Alice Young (16:43:00): > @Alice Young has joined the channel
2023-11-30
Aastha kapoor (02:13:49): > @Aastha kapoor has joined the channel
Junxiang Xu (16:09:39): > @Junxiang Xu has joined the channel
Vivek Nair (17:09:11): > @Vivek Nair has joined the channel
Natalia Sadkov (22:52:34): > @Natalia Sadkov has joined the channel
2023-12-01
Nick Tobin (07:08:00): > @Nick Tobin has joined the channel
Tram Nguyen (10:15:44): > @Tram Nguyen has joined the channel
Sean Davis (11:31:57): > https://datascience.cancer.gov/news-events/news/sharing-cancer-research-software-nih-wants-hear-you - Attachment (datascience.cancer.gov): Sharing Cancer Research Software? NIH Wants to Hear from You! | CBIIT > Are you working with source codes, algorithms, workflows, and other software in your cancer research? NIH wants to hear from you! Respond today to help NIH develop new best-practice guidelines.
Sean Davis (11:59:21): > https://arxiv.org/pdf/2311.16863.pdf
2023-12-02
Nicholas McKenzie (17:11:47): > @Nicholas McKenzie has joined the channel
2023-12-04
Gaby (11:09:31): > @Gaby has joined the channel
2023-12-06
Benedetta Banzi (05:25:33): > @Benedetta Banzi has joined the channel
Camila Rickli (08:25:09): > @Camila Rickli has joined the channel
2023-12-08
Mikolaj Mazurkiewicz (09:14:48): > @Mikolaj Mazurkiewicz has joined the channel
Ravza (09:39:25): > @Ravza has joined the channel
James Dalgleish (09:40:12): > @James Dalgleish has joined the channel
Eric Waltari (17:24:15): > @Eric Waltari has joined the channel
2023-12-11
Russell Bainer (15:58:42): > @Russell Bainer has joined the channel
2023-12-12
Mohammed Toufiq (11:39:23): > @Mohammed Toufiq has joined the channel
2023-12-13
Robert Tekoh (12:07:58): > @Robert Tekoh has joined the channel
Becca Hassett (13:43:30): > @Becca Hassett has joined the channel
2023-12-16
Konstantinos Benekos (13:56:19): > @Konstantinos Benekos has joined the channel
2023-12-17
Sara Mancinelli (10:20:25): > @Sara Mancinelli has joined the channel
Madhur Parihar (21:45:12): > @Madhur Parihar has joined the channel
2023-12-18
Tomasz Włodarczyk (07:38:01): > @Tomasz Włodarczyk has joined the channel
Felipe Faraguti (14:06:10): > @Felipe Faraguti has joined the channel
Daniella M Pierre (18:56:13): > @Daniella M Pierre has joined the channel
2023-12-19
Francisco Gorrostieta (08:34:15): > @Francisco Gorrostieta has joined the channel
2023-12-20
Sean Davis (10:01:19): > https://jhk0530.github.io/gemini.R/R package to use Google’s gemini via API on R.
Juan Henao (11:09:36) (in thread): > Still needs some work to compete with chatgpt API, but the time of benchmarks about AI APIs is coming
2023-12-24
Jesus de la Fuente Cedeno (17:38:31): > @Jesus de la Fuente Cedeno has joined the channel
2023-12-25
Sean Davis (17:27:34): > https://www.infoworld.com/article/3694611/8-chatgpt-tools-for-r-programming.html - Attachment (InfoWorld): 8 ChatGPT tools for R programming > The generative AI technology powering ChatGPT—OpenAI’s GPT-3.5 and GPT-4 LLMs—is available to R users, with a growing collection of packages and apps to choose from.
Cherishma Subhasa (21:21:22): > @Cherishma Subhasa has joined the channel
2023-12-27
Cindy Reichel (14:31:57): > @Cindy Reichel has joined the channel
2023-12-28
Kai (04:23:49): > @Kai has joined the channel
2024-01-04
Artür Manukyan (05:38:38): > @Artür Manukyan has joined the channel
MASHUDU (11:18:56): > @MASHUDU has joined the channel
2024-01-05
Ouso (08:09:05): > @Ouso has joined the channel
2024-01-06
Sean Davis (21:07:57): > https://www.infoworld.com/article/3712061/posit-lays-off-r-markdown-knitr-creator-yihui-xie.html - Attachment (InfoWorld): Posit lays off R Markdown, knitr creator Yihui Xie > The creator of R packages such as R Markdown, knitr, blogdown, and bookdown will continue working as a part-time contractor for Posit to maintain some of his packages.
2024-01-07
Jared Andrews (11:54:44): > Guess they’re really leaning into quarto
Janani Ravi (23:06:33) (in thread): > Shocking!:face_with_open_eyes_and_hand_over_mouth:I love yihui’s:package:s!
Itzel Espinoza (23:49:36): > @Itzel Espinoza has joined the channel
2024-01-08
Maia (16:21:17): > @Maia has joined the channel
2024-01-09
Alan O’C (05:43:48) (in thread): > bizarre
2024-01-10
vjkm (11:55:41): > @vjkm has joined the channel
Yanina Bellini Saibene (14:31:57): > @Yanina Bellini Saibene has joined the channel
Bernie Mulvey (15:01:44): > @Bernie Mulvey has joined the channel
Xin (20:44:20): > @Xin has joined the channel
2024-01-11
Saga (11:51:56): > @Saga has joined the channel
Federico Marini (11:56:54) (in thread): > and/or moving away-ish from R and going towards python/all other languages. Which is not a bad thing per se, but that was a bad way to close a relationship with an employee that gave them so much in terms of output, impact, and “all the other tiny things”
Nilesh Kumar (12:00:10): > @Nilesh Kumar has joined the channel
2024-01-12
Caleb Hallinan (12:24:44): > @Caleb Hallinan has joined the channel
Sander W. van der Laan (12:57:01): > @Sander W. van der Laan has joined the channel
Ephey (15:41:47): > @Ephey has joined the channel
2024-01-15
BirthdayBot (21:37:05): > @BirthdayBot has joined the channel
BirthdayBot (21:37:06): > [Unsupported block type: section] > > [Unsupported block type: actions]
Stevie Pederson (23:19:07) (in thread): > I’m not sure who added this but I’ve just been the victim of identity theft where my name & DOB was used without any other information. I wouldn’t encourage this in a slack forum. Can we please remove it?
Peter Hickey (23:47:58) (in thread): > seconded, can we please remove this
2024-01-16
Dan Gomez (00:38:07): > @Dan Gomez has joined the channel
Lluís Revilla (03:14:24) (in thread): > I received a DM from the bot, from there I went to configuration and removed the permission of this bot to connect to slack (https://community-bioc.slack.com/apps/A0QAZV90X-birthdaybot?did_revoke=1&tab=more_info) . I’m not sure if it will revoke it for everyone but the DM disappeared. - Attachment (Slack): BirthdayBot > Celebrate Birthdays & Anniversaries with BirthdayBot > Trusted by over 40K organizations globally. > > More Than Just Reminders: BirthdayBot is designed for remote and hybrid organizations to enr
Lluís Revilla (03:18:39): > Many thanks to whoever fixed the RSS feed of Bioconductor checks!!:raised_hands:Since the end of December I am receiving regular updates of the state of the packages:smile::partying_face:
Koen Van den Berge (04:02:43): > @Koen Van den Berge has left the channel
st liang (04:53:18): > @st liang has joined the channel
Alan O’C (05:00:04) (in thread): > Hello, I am SSNBot, and I’ve been given the best position in the company: CEO of celebrating social security numbers!
Lori Shepherd (06:45:03): > Glad to hear it’s working now
2024-01-17
Federica Gazzelloni (06:04:52): > 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
Lori Shepherd (06:41:07) (in thread): > It should be removed and we strengthen the settings of slack to ask for admin approval before allowing future apps installations
2024-01-24
Devon Kohler (08:52:16): > Dear friends and colleagues: > > 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, is now accepting applications. The application deadline is February 15, 2024. > > 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/
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
2024-01-26
Sean Davis (12:50:31): > May be of some modest interest to folks here–resources for using and guiding GenAI (like ChatGPT) in education:https://seandavi.github.io/campus-llm-kb/resources_education.html
2024-01-30
Steve Lianoglou (18:07:49): > Today I was working up an analysis where I needed to export some genomic ranges as a *.bed file … > > I thought I’d leverage thertracklayer::export.bed()function to make my life just a bit easier to do that, and when R complained on my call tolibrary(rtacklayer), I figured this is a package that needs making to help with the DIY projects around the homestead …
2024-02-02
Alan O’C (11:21:18): > Has anybody here submitted + revised an F1000 paper? We submitted a latex document originally, and in our post-review revisions are now being asked to track changes their docx with the revised version, which would take… far too long… and be completely useless, in terms of references/figures/basically everything. Is it worthwhile trying to convince them to take the sensible path?
Lena (11:29:15) (in thread): > they don’t let you track changes usinglatexdiff?
Alan O’C (11:30:08) (in thread): > The direct quote (after I said we previously submitted a latex doc) was > > Unfortunately, we do require all version submissions to be made on the word doc of the published article
Alan O’C (11:30:47) (in thread): > But thanks! I’ll suggest that as an alternative
Lena (11:31:03) (in thread): > sorry, I have no experience with them:confused:it does sound unreasonable
Alan O’C (11:33:50) (in thread): > Wondering if@Aaron Lunremembers if he went through this for v2 ofhttps://f1000research.com/articles/5-2122/v2, if so I am more impressed by this than any amount of research or software output since - Attachment (f1000research.com): F1000Research Article: A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. > Read the latest article version by Aaron T.L. Lun, Davis J. McCarthy, John C. Marioni, at F1000Research.
Aaron Lun (11:48:46) (in thread): > My submission was pure latex IIRC, no docx involved.
Kasper D. Hansen (12:03:51) (in thread): > In my understanding this has changed substantially because F1000Res internal workflow has changed
Kasper D. Hansen (12:04:36) (in thread): > It used to be all latex. I have no recent experience, but you’re not the first one mentioning word and that obviously makes it a somewhat less appealing publishing venue
Alan O’C (12:09:30) (in thread): > Thanks all. Yes, there’s no way I would’ve submitted knowing this in advance. For reproducible manuscripts it makes zero sense > > Also should mention the conversion introduced syntax errors first time around so it’s not even working as intended
2024-02-05
Courtney Zirkle (08:34:07): > @Courtney Zirkle has joined the channel
2024-02-06
Yanina Bellini Saibene (11:34:20): > rOpenSci January news!:rocket:The R-Universe now builds MacOS ARM64 binaries for use on Apple Silicon (aka M1/M2/M3) systems!:calendar:Upcoming coworking sessions: R-universe in February, dates/times/timezones in March.:package:New (or re-reviewed!) packages {GLMMcosinor}, {rangr}, {comtradr}:computer:Package news:spiral_note_pad:4 blog posts including our 2023 Code of Conduct Transparency Report:toolbox:Package Development cornerhttps://ropensci.org/blog/2024/01/25/news-january-2024/ - Attachment (ropensci.org): rOpenSci News Digest, January 2024 > MacOS ARM64 binaries for use on Apple Silicon (aka M1/M2/M3) through R-universe; coworking; new packages and package news
2024-02-07
Lluís Revilla (06:46:10): > I’m having trouble posting tosupport.bioconductor.org. I think I saw a message about it somewhere ( a channel or the mailing list) but I cannot find it or post my question but I see other people posting. Is it experiencing some problems?
Lluís Revilla (06:47:12) (in thread): > I either get a problem with the tags (sometimes it tells me that I need to place a comma to create a tag, other’s just nothing) or a problem with the text of my question (without any information about what is wrong).
Vince Carey (07:19:46) (in thread): > Sorry@Lluís Revillawe have made some changes to deal with spam and there are going to be some bumps. Will be back in touch.
Vince Carey (07:25:24) (in thread): > have you tried clearing browser cache and perhaps using incognito mode? i had no problem with a new post with fresh auth via google.
Lori Shepherd (07:36:30) (in thread): > its not a spam issue its a special character issue most likely if you are copying and pasting text from terminal. we lightened the constraints except for a validity check on ascii characters; we haven’t been able to narrow down what browswer or OS is the root cause but that is likely the cause. Also tags are required there are generic tags and all the packages show up as suggestions but we do require a tag. The default can be Bioconductor
Lluís Revilla (07:40:56) (in thread): > I tried different browsers but it might be a character issue. A warning or message of what is wrong would be helpful to know what to fix… > The problem with tags was not that I didn’t use them but that the tags I added aren’t allowed somehow, even if they appear in the menu when I start writing it.
Lluís Revilla (07:42:04) (in thread): > My OS is ubuntu 22.04 on Firefox 122.0.1 or on Chromium Version 121.0.6167.139 (Official Build) snap (64-bit)
Lori Shepherd (07:44:25) (in thread): > You should still be able to use any free form tag you want but you still need to add at least one tag suggested/approved - if it was not having to do with a package, “Bioconductor” is the catch all, there is also “release” , “devel” , I think we added things like “conferences” , etc…
Lluís Revilla (07:54:19) (in thread): > I desist to post the question here. I upgraded the computer, restarted, cleaned the cache and used several browsers the tags are now valid (at the third try) but no clue what/how to fix the text. > For some more context I copied the output of reprex…
2024-02-11
Siraj Farhan (07:54:50): > @Siraj Farhan has joined the channel
2024-02-13
Maria Doyle (08:25:05) (in thread): > @Lluís Revillawere you able to post at support site? I’m having a similar issue trying to post the message in screenshot below on behalf of CoC committee. It won’t post and I can’t see what the issue is. I’m on Mac and have tried Chrome and Firefox (freshly installed). Can anyone tell what may be wrong? - File (PNG): Screenshot 2024-02-13 at 13.22.36.png
Lori Shepherd (08:27:22) (in thread): > can you send me your text so I can try to reproduce
Maria Doyle (08:28:50) (in thread): > yes below, thanks for taking a look > > Hello Bioconductor Community > > > > It is important to reflect often on the importance of upholding [Bioconductor values][1], 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 the [Code of Conduct committee][2] if you consider that some situation doesn’t reflect these values. > > > > Thank you for your dedication to the Bioconductor community. > > > > > > [1]:https://bioconductor.github.io/bioc_coc_multilingual/en-US.html[2]:https://bioconductor.github.io/bioc_coc_multilingual/
Lori Shepherd (08:31:25) (in thread): > Its the issue with special characters — when I paste into a text editor, the apostrophe for Let’s and doesn’t ends up as non ascii characters. And we have a validity check that checks for this.
Lori Shepherd (08:31:43) (in thread): > Let�@~Ys and doesn�@~Yt
Lori Shepherd (08:39:30) (in thread): > so i can look into a solution – were you copying and pasting that from somewhere else or typing directly into the support site block?
Maria Doyle (08:41:24) (in thread): > thaks for find that! I copied and pasted from the message I was sent in Slack
Lluís Revilla (10:48:20) (in thread): > I was not able to post to the support site (or Biostars), there is another question in the support site with the same problem. It might be an encoding issue but it would be nice if it would report that to the user so that we can fix and post
Lori Shepherd (11:20:12) (in thread): > yes looking into if its possible to have an informative message when the encoding validation is triggered
Jenea Adams (13:51:17): > Hello all, I have two announcements fromBWCB: > * On February 28th, 2024 we are hosting a public townhall centering community-building around exploring opportunities for allyship in the computational biology community. We will begin by sharing some insights from our survey results capturing the experiences of various communities within the computational biology field. Many of you here participated in that survey, and we appreciate your input! We welcome you to join us for a conversation that will create space to engage critically together on what we’re learning. > > * RSVP here:https://www.blackwomencompbio.org/event-details/townhall-on-opportunities-for-allyship-in-computational-biology > > * We have just released applications for our 2024grant programs. If you work with colleagues or trainees who could benefit from becoming a member applying, I appreciate you sharing this with them. Applications close on March 1, 2024. - Attachment (BlackWomenCompBio): Townhall on Opportunities for Allyship in Computational Biology | BlackWomenCompBio > All in the STEM community are welcome to join us for flash talks an open discussion on the the current state of opportunities for allyship in the field of computational biology. We will also introduce the BWCB Connect program, an initiative to spark connection and networking for all in the field. - File (PNG): 2.png
Hervé Pagès (19:27:44) (in thread): > This apostrophe is UTF-8. UTF-8 characters are very common, especially in R output (e.g. fancy quotes). Any chance the support site can accept them? The pre-rendering accepts them so it’s kind of unexpected that when I press “Save” my answer (which looked fine in the preview) just disappears and seems to be lost forever (I might have spent a lot of time writing it:sweat:).
2024-02-14
Jamie Whitehouse (04:59:53): > @Jamie Whitehouse has joined the channel
Louis Le Nézet (11:04:08): > Hi, > I would like to invite someone I know to the bioconductor Slack. > How can I do that ?
Alan O’C (11:06:40) (in thread): > Clicking the workspace name gives me a dropdown - File (PNG): Screenshot from 2024-02-14 16-06-14.png
Louis Le Nézet (11:08:07) (in thread): > Thanks a lot for the quick answer !
Patrizia Piotti (12:26:00): > @Patrizia Piotti has joined the channel
2024-02-15
David Rach (09:55:37): > What is your favorite/most-useful R:books:book? I am on a reading binge this year, currently on the last couple chapters of Advanced R, and looking for additional book suggestions:book::worm:
Jacques SERIZAY (13:07:05) (in thread): > Not as well organized as Hadley’s books, butComputational Genomics with Rfrom Altuna Akalin covers most aspects of bioinfo analysis for bulk assays. It has not been updated for quite some time though, and it doesn’t cover at all the tidyomics principles:scream:. - Attachment (compgenomr.github.io): Computational Genomics with R > A guide to computationa genomics using R. The book covers fundemental topics with practical examples for an interdisciplinery audience
Jacques SERIZAY (13:16:16) (in thread): > While this thread is open, any suggestion forpythonpackage development? Package dev approaches in python are a lot more diverse than in R. Any suggestion for a good, clear guide for package dev (not coding)?
Martin Morgan (15:51:03) (in thread): > Since you’re at the end of r4ds, I’d suggest ‘The Art of R Programming’ from Norman Matloff. Most of the book is kind of an anti-r4ds, emphasizing an understanding of the language foundations. Chapters 9 (object-oriented programming) and 13+ (debugging, performance, interfacing to other languages, parallel) are pretty unique (‘dated’ if looked at now, ‘visionary’ if at the time of writing). Maybe especially interesting (and challenging ‘exercises for the reader’) are when Matloff says that something is one way (forloops scale quadratically, so are slow for big data,1:100000allocates a lot of memory) but nowforloops are not particularly slow, and1:100000actually occupies very little space. What changed inR? What lessons can we as (advanced)Rprogrammers learn?
Lluís Revilla (18:11:50) (in thread): > For python package development I recommend to create an R package and wrap it with rpy2:wink:. For R you can read everything on the Big Book of R:https://www.bigbookofr.com/I think there are more than 200 books. - Attachment (bigbookofr.com): Big Book of R > 400+ Free R programming books
Jayaram Kancherla (18:32:44) (in thread): > @Jacques SERIZAYwe put together a guide on how we develop packages in biocpy -https://github.com/BiocPy/developer_guide
2024-02-19
Christine Hou (09:51:28): > @Christine Hou has joined the channel
2024-02-20
francesco patane (04:19:36): > @francesco patane has joined the channel
2024-02-23
Chris Magnano (14:23:45): > @Chris Magnano has joined the channel
Sangmin Park (16:50:11): > @Sangmin Park has joined the channel
2024-02-25
Ritika Gupta (12:26:35): > @Ritika Gupta has joined the channel
2024-02-26
Ramón Fallon (10:35:21): > @Ramón Fallon has joined the channel
2024-02-27
Eleni Liapi (01:03:58): > @Eleni Liapi has joined the channel
leila yesufu (17:29:09): > @leila yesufu has joined the channel
Bukola Agbabiaka (17:29:42): > @Bukola Agbabiaka has joined the channel
Adrian Wanner (18:22:10): > @Adrian Wanner has joined the channel
2024-02-28
Desongu Samuel Kwaghtaver (03:34:37): > @Desongu Samuel Kwaghtaver has joined the channel
taofeeqah bakare (18:22:38): > @taofeeqah bakare has joined the channel
2024-03-01
Ye Meng (04:03:49): > @Ye Meng has joined the channel
Amit Mandal (09:01:03): > @Amit Mandal has joined the channel
2024-03-04
Zohar M Steinberg (04:48:08): > @Zohar M Steinberg has joined the channel
Charlotte Lees (04:49:25): > @Charlotte Lees has joined the channel
Maria F Pudjohartono (04:50:04): > @Maria F Pudjohartono has joined the channel
Anusha Aman (04:50:47): > @Anusha Aman has joined the channel
Ana Dopico (05:02:52): > @Ana Dopico has joined the channel
Vilhelm Suksi (09:23:44): > @Vilhelm Suksi has joined the channel
Isi Irabor (11:09:25): > @Isi Irabor has joined the channel
Linda Uchenwoke (11:18:37): > @Linda Uchenwoke has joined the channel
Adedoja Isaac (11:38:11): > @Adedoja Isaac has joined the channel
samuel alison (11:41:34): > @samuel alison has joined the channel
Melodee Okigbo (11:46:24): > @Melodee Okigbo has joined the channel
George Opondi (11:51:23): > @George Opondi has joined the channel
Ayodeji Ogunbiyi (11:54:08): > @Ayodeji Ogunbiyi has joined the channel
Victoria (Burah) Poromon (12:05:33): > @Victoria (Burah) Poromon has joined the channel
Ayodeji Ogunbiyi (12:06:49): > Hi everyone. Please I need some tips for my contribution to the Bioconductor project with Outreachy (I actually don’t know what to do:sob:)
Sneha Singh (12:07:26): > @Sneha Singh has joined the channel
Chioma Onyido (12:15:08) (in thread): > Hi@Ayodeji Ogunbiyi. Please join the bugsigdb channel for steps on how to make contributions, the community is quite active. > Also your mentors are there to answer any questions you have.:slightly_smiling_face:
Chinedu Ihedioha (12:16:14): > @Chinedu Ihedioha has joined the channel
Fausat Olasubomi Abiola (12:20:40): > @Fausat Olasubomi Abiola has joined the channel
Precious Orakwe (12:26:20): > @Precious Orakwe has joined the channel
Naomi Ibe (12:37:10): > @Naomi Ibe has joined the channel
Adeola Adeniyi (12:37:46): > @Adeola Adeniyi has joined the channel
vishal (12:38:52): > @vishal has joined the channel
Oluwatomisin Omojokun (12:45:33): > @Oluwatomisin Omojokun has joined the channel
Mildred Anashie (12:46:59) (in thread): > Welcome@Ayodeji Ogunbiyi
Jenny (12:52:53): > @Jenny has joined the channel
Jenny (12:58:17): > good day everyone, my name is Jennifer and I am currently learning Java. > I recently got approved to join the outreachy program, I need a mentor to take me through the contribution stage of the program. > Please can anyone help me out?
Jenny (12:59:32) (in thread): > #bugsigdb
Chioma Onyido (12:59:51): > Hi,:wave:this message is for allOutreachy applicants, > Welcome to Bioconductor, Please join the#bugsigdb**** channel**for steps on how to make contributions to the Microbiome Study Curation project, the community is quite active. > > Also your mentors are there to answer any questions you have.:slightly_smiling_face:Goodluck!
Nana (13:09:46): > @Nana has joined the channel
Nekembe Boris (13:09:48): > @Nekembe Boris has joined the channel
Rahila-me (13:18:30): > @Rahila-me has joined the channel
Eniola Adebayo (13:21:15): > @Eniola Adebayo has joined the channel
Adeyemi Favour Adetayo (13:35:15): > @Adeyemi Favour Adetayo has joined the channel
Juliet Ogbu (13:57:20): > @Juliet Ogbu has joined the channel
Oluwaseyifunmi Taiwo (14:15:56): > @Oluwaseyifunmi Taiwo has joined the channel
Habiba Saad (14:16:38): > @Habiba Saad has joined the channel
Sakshi Varshney (14:23:26): > @Sakshi Varshney has joined the channel
Ananya Tomar (15:00:46): > @Ananya Tomar has joined the channel
Bolanle Wahab (15:03:10): > @Bolanle Wahab has joined the channel
Peace Daniel (15:11:41): > @Peace Daniel has joined the channel
Okache Johnpaul (16:22:16): > @Okache Johnpaul has joined the channel
Oluwatosin Adesola (16:33:30): > @Oluwatosin Adesola has joined the channel
Nwuguru Chidiebere (16:38:29): > @Nwuguru Chidiebere has joined the channel
Leenaa Al-Amin (17:21:05): > @Leenaa Al-Amin has joined the channel
Ruth Bamgbose (17:31:36): > @Ruth Bamgbose has joined the channel
Habibat Sakiru (17:57:56): > @Habibat Sakiru has joined the channel
EBERE ADEKOGBE (19:59:19): > @EBERE ADEKOGBE has joined the channel
Alex Eze (20:16:32): > @Alex Eze has joined the channel
Mahalakshmi Sachin (21:04:48): > @Mahalakshmi Sachin has joined the channel
Faith Ifeoluwa Alexander (21:13:30): > @Faith Ifeoluwa Alexander has joined the channel
Amal Hirole (22:13:01): > @Amal Hirole has joined the channel
Manisha Nair (23:09:50): > @Manisha Nair has joined the channel
Angella Namuli (23:16:23): > @Angella Namuli has joined the channel
2024-03-05
Roderick Momin (00:37:29): > @Roderick Momin has joined the channel
Tanya Dwivedi (00:38:18): > @Tanya Dwivedi has joined the channel
Arnab Mukherjee (00:39:08): > @Arnab Mukherjee has joined the channel
Nanlop Blessing Dafwat (00:50:04): > @Nanlop Blessing Dafwat has joined the channel
Samreen Aftab (01:30:06): > @Samreen Aftab has joined the channel
levis Ngigi (01:31:07): > @levis Ngigi has joined the channel
Anshuman Moharana (01:35:05): > @Anshuman Moharana has joined the channel
Blessing Laweh (01:47:38): > @Blessing Laweh has joined the channel
Rodney Ighalo (01:57:54): > @Rodney Ighalo has joined the channel
Vamika Mendiratta (02:06:37): > @Vamika Mendiratta has joined the channel
Erembe Arobo (02:21:03): > @Erembe Arobo has joined the channel
Ogwos (02:59:12): > @Ogwos has joined the channel
Gayathri S (03:04:21): > @Gayathri S has joined the channel
Abiodun Oladejo (03:14:36): > @Abiodun Oladejo has joined the channel
Behroze Aslam (03:33:57): > @Behroze Aslam has joined the channel
Zaynab Aderonke Ogunnubi (03:56:37): > @Zaynab Aderonke Ogunnubi has joined the channel
Nils Eling (04:04:18): > @Nils Eling has joined the channel
Emmanuel Doreen (04:17:28): > @Emmanuel Doreen has joined the channel
abdulwasiu maryam (04:18:48): > @abdulwasiu maryam has joined the channel
Charity Mbabazi (04:43:57): > @Charity Mbabazi has joined the channel
Winifred Young (04:50:12): > @Winifred Young has joined the channel
Amanda Adoyi (05:10:36): > @Amanda Adoyi has joined the channel
Charlie George (05:22:01): > Hi everyone, I’ve been involved in a projectwww.x-net.bioto research interdisciplinary career research barriers in the UK and propose recommendations to address them, much of our research focused on those at the intersection of biomedical science and computation/statistics such as yourselves. We’ve just launched our series of 13 recommendations to UK funders which hope to support and insentise a more collaborative and supportive research culture for all. You can see the tweetorial summarising the efforts herehttps://x.com/CGATist/status/1764926690126401926?s=20please retweet so it reaches as many colleagues as possible. Many thanks:slightly_smiling_face: - Attachment (X (formerly Twitter)): Chris Ponting :blue_heart: (@CGATist) on X > NEWS:tada: Today X-Net launched recommendations to @UKRI_News to tackle barriers for #InterdisciplinaryResearch careers > :point_down:we explain how these were developed with researchers, public & industry > https://t.co/Plrs5pyTIZ > Collaboration among @mrc_hgu @MRC_WIMM @mrcppu @KavliOxford 1/12
Aishat Ijiyode (05:23:24): > @Aishat Ijiyode has joined the channel
Sandra Dindi (05:32:45): > @Sandra Dindi has joined the channel
Temi (05:35:01): > @Temi has joined the channel
Valentina Buoro (05:36:51): > @Valentina Buoro has joined the channel
Hambugger (05:47:26): > @Hambugger has joined the channel
Kum Eugene (05:52:30): > @Kum Eugene has joined the channel
Barakat Akinsiku (06:01:50): > @Barakat Akinsiku has joined the channel
Muqtadirat Yussuff (06:27:21): > @Muqtadirat Yussuff has joined the channel
Iman Ngwepe-Ntshibida (06:54:00): > @Iman Ngwepe-Ntshibida has joined the channel
Ifeyinwa Ohondu (07:06:11): > @Ifeyinwa Ohondu has joined the channel
Emem Eduoku (07:06:11): > @Emem Eduoku has joined the channel
Rimjhim Mittal (07:32:01): > @Rimjhim Mittal has joined the channel
Blessing Peters (07:34:16): > @Blessing Peters has joined the channel
Amarachi Lewachi (07:36:04): > @Amarachi Lewachi has joined the channel
Ima-obong (Aimah) (07:36:52): > @Ima-obong (Aimah) has joined the channel
Semilore Atolagbe (07:53:00): > @Semilore Atolagbe has joined the channel
Abiola Salako (07:58:19): > @Abiola Salako has joined the channel
Adenike Oladimeji-Kasumu (08:03:48): > @Adenike Oladimeji-Kasumu has joined the channel
Arpita Kumbhar (08:08:49): > @Arpita Kumbhar has joined the channel
Suru Olaitan (08:11:02): > @Suru Olaitan has joined the channel
Onyeahialam Gracious (08:43:11): > @Onyeahialam Gracious has joined the channel
PinRathod (08:58:06): > @PinRathod has joined the channel
ESE EIGBADON (09:06:01): > @ESE EIGBADON has joined the channel
Chinazaekpere Ibeh (09:13:52): > @Chinazaekpere Ibeh has joined the channel
Bolarinwa Abosede Julianah (09:22:20): > @Bolarinwa Abosede Julianah has joined the channel
Azhar Ismagulova (10:02:33): > @Azhar Ismagulova has joined the channel
Shreya Badchariya (10:12:18): > @Shreya Badchariya has joined the channel
Giancarlo Castellano (11:16:46): > @Giancarlo Castellano has joined the channel
Deborah Oyawale (11:44:50): > @Deborah Oyawale has joined the channel
Amaka Joyce (11:54:37): > @Amaka Joyce has joined the channel
Divyanshi Singh (12:38:34): > @Divyanshi Singh has joined the channel
Blessing Anumba (12:44:03): > @Blessing Anumba has joined the channel
Prapti Jaduvanshi (12:54:49): > @Prapti Jaduvanshi has joined the channel
Ojoachele Onuh (13:46:45): > @Ojoachele Onuh has joined the channel
Latifat (14:16:47): > @Latifat has joined the channel
Blessing Ene Anyebe (14:20:42): > @Blessing Ene Anyebe has joined the channel
Busingye lillian (14:27:28): > @Busingye lillian has joined the channel
Regina Rukeme Agaren (14:57:57): > @Regina Rukeme Agaren has joined the channel
Semango Nicholas (14:58:40): > @Semango Nicholas has joined the channel
Idiat Alli (15:43:12): > @Idiat Alli has joined the channel
Ikeh Darlington Ikeh (16:10:52): > @Ikeh Darlington Ikeh has joined the channel
Success Ologunsua (16:23:52): > @Success Ologunsua has joined the channel
Chiemelie Carita Ndibe (16:28:29): > @Chiemelie Carita Ndibe has joined the channel
Chioma Agu (16:53:53): > @Chioma Agu has joined the channel
Benedicta Imelda (17:23:59): > @Benedicta Imelda has joined the channel
Khadijah Kamorudeen (17:41:11): > @Khadijah Kamorudeen has joined the channel
Collins Carshy (17:48:26): > @Collins Carshy has joined the channel
Ibukun Hassan (18:01:15): > @Ibukun Hassan has joined the channel
Vivian O (18:44:02): > @Vivian O has joined the channel
Shedrack Sunday (20:30:12): > @Shedrack Sunday has joined the channel
Diamond Eyamu (21:21:23): > @Diamond Eyamu has joined the channel
许春江 (22:11:49): > @许春江 has joined the channel
CE61_Karishma Mandal (22:32:54): > @CE61_Karishma Mandal has joined the channel
Caitlin Page (23:58:27): > @Caitlin Page has joined the channel
2024-03-06
Ishita Pathak (00:03:08): > @Ishita Pathak has joined the channel
Siva (01:24:15): > @Siva has joined the channel
Rukayat Salaudeen (02:47:58): > @Rukayat Salaudeen has joined the channel
Michael Adekanye (02:56:46): > @Michael Adekanye has joined the channel
Kapil (02:57:11): > @Kapil has joined the channel
Ufomba Justina (03:00:53): > @Ufomba Justina has joined the channel
Manideep (03:09:53): > @Manideep has joined the channel
vanessa kamunya (03:24:35): > @vanessa kamunya has joined the channel
Neelam Mahraj (04:42:05): > @Neelam Mahraj has joined the channel
Adegboye Rukayat (04:53:16): > @Adegboye Rukayat has joined the channel
Dolapo Mosuro (05:23:15): > @Dolapo Mosuro has joined the channel
sahir (05:28:40): > @sahir has joined the channel
Nancywrites (06:02:34): > @Nancywrites has joined the channel
Elsie Dickson (06:15:26): > @Elsie Dickson has joined the channel
Mojisayo Awolesi (06:21:23): > @Mojisayo Awolesi has joined the channel
Raihanat Adewuyi (07:09:46): > @Raihanat Adewuyi has joined the channel
Medina Adeniran (07:15:41): > @Medina Adeniran has joined the channel
Faith Omolara Adegoke (07:16:30): > @Faith Omolara Adegoke has joined the channel
Omoleye Jimoh (07:19:49): > @Omoleye Jimoh has joined the channel
Paseda Modupe oluwaseun (07:21:08): > @Paseda Modupe oluwaseun has joined the channel
Janine Makorre (07:42:26): > @Janine Makorre has joined the channel
Grace Paul (08:03:33): > @Grace Paul has joined the channel
Kaycee Pyaar (08:11:17): > @Kaycee Pyaar has joined the channel
Ikechukwu Chibuike (08:56:40): > @Ikechukwu Chibuike has joined the channel
104_Khushnuma Sadaf_ECE-AI2 (08:59:46): > @104_Khushnuma Sadaf_ECE-AI2 has joined the channel
Esther Nelson (09:12:58): > @Esther Nelson has joined the channel
Prakriti Maurya (09:30:51): > @Prakriti Maurya has joined the channel
Tooba Amjad (10:36:49): > @Tooba Amjad has joined the channel
Adejoke Ogunyinka (10:40:07): > @Adejoke Ogunyinka has joined the channel
Preethi grace Manthena (11:05:58): > @Preethi grace Manthena has joined the channel
Oluwatoyosi Victoria Olanrewaju (11:37:13): > @Oluwatoyosi Victoria Olanrewaju has joined the channel
Okhuomon Ajayi (12:06:30): > @Okhuomon Ajayi has joined the channel
Afnan Asif (12:09:14): > @Afnan Asif has joined the channel
ayesha khan (12:11:36): > @ayesha khan has joined the channel
Temitayo Ogidan (12:12:23): > @Temitayo Ogidan has joined the channel
eneje promise (13:09:11): > @eneje promise has joined the channel
Precious Orakwe (13:09:32): > please can someone guide me on how to start contributing
Aleru Divine (13:11:45) (in thread): > Hi@Precious Orakweplease join the#bugsigdbchannel
Marcel Ramos Pérez (13:12:20) (in thread): > Hi Precious, you can join the#outreachychannel for more guidance. Also of relevance:https://community-bioc.slack.com/archives/C35G93GJH/p1709746183127649 - Attachment: Attachment > Welcome Outreachy applicants! Please join #bugsigdb for 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 #general alerts the entire community so it’s better to do introductions on #outreachy. Thank you and good luck!
Anshika Arora (13:38:51): > @Anshika Arora has joined the channel
Aditi Bhadoriya (14:09:01): > @Aditi Bhadoriya has joined the channel
Hamidat Mohammed (14:12:32): > @Hamidat Mohammed has joined the channel
Millicent Adzepa (14:14:53): > @Millicent Adzepa has joined the channel
Abbah Divine (14:32:52): > @Abbah Divine has joined the channel
idiaru Angela (14:33:31): > @idiaru Angela has joined the channel
Devashri (15:11:38): > @Devashri has joined the channel
NWAKAEGO VINCENT (15:52:42): > @NWAKAEGO VINCENT has joined the channel
Perpetual Meninwa (16:14:03): > @Perpetual Meninwa has joined the channel
Osayuki Raymond Okhuarobo (16:23:00): > @Osayuki Raymond Okhuarobo has joined the channel
Blessing Williams (18:27:42): > @Blessing Williams has joined the channel
Praise Agbetuyi (20:05:53): > @Praise Agbetuyi has joined the channel
consolation obazee (22:00:55): > @consolation obazee has joined the channel
Manya Sachdeva (22:52:14): > @Manya Sachdeva has joined the channel
2024-03-07
Precious Chilaka (00:51:37): > @Precious Chilaka has joined the channel
ADAEZE SIMON (01:55:50): > @ADAEZE SIMON has joined the channel
Nitya Singhal (02:08:25): > @Nitya Singhal has joined the channel
Chimdimma Nwachukwu (02:54:59): > @Chimdimma Nwachukwu has joined the channel
Ifenna Muonagolum (03:56:36): > @Ifenna Muonagolum has joined the channel
dehbeie donatus (04:05:32): > @dehbeie donatus has joined the channel
Peace Daniel (04:26:48): > Hi@Mildred Anashiechecking on you:woman-raising-hand:
Mildred Anashie (04:29:12) (in thread): > Hi@Peace DanielThank you:blush:I’mpresent:woman-raising-hand::grin:
Peace Daniel (04:30:46) (in thread): > Great,wasn’tseeing much from you earlier
Mildred Anashie (04:33:02) (in thread): > Oh > Thank you for observing that:hugging_face:
Serah Gituto (06:09:21): > @Serah Gituto has joined the channel
Mehak Sharma (07:21:51): > @Mehak Sharma has joined the channel
Sandeep Indramohan (09:48:59): > @Sandeep Indramohan has joined the channel
Harshita Srivastava (10:21:54): > @Harshita Srivastava has joined the channel
Binita Dhakal (11:25:06): > @Binita Dhakal has joined the channel
wizdom Chris (11:44:28): > @wizdom Chris has joined the channel
Akinbode Mariam (13:12:05): > @Akinbode Mariam has joined the channel
acha rhaah (13:45:15): > @acha rhaah has joined the channel
Brian Till (13:57:25): > @Brian Till has joined the channel
Gurjot Kaur (13:58:49): > @Gurjot Kaur has joined the channel
Chris Awoke (14:06:38): > @Chris Awoke has joined the channel
fetlework gubena arage (14:42:48): > @fetlework gubena arage has joined the channel
Flourish Ralph (15:34:05): > @Flourish Ralph has joined the channel
anushka singh (15:38:59): > @anushka singh has joined the channel
Paavni (22:49:26): > @Paavni has joined the channel
2024-03-08
DataWithPrecision (00:08:43): > @DataWithPrecision has joined the channel
Matthew Idungafa (00:09:15): > @Matthew Idungafa has joined the channel
Blessing Mba (01:05:21): > @Blessing Mba has joined the channel
Derrick Nathan (02:03:48): > @Derrick Nathan has joined the channel
Glorious Katushabe (02:14:56): > @Glorious Katushabe has joined the channel
Komal Verma (04:02:52): > @Komal Verma has joined the channel
Ajayi Mercy (05:29:58): > @Ajayi Mercy has joined the channel
Druscilla Nakanwagi (05:48:16): > @Druscilla Nakanwagi has joined the channel
Sidra Khan (07:27:57): > @Sidra Khan has joined the channel
Riya Jain (09:37:58): > @Riya Jain has joined the channel
Modinat Ganiyu (11:10:01): > @Modinat Ganiyu has joined the channel
Cindy Purity (12:36:23): > @Cindy Purity has joined the channel
sneha goel (12:46:36): > @sneha goel has joined the channel
Welile Dlamini (15:34:58): > @Welile Dlamini has joined the channel
Omeyimi Longe (17:24:54): > @Omeyimi Longe has joined the channel
Evelyn Mary Attah (17:33:48): > @Evelyn Mary Attah has joined the channel
2024-03-09
Farheen Gul (00:33:05): > @Farheen Gul has joined the channel
Joy Gold (01:50:12): > @Joy Gold has joined the channel
Jolade Okunlade (03:56:53): > @Jolade Okunlade has joined the channel
Sahana K (05:39:55): > @Sahana K has joined the channel
Mariam Hammed Gambina (07:55:06): > @Mariam Hammed Gambina has joined the channel
Navya Verma (08:22:26): > @Navya Verma has joined the channel
Hamza Haji (13:21:32): > @Hamza Haji has joined the channel
Aananditaa (13:23:28): > @Aananditaa has joined the channel
Josué Sandoval (15:50:25): > @Josué Sandoval has joined the channel
Dorcas Oladele (20:18:15): > @Dorcas Oladele has joined the channel
2024-03-10
ANUKRATI CHATURVEDI (01:57:06): > @ANUKRATI CHATURVEDI has joined the channel
Chen Jackson (07:08:19): > @Chen Jackson has joined the channel
Irene Ighalo (11:42:42): > @Irene Ighalo has joined the channel
Bhavya Pandey (11:53:12): > @Bhavya Pandey has joined the channel
Bukola Salawu (12:20:49): > @Bukola Salawu has joined the channel
Arnav Puri (14:03:39): > @Arnav Puri has joined the channel
Gonza Gertrude (15:09:06): > @Gonza Gertrude has joined the channel
Juliana Oluwatobi (17:42:37): > @Juliana Oluwatobi has joined the channel
Taiye Michaels (20:57:45): > @Taiye Michaels has joined the channel
2024-03-11
Kelechi Madubuko (06:35:44): > @Kelechi Madubuko has joined the channel
Isha Kashyap (10:17:15): > @Isha Kashyap has joined the channel
Lawrence Franklin Chukwudalu (11:48:39): > @Lawrence Franklin Chukwudalu has joined the channel
Mikhail Spivakov (12:36:49): > @Mikhail Spivakov has joined the channel
Sandeep Pillai (17:44:58): > @Sandeep Pillai has joined the channel
2024-03-12
subhiksha sundaram (00:10:45): > @subhiksha sundaram has joined the channel
Saasha Gupta (03:52:15): > @Saasha Gupta has joined the channel
Munirat (07:44:43): > @Munirat has joined the channel
White Kiky (08:05:19): > @White Kiky has joined the channel
Mkpouto Shedrack (08:14:21): > @Mkpouto Shedrack has joined the channel
Guan Gui (22:14:58): > @Guan Gui has joined the channel
2024-03-13
assel (02:20:32): > @assel has joined the channel
Raony Guimaraes Corrêa Do Carmo Lisboa Cardenas (10:49:34): > @Raony Guimaraes Corrêa Do Carmo Lisboa Cardenas has joined the channel
Jesus Gonzalez (10:57:16): > @Jesus Gonzalez has joined the channel
MizOgelicious (14:13:57): > @MizOgelicious has joined the channel
2024-03-14
Vinay Mannam (10:31:19): > @Vinay Mannam has joined the channel
RGentleman (13:41:11): > @RGentleman has left the channel
2024-03-15
Tung Trinh (02:22:57): > @Tung Trinh has joined the channel
Mindy Kim Graham (18:05:59): > @Mindy Kim Graham has joined the channel
2024-03-17
Taiwo Akinlagun (06:18:32): > @Taiwo Akinlagun has joined the channel
Frank Lloyd Jr. (20:14:45): > @Frank Lloyd Jr. has joined the channel
2024-03-18
Iman (00:44:42): > @Iman has joined the channel
Ajayi Mercy (05:26:10): > @Ajayi Mercy has joined the channel
Hew (05:45:18): > @Hew has joined the channel
Srilakshmi (05:55:38): > @Srilakshmi has joined the channel
Edward Knaven (11:26:14): > @Edward Knaven has joined the channel
Kayla Interdonato (12:21:52): > @Kayla Interdonato has joined the channel
2024-03-19
Nikita Sen (02:36:16): > @Nikita Sen has joined the channel
Shambhavi Sinha (08:41:34): > @Shambhavi Sinha has joined the channel
Jasmine Daly (12:51:33): > @Jasmine Daly has joined the channel
Tara Ternes (13:05:45): > @Tara Ternes has joined the channel
2024-03-20
Taylor Witte (12:58:53): > @Taylor Witte has joined the channel
Cristiana J Meuret (18:03:27): > @Cristiana J Meuret has joined the channel
2024-03-22
Ava Jensen (09:40:14): > @Ava Jensen has joined the channel
Ying Xiong (10:32:57): > @Ying Xiong has joined the channel
Julie White (10:38:24): > @Julie White has joined the channel
Gordon Zheng (12:12:56): > @Gordon Zheng has joined the channel
Daniel Mullen (14:36:07): > @Daniel Mullen has joined the channel
Kelsi Watkins (18:17:43): > @Kelsi Watkins has joined the channel
2024-03-25
Sneha Suman (03:55:34): > @Sneha Suman has joined the channel
Frederik Ziebell (06:25:17): > @Frederik Ziebell has joined the channel
manasvita (21:02:16): > @manasvita has joined the channel
2024-03-26
Hana H. (05:20:53): > @Hana H. has joined the channel
Eve Gardner (13:02:32): > @Eve Gardner has joined the channel
Sara m.morsy (14:25:58): > @Sara m.morsy has joined the channel
Melissa Aidée (20:08:50): > @Melissa Aidée has joined the channel
2024-03-27
abhich (05:38:58): > @abhich has joined the channel
HÀ KHANG ĐẠT (10:42:06): > @HÀ KHANG ĐẠT has joined the channel
Crystal Musser (16:59:45): > @Crystal Musser has joined the channel
Ivan Osinnii (19:10:47): > @Ivan Osinnii has joined the channel
2024-03-28
Mohamed Sharif (09:46:03): > @Mohamed Sharif has joined the channel
Jonas Schuck (14:18:34): > @Jonas Schuck has joined the channel
2024-03-29
Yanina Bellini Saibene (14:49:05): > rOpenSci March news! #RStats:handshake:Leadership changes! Read Karthik farewell post, and Noam post about his new role:globe_with_meridians:Dev Guide 0.9.0: Multilingual Now! And Better:microphone:Yani Interview with Code for Thought podcast:date:Upcoming coworking sessions: Quarto in April with Pao Corrales, “Meet our new Executive Director” in May.:notes:New packages {nuts}, {quadkeyr}, {weatherOz}:package:Package news:spiral_note_pad:Many blog posts:wave:Calls for contributions:hammer_and_wrench:Package Development cornerhttps://ropensci.org/blog/2024/03/29/ropensci-news-march-2024/ - Attachment (ropensci.org): rOpenSci News Digest, March 2024 > Leadership changes at rOpenSci, multilingual dev guide, new packages and package news
2024-04-01
Saumya Yadav (10:06:36): > @Saumya Yadav has joined the channel
2024-04-03
Matúš Kalaš (07:38:23): > @Matúš Kalaš has joined the channel
Lu Zhou (07:40:32): > @Lu Zhou has joined the channel
Marco Rheinnecker (17:57:29): > @Marco Rheinnecker has joined the channel
2024-04-04
Hervé Ménager (04:14:14): > @Hervé Ménager has joined the channel
Alexandru Mizeranschi (09:34:18): > @Alexandru Mizeranschi has joined the channel
Christian Ona (12:22:40): > @Christian Ona has joined the channel
Anqi Zhu (17:37:39): > @Anqi Zhu has joined the channel
2024-04-05
Delaney Baratka (12:21:37): > @Delaney Baratka has joined the channel
2024-04-08
Mariangela Santorsola (11:48:05): > @Mariangela Santorsola has joined the channel
2024-04-09
Amal Boukteb (11:00:44): > @Amal Boukteb has joined the channel
Ludwig Lautenbacher (12:22:44): > @Ludwig Lautenbacher has joined the channel
Raymond Lesiyon (16:47:35): > @Raymond Lesiyon has joined the channel
2024-04-10
Mercedes Guerrero (04:34:00): > @Mercedes Guerrero has joined the channel
Margherita (11:15:09): > @Margherita has joined the channel
2024-04-11
Elton (10:02:16): > @Elton has joined the channel
Chris Chatham (12:56:22): > @Chris Chatham has joined the channel
2024-04-12
Felipe ten Caten (13:22:59): > @Felipe ten Caten has joined the channel
Yanina Bellini Saibene (14:50:10): > From a Researcher (Ashley Juavinett): > > We are conducting a study to understand professional experiences in computing within the context of biology.:computer::herb::microscope:If you are in a biology-related field AND use some amount of computing (e.g. writing code) in your current role, indicate interest in a 1-hour interview with $25 compensation here:https://forms.gle/YXozM6Wx2ZwmruVp8The study is open undergrad/grad students, postdocs, faculty, & folks in industry. > > Please share!:pray: - Attachment (Google Docs): Sign-Up Form: Computing Paths in Biology Interview > Thank you for your interest in participating in an interview to help us learn more about computing paths in biology! Please fill out the following information to indicate your interest. If selected to participate, Austin Zuckerman (Ph.D. student working with Ashley Juavinett) will reach out to you to officially schedule a time and date! The interview will last approximately one hour and you will receive a $25 gift card for participating.
2024-04-13
Yanina Bellini Saibene (14:49:06): > I have the pleasure of chatting at the Sustain Podcast:slightly_smiling_face: > > Yani Bellini Saibene explores funding challenges, sustainability in volunteer models, diversity in open source, addressing global disparities, and community empowerment. > Listen athttps://podcast.sustainoss.org/228If you like it, please share it!:pray:Here are the links: > * LinkedIn > * Discourse > * Mastodon > * Bluesky - Attachment (Sustain): Yani Bellini Saibene on better scientific coding communities > Yani explores funding challenges, sustainability in volunteer models, diversity in open source, addressing global disparities, and community empowerment.
Boyao Zhang (15:30:48): > @Boyao Zhang has joined the channel
Ankitha Ramaiyer (20:47:04): > @Ankitha Ramaiyer has joined the channel
2024-04-16
Siraj Farhan (15:19:03): > Hey all! > > I’m the founder ofSynthia Labs, excited to share our AI agent (like ChatGPT but for Bioinformatics) we’ve been developing toaccelerate bioinformatics tool development. It features capabilities likedirect editing & executing of scripts(Python, R, bash),installing packages,handling large datasetsandintegrating custom Docker imagesCheck out our3-min demohere:https://www.loom.com/share/e94083ed1c354dc1abd32e46c68c3624We’re offeringearly access! Please fill out thisquick formto register your interest:https://forms.gle/b2rV4AnPyGRACMVB6Thanks for helping us advance bioinformatics! - Attachment (Loom): Synthia | An AI Scientist - Attachment (Google Docs): AI in Bioinformatics > Your input will help us understand the current use of language models in bioinformatics and identify the key challenges faced by the community. > Thank you for your valuable insights and support in advancing AI in bioinformatics! > The Synthia Labs Team
2024-04-17
Rachel Ferina (13:56:15): > @Rachel Ferina has joined the channel
2024-04-18
Philipp Sergeev (03:00:21): > @Philipp Sergeev has joined the channel
Weston Elison (15:06:12): > @Weston Elison has joined the channel
Suhn Rhie (16:09:27): > @Suhn Rhie has joined the channel
Rachel Ingraham (18:16:09): > @Rachel Ingraham has joined the channel
2024-04-19
Yixiao Wang (02:36:43): > @Yixiao Wang has joined the channel
S L (07:57:12): > @S L has joined the channel
Terry Noblin (13:32:18): > @Terry Noblin has joined the channel
2024-04-20
Nsobundu Chukwudalu (07:04:19): > @Nsobundu Chukwudalu has joined the channel
2024-04-21
Ziru Chen (21:58:18): > @Ziru Chen has joined the channel
2024-04-22
Yanina Bellini Saibene (08:31:23): > rOpenSci April news!:sparkles::rocket:R-Universe docs get a boost from Google Season of Docs:wave:Help us put together the rOpenSci Community Call calendar for the year!:mega:Our social media campaigns about packages:spiral_calendar_pad:Upcoming coworking sessions:******“Meet our new Executive Director”******in May, TBD in June.:bulb:New packages {baRulho}, {fellingdater}:package:Package news:spiral_note_pad:Blog posts:female-technologist:Calls for contributions:wrench:Package Development cornerhttps://ropensci.org/blog/2024/04/22/ropensci-news-april-2024/ - Attachment (ropensci.org): rOpenSci News Digest, April 2024 > R-universe docs thanks to GSOD, community calls, new packages and package news
Wanling Kratzman (11:24:08): > @Wanling Kratzman has joined the channel
2024-04-23
Emil Funk (07:20:43): > @Emil Funk has joined the channel
2024-04-24
Izabela Mamede (08:26:36): > Hello Bioconductor community, > I’m interested in exploring RNA modifications from nanopore data. Could anyone recommend tools and packages specifically designed for this purpose? Are any inside BioConductor? Additionally, I’m curious if there are any streamlined workflows available for this analysis, or if any research teams are actively working on developing them. Any insights or recommendations would be greatly appreciated. Thank you!
Lance Zhang (09:35:09): > @Lance Zhang has joined the channel
Changqing (19:52:12) (in thread): > NanoMethViz?
2024-04-25
Nan Deng (01:20:57): > @Nan Deng has joined the channel
Izabela Mamede (07:08:49) (in thread): > When I used this for the last time it worked perfect for DNA data, not so much for RNA (good for m6a not m5c etc), and only for methylation. But thanks for the suggestion, I will check if they made any new releases.
AbuZar Khan (07:52:13): > @AbuZar Khan has joined the channel
Peter Hickey (21:07:37) (in thread): > @Shian Su^^^
Shian Su (21:24:33) (in thread): > This is something I’d like to support, but it’s a bit difficult without test data. In theory NanoMethViz works for any kind of modification mapped to a reference. In practice the plots are calibrated for m5c in DNA. I think Nanopore’s ModKit is probably your best bet for some exploratory analysis. > > If you could describe any specific issues you’re encountering I am happy to try and help. I’m personally working on some m6a C.elegans DNA data right now and the data is simultaneously too dense (too many A sites compared to CG motifs I’ve calibrated to) and too sparse (the prevalence of methylation is generally <5%).
2024-04-26
Joel Nitta (01:19:35): > @Joel Nitta has joined the channel
Martin Emons (06:41:51): > @Martin Emons has joined the channel
Izabela Mamede (08:30:17) (in thread): > I am trying ModKit right now! For now I have only one test data of RNA of chikungunya infection in human cells, the ideia would be to see what i can get from it and if it is worth it to sequence more samples/other infections. I really appreciate your suggestions, I am having a similar problem, since NanoMethViz is not fully calibrated for other mods/ or RNA.
2024-04-28
Danielle Callan (08:18:00): > @Danielle Callan has joined the channel
2024-04-29
Jacqui Thompson (09:00:20): > @Jacqui Thompson has joined the channel
Samuel Gunz (09:32:18): > @Samuel Gunz has joined the channel
Jinlong Zhang (22:25:44): > @Jinlong Zhang has joined the channel
2024-04-30
Lambda Moses (03:47:26): > https://youtu.be/S9Do2p4PwtE?feature=shared - Attachment (YouTube): re:bass
Carmine Gelormini (16:28:29): > @Carmine Gelormini has joined the channel
2024-05-01
Lori Shepherd (15:30:19): > 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
Mark Christie (07:56:46): > @Mark Christie has joined the channel
Joe Knecht (18:36:09): > @Joe Knecht has joined the channel
2024-05-03
Zhenyuan Zhou (00:48:55): > @Zhenyuan Zhou has joined the channel
Shivaji maddhesia (01:14:34): > @Shivaji maddhesia has joined the channel
Heshmat A. Borhani (04:16:39): > @Heshmat A. Borhani has joined the channel
Shun (11:23:52): > @Shun has joined the channel
Jessica Valiarovski (12:13:46): > @Jessica Valiarovski has joined the channel
2024-05-04
Florian Tran (12:51:16): > @Florian Tran has joined the channel
Allen Wang (12:59:09): > @Allen Wang has joined the channel
Larry Adeyanju (12:59:50): > @Larry Adeyanju has joined the channel
Carlos Enrique Balcazar Lopez (18:26:03): > @Carlos Enrique Balcazar Lopez has joined the channel
Andy Liu (21:24:17): > @Andy Liu has joined the channel
2024-05-05
Ifra (05:07:08): > @Ifra has joined the channel
Michal Kolář (14:53:47): > @Michal Kolář has joined the channel
2024-05-06
JOAN EMANUEL VILLAMIL SILVA M.D (01:34:14): > @JOAN EMANUEL VILLAMIL SILVA M.D has joined the channel
Matt Stone (13:36:47): > @Matt Stone has joined the channel
Diana Tavares Ferreira (20:49:32): > @Diana Tavares Ferreira has joined the channel
2024-05-07
Cyril Dalmasso (04:55:12): > @Cyril Dalmasso has joined the channel
Rebecca Rees (06:29:27): > @Rebecca Rees has joined the channel
Henri Z (06:51:33): > @Henri Z has joined the channel
Carlo Pecoraro (12:08:07): > @Carlo Pecoraro has joined the channel
Erick Navarro (12:26:28): > @Erick Navarro has joined the channel
2024-05-08
Johannes Mayer (11:46:58): > @Johannes Mayer has joined the channel
Princess Rodriguez (13:10:42): > @Princess Rodriguez has joined the channel
2024-05-09
Philippe Laffont (07:34:39): > @Philippe Laffont has joined the channel
Johnny Cruz (14:10:42): > @Johnny Cruz has joined the channel
2024-05-10
Hugh Warden (10:41:33): > @Hugh Warden has joined the channel
2024-05-11
Chiraz Mehemmai (12:21:03): > @Chiraz Mehemmai has joined the channel
2024-05-14
Kayleigh Ann (19:26:23): > @Kayleigh Ann has joined the channel
Zhe Ren (23:56:53): > @Zhe Ren has joined the channel
2024-05-15
Elisa Gómez de Lope (07:37:58): > @Elisa Gómez de Lope has joined the channel
Niklas Beumer (08:00:44): > @Niklas Beumer has joined the channel
Karrar (09:02:24): > @Karrar has joined the channel
Robin Bram (11:29:13): > @Robin Bram has joined the channel
2024-05-16
Ryan Corfixsen (14:37:21): > @Ryan Corfixsen has joined the channel
2024-05-17
Kelvin Lew (02:40:32): > @Kelvin Lew has joined the channel
2024-05-20
Rachel A (05:00:45): > @Rachel A has joined the channel
Lin Luo (05:01:23): > @Lin Luo has joined the channel
2024-05-21
Christopher Yogodzinski (09:19:14): > @Christopher Yogodzinski has joined the channel
2024-05-22
Stevie Pederson (10:12:26) (in thread): > OMG!!! Their system literally removes all line breaks from your code!!! Their solution is to ask you to re-submit each code chunk as an individual, standalone Word document so they can see the formatting, despite having all of the code correctly formatted (& tested) in the original submission. Thanks for warning me@Alan O’Cand I very much wish I’d listened. Although I must admit, no-one in their right mind would’ve imagined a system that does what they’re doing
Will Hore-Lacy (20:06:10): > @Will Hore-Lacy has joined the channel
Louise (20:06:10): > @Louise has joined the channel
2024-05-23
Ely Seraidarian (03:32:20): > @Ely Seraidarian has joined the channel
shishr (04:21:25): > @shishr has joined the channel
Retu Haikonen (05:07:57): > @Retu Haikonen has joined the channel
Dominik Rabsch (05:57:12): > @Dominik Rabsch has joined the channel
Dag Stockstad (07:08:48): > @Dag Stockstad has joined the channel
Kelvin Muithya (09:55:20): > @Kelvin Muithya has joined the channel
Lori Shepherd (14:21:13): > 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
Yanina Bellini Saibene (08:43:42): > rOpenSci May news!:sparkles::label:rOpenSci in the Research Organization Registry:star-struck:What are the rOpenSci Champions up to now?:calendar:Upcoming coworking sessions: “R in the Wild” in June, “Git and Github” in July:deciduous_tree:New package {dendroNetwork}:package:Package news:spiral_note_pad:Communication Tips for your Open-Source Project:wave:Calls for contributions:toolbox:Package Development cornerhttps://ropensci.org/blog/2024/05/24/ropensci-news-may-2024/ - Attachment (ropensci.org): rOpenSci News Digest, May 2024 > Champions program update, metadat, new packages and package news
2024-05-27
何璇 (03:26:58): > @何璇 has joined the channel
Nicolai Karcher (08:31:14): > @Nicolai Karcher has joined the channel
2024-05-28
Jenny Drnevich (11:28:01): > For anyone with experience with NIH’s biosketch format - the instructions explicitly say we can cite research products like educational curricula or software, but “Use of hyperlinks and URLs to cite these items is not allowed.”. How in the world are we supposed to cite things like this that solely exist on line and are not published?! Even more confusing is the link they give to the FAQ about how to cite interim research projects in the proper format says to use a DOI and gives a URL in their example! I thought people here would likely have software that fits in this category and could share how they cite it in NIH’s biosketch.https://grants.nih.gov/grants/how-to-apply-application-guide/forms-h/general/g.240-r&r-seniorkey-person-profile-(expanded)-form.htm#Instructions
Marouen Ben Guebila (11:37:06) (in thread): > Hey Jenny, I think it is ok to use URLs in the new Biosketch format. Hyperlinks however are not allowed because they may be used to trace back reviewers. (https://netzoo.github.iovs https://netzoo.gitub.io)
Jenny Drnevich (11:51:48) (in thread): > I could see why they don’t want embedded hyperlinks but the instructions also say no URLs. This is the first time my biosketch has gotten flagged and I’ve had them in for years, so I wondered if this was a new requirement?
Marouen Ben Guebila (12:03:42) (in thread): > Oh this seems new then, I’ve gotten away with URLs without hyperlinks in the past, so they may be enforcing it now.
Frederick Tan (12:04:42) (in thread): > Comments in this post suggest there is some enforcement variability between institutes > * https://www.nia.nih.gov/research/blog/2021/04/missing-links-why-nih-doesnt-allow-hyperlinks-grant-applications
Jenny Drnevich (12:07:08) (in thread): > Thanks, Marouen and Fred!
Jenny Drnevich (12:14:24) (in thread): > And of course there is conflicting information from NIH about this! “Douse hyperlinks in relevant citations and publications included in biosketches and publication list attachments”https://nexus.od.nih.gov/all/2019/05/13/the-dos-donts-of-hyperlinks-in-grant-applications/ - Attachment (nexus.od.nih.gov): The Do’s & Don’ts of Hyperlinks in Grant Applications > It would be hard to read more than a couple paragraphs on the internet these days without encountering a hyperlink to a definition or additional clarifying information. Hyperlinks are everywhere. So, why does NIH limit the use of hyperlinks in grant applications?
2024-05-29
Ezekiel Ekanem (16:02:35): > @Ezekiel Ekanem has joined the channel
2024-05-30
Aedin Culhane (04:42:29) (in thread): > Bioconductor packages all have DOI.So can we just provide the doi but not hyperlink
Jiya Chaudhary (06:05:15): > @Jiya Chaudhary has joined the channel
Jenny Drnevich (08:22:13) (in thread): > Update: turns out my Grants & Contracts just required me to take out embedded links but plain text to the URL was fine. Also, following NIH’s rabbit hole led me to this guide they have on how to properly cite websites:https://www.ncbi.nlm.nih.gov/books/NBK7274/
Joshua Hamilton (14:53:34): > @Joshua Hamilton has joined the channel
Marco Blanchette (16:05:47): > @Marco Blanchette has joined the channel
2024-05-31
Bradley Woolf (11:11:20): > @Bradley Woolf has joined the channel
2024-06-02
Muskan Singh (03:21:42): > @Muskan Singh has joined the channel
Sathish Kumar (13:26:59): > @Sathish Kumar has joined the channel
2024-06-03
Anthony Christidis (14:47:57): > @Anthony Christidis has joined the channel
2024-06-04
David Michaels (10:06:11): > @David Michaels has joined the channel
Hossein Valipour Kahrood (21:39:41): > @Hossein Valipour Kahrood has joined the channel
2024-06-05
Adrian Hirt (05:45:31): > @Adrian Hirt has joined the channel
Egor Semenchenko (10:43:01): > @Egor Semenchenko has joined the channel
贺宇 (23:53:22): > @贺宇 has joined the channel
2024-06-07
David Mayer (09:41:07): > @David Mayer has joined the channel
Latrice Landry (13:47:57): > @Latrice Landry has joined the channel
2024-06-09
Saejeong Park (10:21:20): > @Saejeong Park has joined the channel
2024-06-10
luyao wang (08:30:14): > @luyao wang has joined the channel
Harshitha (09:33:04): > @Harshitha has joined the channel
Giovanni Palla (11:17:29): > :star2:Join Us at the Scverse Conference 2024!:star2::spiral_calendar_pad:Dates: September 10-12, 2024:round_pushpin:Location:Munich, Germany:memo:Details & Registration:Scverse Conference 2024Scverse is hosting its first conference in Munich. It will hosts talks, poster sessions and workshop on open source software for single cell and spatial genomics.Speakers: > * Fabian Theis- Helmholtz Munich > * Alex Wolf- Lamin > * Angela Pisco- Insitro > * Rob Patro- University of Maryland > * Christina Leslie- MSKCC > * Maria Brbic- EPFL > :earth_africa:Travel Grants Available: Need support to attend? We’re offering travel grants. Don’t let anything hold you back from this opportunity!:rocket:Call for Participation: We’re still accepting abstract submissions and workshop proposals! Contribute your ideas and engage with peers and leaders in the field.:link:Submit Your Ideas:Abstracts & WorkshopsMark your calendars and get ready for an enlightening experience. We’re excited to see you there!:loudspeaker:Spread the Word: Help us make Scverse Conference 2024 a milestone event by sharing this announcement with your colleagues and across your networks! > > #scverse #CompBio #OpenSource
William Hung (11:50:11): > @William Hung has joined the channel
Justin Landis (13:15:49): > @Justin Landis has joined the channel
Jared Andrews (17:19:52): > TheKIDS24 BioHackathonsignup is now OPEN!:date:Event Date:September 4-6, 2024:round_pushpin:Location:St. Jude Children’s Research Hospital - Memphis, TN:computer:Participation:In-person and Virtual > Join us for three days of intensive coding full of innovation, collaboration, and fun! Whether you’re attending in person or joining us virtually, this is your chance to make a difference and showcase your skills. Don’t miss out on this incredible opportunity to be part of something impactful.Register now and secure your spot!Register HereIf you have any questions please emailbiohackathon@stjude.orgWe can’t wait to see you there!:rocket:I am involved in planning this event at St. Jude, and we’re looking for enthusiastic folks to take a look. Come help build something cool and useful, see what St. Jude is about, and learn some new skills! Feel free to post here or DM me with any questions. > > Students and trainees are very welcome, so if anyone in your group/institution may be interested, please pass it along! Limited travel awards will be available.
2024-06-11
Laurent Gatto (03:28:09) (in thread): > Hi Giovanni - you mention in your post that travel grants are available. Are these advertised on the conference page? I can’t find them.
Saurabh Verma (17:20:58): > @Saurabh Verma has joined the channel
Vince Carey (22:22:47): - File (PNG): image.png
2024-06-12
Giovanni Palla (09:02:59) (in thread): > hi@Laurent Gattowe just added info here:https://scverse.org/conference2024/infounder Travel Grant
Kailasadatta Boggaram (12:11:13): > @Kailasadatta Boggaram has joined the channel
Liliana (19:05:00): > @Liliana has joined the channel
2024-06-13
Shinji Tokunaga (00:00:53): > @Shinji Tokunaga has joined the channel
JACOB A DE JESUS-CANDELARIO (06:19:54): > @JACOB A DE JESUS-CANDELARIO has joined the channel
Ekaterina Akimova (07:20:14): > @Ekaterina Akimova has joined the channel
Jane Lyon (09:30:59): > @Jane Lyon has joined the channel
Jian He (18:46:49): > @Jian He has joined the channel
2024-06-17
Ke Yang (11:49:19): > @Ke Yang has joined the channel
2024-06-20
Pablo Lopez-Colon (13:39:11): > @Pablo Lopez-Colon has joined the channel
2024-06-21
Jamie Whitehouse (07:06:17): > @Jamie Whitehouse has left the channel
Yanina Bellini Saibene (12:59:17): > rOpenSci June news!:sparkles:#RStats:handshake:rOpenSci takes over maintenance of the {goodpractice} package:spiral_note_pad:rOpenSci at CZI Open Science 2024:calendar:The rOpenSci team & community at upcoming events:calendar:Upcoming coworking sessions: “Git and Github” in July, ” Building your first R package” in August:ocean:New packages {goodpractice}, {mregions2}, {rOPTRAM}:package:Package news:spiral_note_pad:Blog posts:wave:Calls for contributions:toolbox:Package Development cornerhttps://ropensci.org/blog/2024/06/21/ropensci-news-june-2024/ - Attachment (ropensci.org): rOpenSci News Digest, June 2024 > New goodpractice maintainer, CZI meeting report, rOpenSci community at upcoming events, new packages and package news
Rachael (13:26:59): > @Rachael has joined the channel
2024-06-24
Manoj M Wagle (09:29:53): > @Manoj M Wagle has joined the channel
Sydney Grant (11:54:54): > @Sydney Grant has joined the channel
2024-06-25
Lluís Revilla (09:29:01): > Hello:wave:! Is anyone from the community going to useR!2024 in Salzburg? I’ll be there and I’ll have time to meet with other Bioconductor people
2024-06-26
Bianka Berki (05:46:03): > @Bianka Berki has joined the channel
Danielle Callan (11:48:47): > I’d like to share something I’m excited about: > > TheMicrobiomeDBteam recently developed a suite of R packages to accompany the website (if you aren’t familiar, check it out!). It supports the same types of analyses (alpha diversity, beta diversity, differential abundance, correlations, etc) as the site, via an API thats designed to be user-friendly and question-centric. Its built on a custom data container that is flexible enough to support a wide variety of data, while performant enough to also serve as the backbone of the site. You can import your own data from TreeSummarizedExperiments (and thanks to the great folks building mia, various other formats as well) or work with our curated data. > > Find more details here:https://microbiomedb.github.io/MicrobiomeDB/We’d love feedback! So don’t hesitate to reach out. There is aDiscord Server, as well, if anyone were interested.
2024-06-27
Ahmed Salah Hassan (09:56:51): > @Ahmed Salah Hassan has joined the channel
Brian Richards (11:34:32): > @Brian Richards has joined the channel
Sean Davis (17:17:25): > https://github.com/posit-dev/positron
2024-06-28
Jonathan Bobak (06:12:37): > @Jonathan Bobak has joined the channel
Marta Rusmini (06:30:32): > @Marta Rusmini has joined the channel
Jacques SERIZAY (10:43:19) (in thread): > That’s the successor of Rstudio, is that right? Integration with VScode features might be interesting:face_with_monocle:
Sean Davis (11:09:32) (in thread): > I guess it might play out that way. Yes, VSCode is a fantastic framework on which to build.
Kiefer (14:51:44): > @Kiefer has joined the channel
2024-06-30
Clara Tejido (12:49:04): > @Clara Tejido has joined the channel
Nicolas Peterson (13:07:47): > @Nicolas Peterson has joined the channel
2024-07-01
Steffen Neumann (07:05:25): > Hi, we have a not-really BioC question, more R basics: We develop a package which depends on another one. Duh. > The dependency ishttps://github.com/PecanProject/pecan/tree/develop/modules/rtmbut also onhttps://pecanproject.r-universe.dev/PEcAnRTMOur github actions fail because it can’t resolve this package. > We tried Remotes: PEcAnRTM=github::PecanProject/pecan/modules/rtm/. (without the trailing dot you get a 404, now we getdeps::.: ! pkgdepends resolution error for deps::..Note that the directory name != package name). > While you can install.packages('PEcAnRTM', repos = '[https://pecanproject.r-universe.dev](https://pecanproject.r-universe.dev)'), theDESCRIPTION/Additional_repositoriesis only supported in R CMD check, not when actually installing.
Kerry (10:06:23) (in thread): > this is github package issue 404 issue with the credentials. > usethis::create_github_token() > > I tried to install the PEcAnRTM and failed to compile, so I think there may be an issue with the package
Kerry (10:13:59) (in thread): > devtools::install_github(“PecanProject/pecan”, subdir=“modules/rtm”, ref=‘develop’,auth_token = “addintokenhere”) > > however, I’m getting the zero-exit status as I’m missing two dependencies ERROR: dependencies ‘PEcAn.logger’, ‘PEcAn.assim.batch’ are not available for package ‘PEcAnRTM’
Joyce Qiu (10:55:43): > @Joyce Qiu has joined the channel
Steffen Neumann (11:03:30) (in thread): > Thanks for trying ! We are currently exploring whether we can add their CRAN-like repo to the Github actions. Will keep you posted…
2024-07-02
Fiona Roche (06:25:32): > @Fiona Roche has joined the channel
Tiago Nardi (10:33:31): > @Tiago Nardi has joined the channel
Diána Pejtsik (10:53:36): > @Diána Pejtsik has joined the channel
Lluís Revilla (12:08:07) (in thread): > You can add the additional repository in repos in bothBiocManager::installandinstall.packages I think there is a way to add it in the r-lib actions too
Steffen Neumann (12:09:36) (in thread): > Thanks for the tip! These calls were not the problem, GitHub actions was. Resolved now
Constanza Perez (18:53:22): > @Constanza Perez has joined the channel
2024-07-03
Neel Shetty (13:52:51): > @Neel Shetty has joined the channel
2024-07-04
Sounkou Mahamane Toure (15:24:51): > @Sounkou Mahamane Toure has joined the channel
2024-07-05
Antonin Thiébaut (04:36:43): > @Antonin Thiébaut has joined the channel
Vanessa Gonzalez Ribao (05:31:09): > @Vanessa Gonzalez Ribao has joined the channel
Rüçhan Ekren (06:49:49): > @Rüçhan Ekren has joined the channel
Dominik Burri (09:09:10): > @Dominik Burri has joined the channel
Reinhold Koch (11:22:56): > @Reinhold Koch has joined the channel
2024-07-08
Sean Davis (09:19:34): > https://github.com/seandavi/awesome-single-cellstill looking for updates. There is no Bioconductor section–would love to see that contribution!
Hervé Pagès (11:00:55) (in thread): > The URL to the OSCA book has changed a couple of years ago. The new URL ishttps://bioconductor.org/books/release/OSCA/ - Attachment (bioconductor.org): Orchestrating Single-Cell Analysis with Bioconductor > Or: how I learned to stop worrying and love the t-SNEs.
Sean Davis (11:09:59) (in thread): > Thanks,@Hervé Pagès. Fixed.
Lorna Morris (11:25:56): > @Lorna Morris has joined the channel
2024-07-09
Xiangfei Xie (11:19:05): > @Xiangfei Xie has joined the channel
Mukta (12:22:10): > @Mukta has joined the channel
Vilhelm Suksi (18:25:58): > @Vilhelm Suksi has joined the channel
Sean Davis (19:55:40): > https://www.nationalacademies.org/our-work/sustaining-community-engagement-in-genomics-research-a-workshop - Attachment (nationalacademies.org): Sustaining Community Engagement in Genomics Research A Workshop | National Academies > Learn more from the National Academies of Sciences, Engineering, and Medicine
2024-07-10
Miha (04:54:05): > @Miha has joined the channel
Angie Aguirre-Tobar (13:04:54): > @Angie Aguirre-Tobar has joined the channel
Axel (20:55:05): > @Axel has joined the channel
Adam (21:33:47): > @Adam has joined the channel
2024-07-11
Hothri Moka (06:00:52): > @Hothri Moka has joined the channel
2024-07-12
Camila Pereira Perico (15:05:43): > @Camila Pereira Perico has joined the channel
2024-07-14
Sudipta Hazra (17:40:28): > @Sudipta Hazra has joined the channel
2024-07-15
Cate Ouma (16:48:07): > @Cate Ouma has joined the channel
2024-07-16
Hiru (06:53:40): > @Hiru has joined the channel
Tom Schwarzl (10:14:11): > @Tom Schwarzl has joined the channel
2024-07-17
천유경 (02:25:46): > @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
Peter(Yizhou) Huang (10:51:03): > @Peter(Yizhou) Huang has joined the channel
Mercedeh Movassagh (13:51:23): > @Mercedeh Movassagh has joined the channel
2024-07-21
sofie shankar (05:43:52): > @sofie shankar has joined the channel
2024-07-22
Meghana GC (09:49:37): > @Meghana GC has joined the channel
2024-07-23
Jamie Park (11:56:09): > @Jamie Park has joined the channel
Tuulu (15:11:42): > @Tuulu has joined the channel
Shaurita (17:37:55): > @Shaurita has joined the channel
2024-07-24
Gigi (08:39:46): > @Gigi has joined the channel
Albert Sylvester (09:20:26): > @Albert Sylvester has joined the channel
Kavya Ayalasomayajula (12:46:04): > @Kavya Ayalasomayajula has joined the channel
Nicholas Lai (16:43:14): > @Nicholas Lai has joined the channel
2024-07-25
Gaurav (13:14:05): > @Gaurav has joined the channel
Pascal Belleau (14:07:31): > @Pascal Belleau has joined the channel
Anh Nguyet Vu (15:12:10): > @Anh Nguyet Vu has joined the channel
Jorge Kageyama (16:34:28): > @Jorge Kageyama has joined the channel
Michael (21:46:37): > @Michael has joined the channel
2024-07-26
Nicholas Lai (11:14:44): > Hi! I emailedhubs@bioconductor.orgbut haven’t heard back yet about adding my team’s dataset to ExperimentHub, is there a point person I can reach out to to follow up?
Lori Shepherd (11:51:26): > please be patient most of the team is limited this week due to the annual conference
Vipul Singhal (11:53:20): > @Vipul Singhal has joined the channel
Ziyin Zhao (13:27:48): > @Ziyin Zhao has joined the channel
Jenea Adams (13:29:14): > Join BWCB’s next town hall event on August 14th! > > A Community Discussion On Evaluating the Alignment of Training with the Field’s Diverse Needs. All are welcome and RSVPs are open now:slightly_smiling_face:https://www.blackwomencompbio.org/event-details/town-hall-future-proofing-compbio - Attachment (BlackWomenCompBio): Town Hall: Future-Proofing CompBio | BlackWomenCompBio > A Community Discussion On Evaluating the Alignment of Trainings with the Field’s Diverse Needs.
Taerim Lee (16:11:15): > @Taerim Lee has joined the channel
Patricia Schnepp (16:43:58): > @Patricia Schnepp has joined the channel
Hiba Ben Aribi (17:01:38): > @Hiba Ben Aribi has joined the channel
My Nguyen (19:43:28): > @My Nguyen has joined the channel
Qiwen Octavia Huang (19:47:25): > @Qiwen Octavia Huang has joined the channel
2024-07-27
Iaroslav (14:03:55): > @Iaroslav has joined the channel
Anh Nguyet Vu (20:09:37): > @Anh Nguyet Vu has joined the channel
2024-07-29
Priscila Calle (15:58:39): > @Priscila Calle has joined the channel
2024-07-30
Li-Fang Yeo (02:42:29): > @Li-Fang Yeo has joined the channel
C. Mirzayi (please do not tag this account) (14:25:50): > This is the first time I’ve seen R referenced in a novel before (Exordia by Seth Dickinson). - File (PNG): image.png
Qiyi Yu (23:26:47): > @Qiyi Yu has joined the channel
2024-07-31
Jorg Doku (15:57:34): > @Jorg Doku has joined the channel
Zahraa W Alsafwani (17:01:39): > @Zahraa W Alsafwani has joined the channel
daohuymanh (23:57:18): > @daohuymanh has joined the channel
2024-08-01
Matt H (08:49:53): > @Matt H has joined the channel
Michael Lawrence (14:31:24) (in thread): > I have certainly cursed R more than thrice. Chaya did not try hard enough.
Gabriel Grajeda (15:58:11): > @Gabriel Grajeda has joined the channel
2024-08-02
Ilya Kabanov (07:30:58): > @Ilya Kabanov has joined the channel
meral hakam (08:47:04): > @meral hakam has joined the channel
2024-08-04
Adeshile Oluwatosin (10:02:12): > @Adeshile Oluwatosin has joined the channel
sunnyday (14:55:27): > @sunnyday has joined the channel
2024-08-06
WJ P (01:18:02): > @WJ P has joined the channel
Anton Ribbenstedt (09:26:00): > @Anton Ribbenstedt has joined the channel
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
Cedric Dewas (04:41:33): > @Cedric Dewas has joined the channel
Varun Kumar Kesherwani (10:01:52): > @Varun Kumar Kesherwani has joined the channel
Hayden Spence (12:15:43): > @Hayden Spence has joined the channel
Frédéric Bertrand (16:52:31): > @Frédéric Bertrand has joined the channel
2024-08-09
Irene Rigato (05:07:12): > @Irene Rigato has joined the channel
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
Headtlove E. Dadzie (10:50:55): > @Headtlove E. Dadzie has joined the channel
Natalie Whitaker-Allen (10:59:09): > @Natalie Whitaker-Allen has joined the channel
Gobi Dasu (15:01:45): > @Gobi Dasu has joined the channel
Arash Bagherabadi (19:57:01): > @Arash Bagherabadi has joined the channel
2024-08-14
xueyao (11:38:26): > @xueyao has joined the channel
Kylie Bemis (22:39:15): > @Kylie Bemis has left the channel
2024-08-16
Camila Pereira Perico (19:13:20): > Hello bioconductor community. > I have a question regarding the versions submitted to bioconductor. > I submitted a version of my package via git. Shortly afterwards, I added some changes and submitted a new version. > The old version had a ‘check’ error and I received an e-mail informing me of the error. Unfortunately, I can’t upload the fixes for the old version and I keep getting emails informing me of the error. > > Would it be worth contacting bioconductor to remove the old version? Could you help me?
Lori Shepherd (19:52:46) (in thread): > You should be able to update with the newer version of the code to Bioconductor. If you have trouble pushing to git we can assist. Keep in mind for changes to take place you need a valid version bump. Also keep in mind there are two active branches at all times, release and devel. Is it possible you only updated one branch and are still getting emails for the other branch?
Camila Pereira Perico (20:01:44) (in thread): > Hi Lori, thank you very much for your reply. > I don’t know if this is the problem. The package is rSWeeP. The release version is 1.16.0. The faulty version is 1.16.1 and the latest version (devel) that is working correctly is 1.17.2. > I’m just worried that I’m still getting notifications about this old version, because version 1.17.2 has been checked and is OK. > Do I need to take any action?
Lori Shepherd (20:35:56) (in thread): > You should push changes to fix release to the RELEASE_3_19 branch and bump to 1.16.2.
Camila Pereira Perico (20:49:38) (in thread): > Got it. Thank you so much for your help Lori.
Lori Shepherd (20:51:15) (in thread): > Let us know if you have any other questions or concerns.:grin:
2024-08-17
ari-ds_8bioc (14:10:50): > @ari-ds_8bioc has joined the channel
2024-08-19
Angelique Trusler (09:01:09): > @Angelique Trusler has joined the channel
Rema Gesaka (09:35:05): > @Rema Gesaka has joined the channel
Leah Everhart (18:31:38): > @Leah Everhart has joined the channel
2024-08-20
Aaishah Mahadeo (06:51:47): > @Aaishah Mahadeo has joined the channel
Alisha Mahadeo (06:56:49): > @Alisha Mahadeo has joined the channel
Josefina Suils (08:34:22): > @Josefina Suils has joined the channel
2024-08-27
Bharat Mishra (11:35:40): > @Bharat Mishra has joined the channel
NILESH KUMAR (11:35:54): > @NILESH KUMAR has joined the channel
2024-08-29
melissa hahn (07:16:15): > @melissa hahn has joined the channel
Shloka Shukla (18:55:01): > @Shloka Shukla has joined the channel
2024-08-30
David Barnett (06:30:58): > @David Barnett has joined the channel
Yanina Bellini Saibene (12:11:31): > August news!:sparkles:#RStats:rocket:Community call: Navigating the R ecosystem using R-Universe!:studio_microphone:Webinar: Screen Reader Accessible Tools and Resources for Learning and Working with R:writing_hand:Blog post series: Two years and twelve projects as Community Manager at rOpenSci:bar_chart:Our stats on all CRAN packages now updated daily:wave:The rOpenSci community at upcoming events:robot_face:New package {karel}:package:Package news:spiral_note_pad:Blog posts:wave:Calls for contributions:toolbox:Package Development cornerhttps://ropensci.org/blog/2024/08/30/news-august-2024/ - Attachment (ropensci.org): rOpenSci News Digest, August 2024 > Screen reader acessibility webinar, R-universe community call, CRAN stats, new package and package news
Christopher Bulow (14:15:49): > @Christopher Bulow has joined the channel
2024-09-01
Vince Carey (10:23:56): > https://developers.slashdot.org/comments.pl?sid=23440588&cid=64753016 - Attachment (developers.slashdot.org): VS Code Fork ‘Cursor’ - the ChatGPT of Coding? - Slashdot > So I pasted it into Claude and got this and this test case, from which I get this output.You’re the one tasking this problem, so you tell us whether it works and whether you want improvements anywhere. This took seconds, and even if you’re not happy with it, it’s bare minimum a framework (and reque…
2024-09-02
Laurent Gatto (03:20:21): > The package landing pages have a ‘In Bioconductor since’ field that gives the years since a package is in Bioc and it’s fifst Bioc and R versions. I can get all sorts of information about a package with biocViews package, but apparently not this one. Does anyone know of the ‘In Bioconductor since’ is available programmatically, or is it somehow derived from the version (and if so, how).
Laurent Gatto (03:32:37) (in thread): > BiocPkgTools doesn’t have this information either, as far as I can see.
Laurent Gatto (03:35:22) (in thread): > Progress: I can extract the first download stats (which should reflect month/year of first release) fromBiocPkgTools::biocDownloadStats()
Laurent Gatto (04:45:42) (in thread): > Although these only go until 2009.
Lori Shepherd (06:24:36) (in thread): > I can look tomorrow since today’s the holiday but yes it’s programmatically. I think it’s a cross from when it’s in the manifest and the release dates. Which is why I think at some point we can only do a year+ from when we started using manifests. I’ll look officially tomorrow tho
Laurent Gatto (06:49:05) (in thread): > Thank you
Lluís Revilla (10:57:24) (in thread): > The download include the devel branch. If a package is accepted after a new Bioconductor version it might have more months than being published. Maybe you could check the commit date of version changes in the major.minor
2024-09-03
Lori Shepherd (09:00:39) (in thread): > confirmed it does a cross check against the release dates and manifests
2024-09-04
Matthew Sutcliffe (13:35:54): > @Matthew Sutcliffe has joined the channel
2024-09-06
gilda williams (00:00:56): > @gilda williams has joined the channel
Edward Osei Gyimah (15:15:56): > @Edward Osei Gyimah has joined the channel
2024-09-07
Noam Ross (13:09:53): > @Noam Ross has joined the channel
Tyler Sagendorf (14:23:50): > @Tyler Sagendorf has joined the channel
2024-09-08
semra ugur (14:39:37): > @semra ugur has joined the channel
2024-09-09
Egon Willighagen (01:43:32): > @Egon Willighagen has joined the channel
Geoffrey Yang (07:03:41): > @Geoffrey Yang has joined the channel
2024-09-10
Alex Qin (03:45:29): > @Alex Qin has joined the channel
Philippa Doherty (09:46:51): > @Philippa Doherty has joined the channel
Jieran Sun (17:10:10): > @Jieran Sun has joined the channel
2024-09-11
Dibyaswarupa Mohanty (12:07:05): > @Dibyaswarupa Mohanty has joined the channel
2024-09-12
Kat Cheung (11:09:12): > @Kat Cheung has joined the channel
Arya Soman (12:44:32): > @Arya Soman has joined the channel
2024-09-13
Gobi Dasu (18:23:49): > I wanted to share this and get some feedback:https://blog.ldtalentwork.com/2019/03/13/how-to-integrate-scraped-products-into-your-woocommerce-site/. - Attachment (LD Talent Blog): How to integrate scraped products into your Woocommerce site - LD Talent Blog > What is scraping ? Web scraping is a process through which certain websites are crawled or scraped and important information extracted from them according to pre-defined specifications. This information is then formatted and stored in a database for business applications. What’s woocommerce ? WooCommerce is an open-source e-commerce plugin for WordPress. It is designed for …
2024-09-14
Katarzyna Zoltowska (10:10:48): > @Katarzyna Zoltowska has joined the channel
Jonathan Weber (16:41:09): > @Jonathan Weber has joined the channel
2024-09-15
Yasmine Elnasharty (08:30:55): > @Yasmine Elnasharty has joined the channel
2024-09-16
Nesrine Gharbi (10:00:52): > @Nesrine Gharbi has joined the channel
Sean Davis (17:00:27): > The Bioconductor Zenodo community is open and available for submissions. Here is the list of submissions so far:https://zenodo.org/communities/bioconductor/records?q=&l=list&p=1&s=10&sort=newest
2024-09-17
Shantanu Shukla (18:26:18): > @Shantanu Shukla has joined the channel
2024-09-18
Marcela Vega (14:29:35): > @Marcela Vega has joined the channel
2024-09-19
Cinque Imperia (14:12:14): > @Cinque Imperia has joined the channel
Jonathan Wang (14:40:35): > @Jonathan Wang has joined the channel
2024-09-20
Camille Guillermin (09:28:56): > @Camille Guillermin has joined the channel
2024-09-21
Sagar Thapa Magar (14:19:31): > @Sagar Thapa Magar has joined the channel
2024-09-23
My Nguyen (16:17:41): > @My Nguyen has joined the channel
2024-09-24
Drashti Patil (02:27:39): > @Drashti Patil has joined the channel
Tobi Ogunbowale (05:57:22): > @Tobi Ogunbowale has joined the channel
Jasmine Baker (12:48:29): > @Jasmine Baker has joined the channel
Candace Savonen (15:29:05): > @Candace Savonen has joined the channel
2024-09-25
Eman Elrefaei (00:51:22): > @Eman Elrefaei has joined the channel
Alison Ludzki (01:37:20): > @Alison Ludzki has joined the channel
Imran Khan (08:55:28): > @Imran Khan has joined the channel
2024-09-26
Thibaut Armel Chérif GNIMADI (09:00:14): > @Thibaut Armel Chérif GNIMADI has joined the channel
2024-09-27
Yanina Bellini Saibene (08:34:17): > :sparkles:rOpenSci September news
:link:Materials: Screen Reader Accessible Tools and Resources for Learning and Working with R:rocket:Community call recording: Navigating the R ecosystem using R-universe:microphone:Podcast: Noam Ross, rOpenSci, and Communities Empowering Open Science:wave:The rOpenSci community at upcoming events:calendar:Next coworking events:dna:New packages {eDNAjoin}, {rix}:package:Package news:writing_hand:Blog posts:pray:Calls for contributions:toolbox:Package Development cornerhttps://ropensci.org/blog/2024/09/27/news-september-2024/ - Attachment (ropensci.org): rOpenSci News Digest, September 2024 > Screen Reader Accessible Tools materials, R-Universe, training resources, coworking, new package and package news
Kevin Leuthold (12:45:37): > @Kevin Leuthold has joined the channel
2024-09-28
Ahmed Hasan (04:47:24): > @Ahmed Hasan has joined the channel
Sohanur Rahaman Sohan (04:49:57): > @Sohanur Rahaman Sohan has joined the channel
2024-09-29
Vimal Keerthi (14:35:03): > @Vimal Keerthi has joined the channel
2024-09-30
Caroline Schreiber (10:44:50): > @Caroline Schreiber has joined the channel
2024-10-01
Basirat Kareem (12:21:10): > @Basirat Kareem has joined the channel
Kate Rasheed (12:32:52): > @Kate Rasheed has joined the channel
Chiamaka Johnfred (12:38:40): > @Chiamaka Johnfred has joined the channel
adeyemo oluwatobi (12:58:19): > @adeyemo oluwatobi has joined the channel
Eseoghene Orhorho (13:00:54): > @Eseoghene Orhorho has joined the channel
Chioma Peters (13:01:52): > @Chioma Peters has joined the channel
Maris Chukwuma (13:09:50): > @Maris Chukwuma has joined the channel
arsema doji (13:19:21): > @arsema doji has joined the channel
adekemi balogun (14:00:11): > @adekemi balogun has joined the channel
tega abamba (14:36:59): > @tega abamba has joined the channel
Igwe Maryann (14:39:05): > @Igwe Maryann has joined the channel
aziz gueye (14:46:58): > @aziz gueye has joined the channel
Jatinder Mahajan (14:51:24): > @Jatinder Mahajan has joined the channel
Martha Kisakye (15:01:03): > @Martha Kisakye has joined the channel
Paavni Goyal (15:11:44): > @Paavni Goyal has joined the channel
Mary Agekameh (15:26:38): > @Mary Agekameh has joined the channel
Agatha (15:30:05): > @Agatha has joined the channel
Balikis sulaimon (15:30:56): > @Balikis sulaimon has joined the channel
BOLARINWA AISHAT (15:52:34): > @BOLARINWA AISHAT has joined the channel
Klangi (16:13:36): > @Klangi has joined the channel
Chinwendu Joy Enyidiegwu (16:20:26): > @Chinwendu Joy Enyidiegwu has joined the channel
Blessdamy (16:37:28): > @Blessdamy has joined the channel
Amrita Das (17:47:58): > @Amrita Das has joined the channel
Peace Anosike (18:52:23): > @Peace Anosike has joined the channel
Samuel Ogunleye (19:57:01): > @Samuel Ogunleye has joined the channel
Eniola Kolawole (20:08:27): > @Eniola Kolawole has joined the channel
Royyale C (20:53:03): > @Royyale C has joined the channel
Mohammed Abubakar (23:36:37): > @Mohammed Abubakar has joined the channel
2024-10-02
Obuli Abraham (00:31:56): > @Obuli Abraham has joined the channel
Hamail Sultan (00:44:43): > @Hamail Sultan has joined the channel
masembe brian (01:27:12): > @masembe brian has joined the channel
Abraham Cruz (02:31:09): > @Abraham Cruz has joined the channel
Arpita (03:11:19): > @Arpita has joined the channel
Ruqayyah (03:35:54): > @Ruqayyah has joined the channel
Rebecca Makinde (03:43:39): > @Rebecca Makinde has joined the channel
Mohamed Osman Omar (03:58:29): > @Mohamed Osman Omar has joined the channel
Alexander Dietrich (04:19:02): > @Alexander Dietrich has joined the channel
Lorenzo (04:29:31): > @Lorenzo has joined the channel
Joy (04:34:47): > @Joy has joined the channel
inyang john (05:36:55): > @inyang john has joined the channel
Ekunola Paul O. (06:03:09): > @Ekunola Paul O. has joined the channel
Onyinyechi (06:33:43): > @Onyinyechi has joined the channel
Sumaiya Rafique (06:43:29): > @Sumaiya Rafique has joined the channel
James Efienemokwu (10:13:17): > @James Efienemokwu has joined the channel
Dorcas Samuel (11:31:08): > @Dorcas Samuel has joined the channel
Harun Cerkezi (13:37:06): > @Harun Cerkezi has joined the channel
Veronicah Wags (14:51:51): > @Veronicah Wags has joined the channel
Daud Ahmed (17:00:53): > @Daud Ahmed has joined the channel
Seyi Kuforiji (17:08:56): > @Seyi Kuforiji has joined the channel
Mojolaoluwa Oyewale (18:00:10): > @Mojolaoluwa Oyewale has joined the channel
Mariam Akinbode (18:24:03): > @Mariam Akinbode has joined the channel
Eva Hamrud (18:52:36): > @Eva Hamrud has joined the channel
Collins Gichangi (19:57:10): > @Collins Gichangi has joined the channel
Dan-Aletor Daniela (20:02:43): > @Dan-Aletor Daniela has joined the channel
Rhaenyra Liang (21:35:28): > @Rhaenyra Liang has joined the channel
Julia A Brettschneider (22:37:56): > @Julia A Brettschneider has joined the channel
2024-10-03
Samted Uche (teddyCodex) (00:42:37): > @Samted Uche (teddyCodex) has joined the channel
Bheki Daweti (04:26:30): > @Bheki Daweti has joined the channel
Olive Oparaocha (05:03:00): > @Olive Oparaocha has joined the channel
Aniebiet Afia (05:36:34): > @Aniebiet Afia has joined the channel
Cynthia Iwuoha (07:41:59): > @Cynthia Iwuoha has joined the channel
Immaculate Atim (08:46:13): > @Immaculate Atim has joined the channel
Toluwalase Abigail (10:33:11): > @Toluwalase Abigail has joined the channel
rhoda (11:15:02): > @rhoda has joined the channel
Yoko C (12:58:22): > @Yoko C has joined the channel
Tanishka Goel (13:57:08): > @Tanishka Goel has joined the channel
Himanshi Srestha (14:43:35): > @Himanshi Srestha has joined the channel
Jessica Oviahon (20:29:03): > @Jessica Oviahon has joined the channel
Inimfon Ebong (21:12:15): > @Inimfon Ebong has joined the channel
Teresia (23:05:20): > @Teresia has joined the channel
2024-10-04
Agnes Obianuju Anosike (02:02:46): > @Agnes Obianuju Anosike has joined the channel
Monisa Hasnain (02:03:38): > @Monisa Hasnain has joined the channel
Princess Rehoboth Asuelimen (05:18:06): > @Princess Rehoboth Asuelimen has joined the channel
Ameerat Bibire (07:59:47): > @Ameerat Bibire has joined the channel
Shachi (14:08:41): > @Shachi has joined the channel
Awa (14:59:24): > @Awa has joined the channel
Zara Adwan (16:41:59): > @Zara Adwan has joined the channel
Samuel Nnanna (17:26:02): > @Samuel Nnanna has joined the channel
Rohit Gupta (22:46:04): > @Rohit Gupta has joined the channel
2024-10-05
Rhoda Wambui (03:55:36): > @Rhoda Wambui has joined the channel
Ochogwu Emmanuel (05:16:25): > @Ochogwu Emmanuel has joined the channel
Khushal Sarode (05:25:02): > @Khushal Sarode has joined the channel
Ifeoma Okafor (08:54:28): > @Ifeoma Okafor has joined the channel
Ebele Lynda Okolo (13:27:50): > @Ebele Lynda Okolo has joined the channel
Rita Kusi-Appiah (22:24:53): > @Rita Kusi-Appiah has joined the channel
2024-10-06
Oromidayo Owolabi (12:48:35): > @Oromidayo Owolabi has joined the channel
2024-10-07
jubril adeyi (07:21:57): > @jubril adeyi has joined the channel
mbeas (11:07:35): > @mbeas has joined the channel
Axxhie (17:04:52): > @Axxhie has joined the channel
2024-10-08
Vaishali Rawat (06:03:21): > @Vaishali Rawat has joined the channel
2024-10-09
Richie (15:30:35): > @Richie has joined the channel
2024-10-10
Tasha Daije (02:55:25): > @Tasha Daije has joined the channel
Ebuka Chinwuba (08:35:32): > @Ebuka Chinwuba has joined the channel
Daniel Marvin (11:01:49): > @Daniel Marvin has joined the channel
Claire Weber (13:33:48): > @Claire Weber has joined the channel
Charles Ebong (18:01:26): > @Charles Ebong has joined the channel
Larissa T Grizzo Thomassian (20:39:50): > @Larissa T Grizzo Thomassian has joined the channel
2024-10-11
Ji Hen Lau (01:33:02): > @Ji Hen Lau has joined the channel
2024-10-12
Francisco Ignacio Oñate Vidal (00:47:56): > @Francisco Ignacio Oñate Vidal has joined the channel
2024-10-14
杨新宇 (04:02:38): > @杨新宇 has joined the channel
Tino (08:02:37): > @Tino has joined the channel
vandana maddi (09:33:00): > @vandana maddi has joined the channel
Vivek (13:57:01): > @Vivek has joined the channel
Sunil Revuri (13:57:27): > @Sunil Revuri has joined the channel
2024-10-15
Negin Valizadegan (00:58:24): > @Negin Valizadegan has joined the channel
2024-10-16
Victoria Olumide (04:36:35): > @Victoria Olumide has joined the channel
Shah zaib (05:29:24): > @Shah zaib has joined the channel
chengyi ma (21:16:59): > @chengyi ma has joined the channel
2024-10-17
Fanny (10:42:12): > @Fanny has joined the channel
2024-10-19
李泽西 (03:24:02): > @李泽西 has joined the channel
2024-10-20
Hong Qin (17:42:01): > @Hong Qin has joined the channel
2024-10-21
L S (04:51:55): > @L S has joined the channel
Liezel Tamon (04:52:25): > @Liezel Tamon has joined the channel
Heather (04:52:53): > @Heather has joined the channel
Lucy Hamer (04:52:55): > @Lucy Hamer has joined the channel
May Sallam (04:53:21): > @May Sallam has joined the channel
Nicole Kerekes (04:53:35): > @Nicole Kerekes has joined the channel
Elena Navarro-Guerrero (05:35:18): > @Elena Navarro-Guerrero has joined the channel
Praharshit Sharma (11:52:44): > @Praharshit Sharma has joined the channel
2024-10-22
Liyang Fei (00:07:23): > @Liyang Fei has joined the channel
Edward Zhao (02:59:41): > @Edward Zhao has joined the channel
Ekaterina Akimova (10:34:34): > @Ekaterina Akimova has joined the channel
Wah Vanessa (12:01:33): > @Wah Vanessa has joined the channel
Alina Jana Arneth (19:31:16): > @Alina Jana Arneth has joined the channel
2024-10-23
anusha_R (08:59:02): > @anusha_R has joined the channel
Lei (20:53:34): > @Lei has joined the channel
2024-10-24
Mercy Cherop (12:54:26): > @Mercy Cherop has joined the channel
Yang Liao (22:20:16): > @Yang Liao has joined the channel
Nomsa Ngoma (23:07:53): > @Nomsa Ngoma has joined the channel
Nur Shahir (23:19:05): > @Nur Shahir has joined the channel
2024-10-25
Benjamin Story (08:00:50): > @Benjamin Story has joined the channel
2024-10-26
정모세 (15:55:33): > @정모세 has joined the channel
2024-10-27
jesson (22:45:05): > @jesson has joined the channel
2024-10-28
Chris Thomas (15:16:59): > @Chris Thomas has joined the channel
Qile Yang (19:01:28): > @Qile Yang has joined the channel
2024-10-29
Travis Blimkie (11:17:19): > @Travis Blimkie has joined the channel
2024-10-30
Inge R Holtman (09:16:53): > @Inge R Holtman has joined the channel
Senbai Kang (09:20:20): > @Senbai Kang has joined the channel
Alessa Ringel (11:28:52): > @Alessa Ringel has joined the channel
FAIZAN (12:26:34): > @FAIZAN has joined the channel
Lori Shepherd (16:31:13): > 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.
Chen Zhan (21:35:43): > @Chen Zhan has joined the channel
2024-10-31
Nusrat Afrin (00:33:52): > @Nusrat Afrin has joined the channel
2024-11-02
skuba (13:40:19): > @skuba has joined the channel
Debprasad Dutta (21:34:25): > @Debprasad Dutta has joined the channel
2024-11-04
Sean Davis (09:44:42): > There has been a recent flurry of spatial methods added tohttps://github.com/seandavi/awesome-single-cell. Would love to see more additions….
Wouter-Michiel Adrien Maria Vierdag (10:43:13): > @Wouter-Michiel Adrien Maria Vierdag has joined the channel
Fanding Zhou (12:41:50): > @Fanding Zhou has joined the channel
khushi ahuja (16:13:57): > @khushi ahuja has joined the channel
Tania Araceli Barreda Galvez (17:20:58): > @Tania Araceli Barreda Galvez has joined the channel
2024-11-05
Chris (09:16:56): > @Chris has joined the channel
Lulevere Beqiri (12:21:40): > @Lulevere Beqiri has joined the channel
2024-11-06
Claire Rioualen (13:03:33): > Edit- nvm, wrong slack space:sweat_smile:Sorry for cross posting - anybody has a magic remedy for karaoke-induced sore throat?:smiling_face_with_tear:
Ethan (13:17:37): > @Ethan has joined the channel
Sam El-Kamand (21:38:52): > @Sam El-Kamand has joined the channel
Malvika Kharbanda (21:49:05): > @Malvika Kharbanda has joined the channel
Michael Nakai (21:49:53): > @Michael Nakai has joined the channel
Merridee Wouters (21:50:12): > @Merridee Wouters has joined the channel
Dharmesh Dinesh Bhuva (21:52:21): > @Dharmesh Dinesh Bhuva has joined the channel
2024-11-07
Cecilia M (07:12:32): > @Cecilia M has joined the channel
Christina Simoglou Karali (10:28:17): > @Christina Simoglou Karali has left the channel
Shreya Rao (22:08:28): > @Shreya Rao has joined the channel
2024-11-08
Launlab (07:27:11): > @Launlab has joined the channel
2024-11-10
贺宇 (22:59:24): > @贺宇 has joined the channel
2024-11-11
Josh Steier (12:24:29): > @Josh Steier has joined the channel
Harry Mueller (18:04:03): > @Harry Mueller has joined the channel
2024-11-13
RITU VERMA (05:51:09): > @RITU VERMA has joined the channel
Sergius Nyah (07:58:35): > @Sergius Nyah has joined the channel
Jeremy Clark (10:20:30): > @Jeremy Clark has joined the channel
Mihail Anton (10:20:45): > @Mihail Anton has joined the channel
Jahanbanoo Shahryari (17:41:19): > @Jahanbanoo Shahryari has joined the channel
2024-11-14
Lillian Dillard (10:49:52): > @Lillian Dillard has joined the channel
2024-11-15
Haroon (06:53:53): > @Haroon has joined the channel
Alex Han (13:33:04): > @Alex Han has joined the channel
2024-11-16
hongjun liu (16:53:26): > @hongjun liu has joined the channel
2024-11-17
Gen B (14:50:12): > @Gen B has joined the channel
2024-11-18
Roy Francis (12:30:12): > @Roy Francis has joined the channel
Lauren Witzgall (14:15:06): > @Lauren Witzgall has joined the channel
Toby Hodges (14:17:20): > @Toby Hodges has joined the channel
2024-11-19
Thomaz Bastiaanssen (10:31:27): > @Thomaz Bastiaanssen has joined the channel
2024-11-20
Y. Schumann (03:57:09): > @Y. Schumann has joined the channel
Emanuele Pitino (10:30:07): > @Emanuele Pitino has joined the channel
Mengrui Zhang (12:39:26): > @Mengrui Zhang has joined the channel
2024-11-21
Tehniyat zahra (04:59:11): > @Tehniyat zahra has joined the channel
Sean Davis (16:26:23): > A little off-topic, but here is a set of medical-student-curated AI in medicine resources that my students chose to engage with (self-directed learning) during our AI in medicine course. It includes ethics, legal, clinical, research, technical topics in the form of videos, papers, podcasts, blog posts, etc. Particularly for clinical colleagues asking you about AI, this list (though long) has been through at least one medical student’s hands.https://bit.ly/ai-med-resources - Attachment (Google Docs): Contributed AI Learning Resources
Meg Urisko (17:13:34): > @Meg Urisko has joined the channel
Luyang Luo (18:38:01): > @Luyang Luo has joined the channel
2024-11-23
Rachel Wise (01:03:56): > @Rachel Wise has joined the channel
Zheng Pan (20:22:53): > @Zheng Pan has joined the channel
2024-11-24
Srushti (06:38:42): > @Srushti has joined the channel
2024-11-25
Júlia Mir (06:10:00): > @Júlia Mir has joined the channel
Hong Zhang (14:35:50): > @Hong Zhang has joined the channel
xinwen (16:47:16): > @xinwen has joined the channel
2024-11-26
Hassan Diab (05:52:55): > @Hassan Diab has joined the channel
Vinzent Risch (08:33:39): > @Vinzent Risch has joined the channel
Trevor Ham (15:24:39): > @Trevor Ham has joined the channel
2024-11-27
CECILIA RIANI (05:33:06): > @CECILIA RIANI has joined the channel
Omar Holayell (09:17:19): > @Omar Holayell has joined the channel
2024-11-28
Dan (08:27:28): > @Dan has joined the channel
2024-11-29
Yanina Bellini Saibene (05:54:43): > November news!:pie:#RStats:wave:Looking for Maintainers to Support First-Time Contributors:rocket:A faster R-Universe!:studio_microphone:@yabellini@fosstodon.org’s s keynote talk at CarpentryConnect and BioNT 2024:globe_with_meridians:Tradução + Hackathon = Traslatón rOpenSci:video_camera:Community Call “A comunidade R fala português” Resources:pray:Give Thanks with the allcontributors Package:calendar:Coworking:raising_hand:Calls for contributions:toolbox:Package development cornerhttps://ropensci.org/blog/2024/11/29/news-november-2024/ - Attachment (ropensci.org): rOpenSci News Digest, November 2024 > Support first-time contributors, fast R-universe, give thanks to contributors
Freddy Drennan (11:42:22): > @Freddy Drennan has joined the channel
2024-11-30
Юлия Прозоровская (04:44:30): > @Юлия Прозоровская has joined the channel
2024-12-02
Yi Ren (03:37:34): > @Yi Ren has joined the channel
Nanako S (21:02:43): > @Nanako S has joined the channel
2024-12-03
Sadie W (16:04:55): > @Sadie W has joined the channel
Farid Agushybana (20:08:08): > @Farid Agushybana has joined the channel
Rutuja (21:15:30): > @Rutuja has joined the channel
2024-12-04
Ben Valderrama (11:20:56): > @Ben Valderrama has joined the channel
2024-12-05
geng joe (08:25:50): > @geng joe has joined the channel
2024-12-06
Grace Kenney (14:31:25): > @Grace Kenney has joined the channel
2024-12-08
Elihu (08:17:57): > @Elihu has joined the channel
Md.tarikul Islam (20:34:51): > @Md.tarikul Islam has joined the channel
2024-12-11
Peiying Cai (07:21:36): > @Peiying Cai has joined the channel
2024-12-12
Aina Pérez Rodas (08:11:36): > @Aina Pérez Rodas has joined the channel
Yujin Cho (08:20:38): > @Yujin Cho has joined the channel
Julian Stamp (11:56:41): > @Julian Stamp has joined the channel
Wander Labaere (12:25:03): > @Wander Labaere has joined the channel
2024-12-13
Kateřina Matějková (05:07:44): > @Kateřina Matějková has joined the channel
Jan (06:15:48): > @Jan has joined the channel
Karima Diafi (17:31:01): > @Karima Diafi has joined the channel
2024-12-14
Jan Nawrocki (05:15:46): > @Jan Nawrocki has joined the channel
dupgen sherpa (05:56:11): > @dupgen sherpa has joined the channel
2024-12-17
Ouma Ronald (02:14:52): > @Ouma Ronald has joined the channel
Grainne OMahoney (06:44:38): > @Grainne OMahoney has joined the channel
2024-12-18
Edward Chen (04:14:19): > @Edward Chen has joined the channel
Yanina Bellini Saibene (07:06:21): > Nice to close the year accomplishing objectives :-):sunglasses::grin:Very proud of this guide that we generated in rOpenSci: everything we developed and learned during the translations and localizations of our content is detailed in this book: the processes, the roles, and the technical tools. > > We hope it will be helpful to other groups and communities!:writing_hand:Blog post ByYanina Bellini Saibene,Maëlle Salmon,Pao Corrales,Elio Campitelli– Edited bySteffi LaZerte:https://ropensci.org/blog/2024/12/17/localization-guide/:toolbox:rOpenSci Localization and Translation Guidelines. Why and how we localize and translate our resources:https://translationguide.ropensci.orgBoth content are in English and Spanish. Feedback is appreciated.:slightly_smiling_face:
Maria Doyle (07:17:48) (in thread): > Congrats on the guide, Yani! Thanks for sharing – it looks like a great resource. It might also be worth posting in#documentation-translation!
Yanina Bellini Saibene (07:20:52) (in thread): > Thanks@Maria Doyle! Shared there too:slightly_smiling_face:
Michael Totty (15:00:51): > @Michael Totty has joined the channel
2024-12-19
Abdoul Oudouss Diakité (01:27:22): > @Abdoul Oudouss Diakité has joined the channel
Łucja Płachecka (09:47:58): > @Łucja Płachecka has joined the channel
Rafaat Waheed (14:26:06): > @Rafaat Waheed has joined the channel
Josie (14:38:44): > @Josie has joined the channel
Ndukauba Oluchi (14:55:01): > @Ndukauba Oluchi has joined the channel
2024-12-21
Davide (13:09:57): > @Davide has joined the channel
2024-12-23
Ying Xu (21:56:40): > @Ying Xu has joined the channel
2024-12-24
willie (06:30:33): > @willie has joined the channel
2024-12-26
Taofeecoh Adesanu (11:36:45): > @Taofeecoh Adesanu has joined the channel
Rasmus Hindström (14:35:07): > @Rasmus Hindström has joined the channel
2024-12-27
加茂浅葱 (05:11:38): > @加茂浅葱 has joined the channel
2024-12-28
Tejaswi Velugapally (05:23:28): > @Tejaswi Velugapally has joined the channel
Egon Willighagen (05:24:21): > @Egon Willighagen has left the channel
Atoni Evans (07:26:42): > @Atoni Evans has joined the channel
Michael Hungbo (07:27:48): > @Michael Hungbo has joined the channel
apekshya kandel (07:53:05): > @apekshya kandel has joined the channel
Pascal-Onaho (07:54:04): > @Pascal-Onaho has joined the channel
Kayode Raheem (08:16:47): > @Kayode Raheem has joined the channel
megha joshi (10:11:32): > @megha joshi has joined the channel
Radwa Sharaf (14:42:15): > @Radwa Sharaf has joined the channel
Anifowose Samuel (17:22:28): > @Anifowose Samuel has joined the channel
Samson (18:20:01): > @Samson has joined the channel
John Bruce (18:20:04): > @John Bruce has joined the channel
Oghale (21:41:29): > @Oghale has joined the channel
2024-12-29
Innas Widiasti (00:18:25): > @Innas Widiasti has joined the channel
Yahya Jahun (03:59:07): > @Yahya Jahun has joined the channel
Andrew Su (12:17:41): > @Andrew Su has joined the channel
2024-12-30
Victor Achor (00:31:06): > @Victor Achor has joined the channel
Mustapha Dibbasey (02:41:01): > @Mustapha Dibbasey has joined the channel
2025-01-01
Pariksheet Nanda (15:46:51): > @Pariksheet Nanda has joined the channel
2025-01-02
George Kitundu (00:38:32): > @George Kitundu has joined the channel
Gloria Amor Arroyo (08:18:46): > @Gloria Amor Arroyo has joined the channel
Najuma Najeem (10:58:22): > @Najuma Najeem has joined the channel
Jason Laird (12:32:35): > @Jason Laird has joined the channel
2025-01-05
Muku Bhandari (06:53:05): > @Muku Bhandari has joined the channel
Ammar Naggar (19:52:21): > @Ammar Naggar has joined the channel
Ilariya Tarasova (22:25:02): > @Ilariya Tarasova has joined the channel
2025-01-06
jianwei (10:31:01): > @jianwei has joined the channel
2025-01-08
Pei-Han Chung (02:56:53): > @Pei-Han Chung has joined the channel
Rahman Nurudeen (04:13:59): > @Rahman Nurudeen has joined the channel
2025-01-09
Adnan (08:32:53): > @Adnan has joined the channel
Mahesh Jethalia (08:59:51): > @Mahesh Jethalia has joined the channel
Ahlam Khaled Ahmed (10:45:53): > @Ahlam Khaled Ahmed has joined the channel
Ammar Sabir Cheema (11:24:26): > @Ammar Sabir Cheema has joined the channel
Sage Allen (16:09:33): > @Sage Allen has joined the channel
2025-01-10
Brian Repko (09:25:20): > @Brian Repko has joined the channel
hemant c naik (11:34:48): > @hemant c naik has joined the channel
2025-01-11
Mateus Falco (09:53:44): > @Mateus Falco has joined the channel
Kimberly Hoang (18:30:28): > @Kimberly Hoang has joined the channel
Shahenda Soliman (21:39:06): > @Shahenda Soliman has joined the channel
2025-01-13
Gijs Tukkers (08:36:43): > @Gijs Tukkers has joined the channel
neslihan oztas (10:03:42): > @neslihan oztas has joined the channel
Chidera (14:51:46): > @Chidera has joined the channel
2025-01-14
Karen Pendergrass (01:39:38): > @Karen Pendergrass has joined the channel
Sumona Akter (01:43:58): > @Sumona Akter has joined the channel
Laura Perasto (04:21:02): > @Laura Perasto has joined the channel
2025-01-16
Jeremiah Akintomide (09:06:51): > @Jeremiah Akintomide has joined the channel
David Akwuru (09:07:08): > @David Akwuru has joined the channel
2025-01-17
Bo (12:11:36): > @Bo has joined the channel
2025-01-21
Lydia Levesque (20:20:03): > @Lydia Levesque has joined the channel
2025-01-24
nyasita ondari (15:58:05): > @nyasita ondari has joined the channel
2025-01-27
Mike (01:44:13): > @Mike has joined the channel
Chetan (19:23:14): > @Chetan has joined the channel
2025-01-28
Susan (01:19:53): > @Susan has joined the channel
Nazgul (11:14:47): > @Nazgul has joined the channel
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
Jessica Holmes (10:39:10): > @Jessica Holmes has joined the channel
Karla Ximena González Platas (11:26:42): > @Karla Ximena González Platas has joined the channel
Mohamed Omar (17:16:19): > @Mohamed Omar has joined the channel
2025-01-30
Ian McCue (12:43:24): > @Ian McCue has joined the channel
Janine Makorre (23:04:36): > @Janine Makorre has left the channel
2025-01-31
Bastien CHASSAGNOL (17:01:27): > @Bastien CHASSAGNOL has joined the channel
Lucas Hueffed (18:05:21): > @Lucas Hueffed has joined the channel
2025-02-02
Mariam (04:09:04): > @Mariam has joined the channel
Sarah Choi (18:30:24): > @Sarah Choi has joined the channel
2025-02-03
Andrew Dahik (20:10:22): > @Andrew Dahik has joined the channel
Sophie Müller (22:20:40): > @Sophie Müller has joined the channel
inan z (23:36:05): > @inan z has joined the channel
2025-02-05
Yanina Bellini Saibene (11:10:56): > [Blog post] Open Science and Open Source only with Diversity, Equity, Inclusion, and Accessibility by The rOpenSci Team. > > Including all of humanity is and always will be at the heart of open science.https://ropensci.org/blog/2025/02/05/no-science-without-deia/ - Attachment (ropensci.org): Open Science and Open Source only with Diversity, Equity, Inclusion, and Accessibility > Including all of humanity is and always will be at the heart of open science.
Akriti (21:37:14): > @Akriti has joined the channel
2025-02-06
Ouma Ronald (01:58:14) (in thread): > hi@Yanina Bellini Saibene. Is this also another opensource community under microbiome? Just wanted to know.
Yanina Bellini Saibene (03:35:14) (in thread): > Hi Ouma, Idon’tthink so, what microbiome is?
Yanina Bellini Saibene (03:37:28) (in thread): > We are fiscal sponsored by NumFOCUS if that helps with your question
Ouma Ronald (03:39:38) (in thread): > I read the message but didn’t get it right and that’s why I asked if its another community but under community-bioc
Maria Doyle (05:42:59) (in thread): > Hi Ouma, > Just to clarify, rOpenSci is a separate open-source community focused on general R packages. You can learn more about them athttps://ropensci.org/. Bioconductor focuses on bioinformatics and computational biology, including microbiome research. Both communities share a commitment to open science and open source. > Hope this helps clear things up! - Attachment (ropensci.org): rOpenSci > Open Tools and R Packages for Open Science
Kalyanee (09:05:33): > @Kalyanee has joined the channel
NOAH (09:07:27): > @NOAH has joined the channel
Liz Hare (11:38:27): > @Liz Hare has joined the channel
Nishi Hembrom (21:15:15): > @Nishi Hembrom has joined the channel
2025-02-07
Taha Ahmad (14:52:18): > @Taha Ahmad has joined the channel
2025-02-09
Sarah (02:42:39): > @Sarah has joined the channel
Elisabetta Toni (05:32:40): > @Elisabetta Toni has joined the channel
Mark (23:31:20): > @Mark has joined the channel
2025-02-10
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
2025-02-12
雨果的阿东 (00:44:03): > @雨果的阿东 has joined the channel
zetianjia (07:37:53): > @zetianjia has joined the channel
Ario Moniri (08:11:13): > @Ario Moniri has joined the channel
2025-02-13
NİLÜFER YILDIRIM (07:57:16): > @NİLÜFER YILDIRIM has joined the channel
Anushka Paharia (09:22:19): > @Anushka Paharia has joined the channel
2025-02-14
Kathleen Watt (08:01:21): > @Kathleen Watt has joined the channel
2025-02-16
Aaron finch (07:53:01): > @Aaron finch has joined the channel
Frank Melo (18:57:35): > @Frank Melo has joined the channel
2025-02-17
Mona Abd El-Aty (10:45:59): > @Mona Abd El-Aty has joined the channel
Giorgia Mori (17:31:28): > @Giorgia Mori has joined the channel
sameer mudbhari (23:54:59): > @sameer mudbhari has joined the channel
2025-02-19
Josias Rodrigues (17:40:46): > @Josias Rodrigues has joined the channel
Mike Oliphant (21:31:49): > @Mike Oliphant has joined the channel
2025-02-20
Georgia Whitton (06:45:01): > @Georgia Whitton has joined the channel
James Nemesh (09:08:08): > @James Nemesh has joined the channel
2025-02-21
Michael Barth (13:39:49): > @Michael Barth has joined the channel
2025-02-22
Mariana Rouni (04:52:53): > @Mariana Rouni has joined the channel
2025-02-25
Jacob Appelbaum (16:31:29): > @Jacob Appelbaum has joined the channel
2025-02-27
Jan Paweł Jastrzębski (09:26:45): > @Jan Paweł Jastrzębski has joined the channel
Anna Sai (19:27:29): > @Anna Sai has joined the channel
2025-02-28
Flora Oladipupo (03:30:42): > @Flora Oladipupo has joined the channel
Saloni Sharma (05:09:09): > @Saloni Sharma has joined the channel
Sergio (05:46:54): > @Sergio has joined the channel
2025-03-02
Sean Davis (07:10:16): > Over the last 48 hours, critical biomedical data infrastructure such as pubmed, NCBI, and some NIH institutional sites have been either down or only intermittently functional. I put together a status page here:https://stats.uptimerobot.com/Zrqh8AhvKnto track a few of these resources. I can add up to 40 more sites. Let me know (in a thread, please) if you have additional US government sites that are critical to your work that you want to track. And, of course, feel free to share with colleagues and politicians for visibility and awareness.
Izabela Mamede (09:24:03) (in thread): > Hey! Thanks for the resource, it is very useful. Could you add blasthttps://blast.ncbi.nlm.nih.gov?
Vince Carey (10:10:15) (in thread): > the uptimerobot system may be inaccurate concerningreporter.nih.gov… which is slow but seems to be up at this time
Sean Davis (10:12:06) (in thread): > Thx,@Vince Carey. I adjusted the timeout.
Martin Morgan (12:29:17) (in thread): > I noticed thathttps://ccr.cancer.govis tagged as ‘forbidden’, but is accessible via my browser. Also, I wonder if the time zone could be changed to EST (or dynamic based on origin of request) to reflect the US basis of the results. And perhaps there are pages to be linked to where planned / known service interruptions are provided for some of these sites?
Godfrey Wagutu (13:10:21): > @Godfrey Wagutu has joined the channel
isoah gracious (13:29:09): > @isoah gracious has joined the channel
Sean Davis (13:34:59) (in thread): > I’ve gotten a TON of interest from folks about this coffee-time project. The infrastructure is actually a commercial service, so I don’t have much control over it. Given the interest, urgency, and importance, I’ll probably put in a little time to work on a more configurable, open version.
Nithya kruthi (18:56:52): > @Nithya kruthi has joined the channel
2025-03-03
JIBAN JYOTI DASH (05:13:38): > @JIBAN JYOTI DASH has joined the channel
Sean Davis (12:55:44): > The Cold Spring Harbor Lab course,https://meetings.cshl.edu/courses.aspx?course=C-DATA, has extended the deadline for application to March 15. There is a cost associated with the course, but there are funds for financial hardship or need available. - Attachment (meetings.cshl.edu): Statistical Analysis of Genome Scale Data > Cold Spring Harbor Laboratory Meetings & Courses – a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
W Sun (18:06:20): > @W Sun has joined the channel
2025-03-04
Gabriela Santos (14:17:53): > @Gabriela Santos has joined the channel
yoghesh g (22:38:34): > @yoghesh g has joined the channel
2025-03-05
Julien Roux (01:28:38): > The abstract call for the BC2 conference (Basel, Switzerland, 8-10 Sept) is closing tomorrow, March 6th. There are quite some sessions of this bioinformatics-oriented conference that could be a good fit for people here
- Attachment (bc2.ch): Scientific programme > The [BC]2 Basel Computational Biology Conference is Switzerland’s main event in the domain of Computational Biology and one of the major events of its kind in Europe. The conference unites scientists from academia, industry and healthcare.
Scott Chamberlain (13:43:48): > @Scott Chamberlain has joined the channel
Jennifer Velez (13:47:30): > @Jennifer Velez has joined the channel
Benjamin Hernandez Rodriguez (22:24:47): > @Benjamin Hernandez Rodriguez has joined the channel
Stephen Russell (23:14:50): > @Stephen Russell has joined the channel
2025-03-06
Sean Davis (06:22:36): > For folks working in cancer genetics/somatic mutation space, would love additional contributions to:https://github.com/seandavi/awesome-cancer-variant-resources
Ludwig Geistlinger (08:40:20) (in thread): > re: Variant Effect Prediction tools and databases. Would we want to addAlphaMissense+AlphaMissenseR? Can open a PR. - Attachment (Zenodo): Predictions for AlphaMissense > This repository provide AlphaMissense predictions. Please see the README for more details. For questions about AlphaMissense or the prediction Database please email mailto:alphamissense@google.com|alphamissense@google.com. - Attachment (Bioconductor): AlphaMissenseR
Kate Penrose (09:29:59): > @Kate Penrose has joined the channel
Sean Davis (10:45:21) (in thread): > Awesome!
Sean Davis (10:48:42) (in thread): > Thanks, all, for the feedback in realtime!
Sean Davis (10:49:58) (in thread): > The NIH folks reached out to let me know that this was not a planned event. I didn’t get more details nor did I ask for them.
Sean Davis (10:52:02) (in thread): > A positive result was the increased visibility and news coverage of some of these critical resources. Hopefully, it was a singular blip.
Robert Castelo (13:11:25) (in thread): > You may also want to add the Bioconductor packageGenomicScoresthat provides access to different types of genomic scores including conservation, minor allele frequencies or pathogeniticy, such as CADD or AlphaMissense scores (see section 7 of itsvignette). - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.
2025-03-09
yuvashree v (04:12:15): > @yuvashree v has joined the channel
2025-03-10
Sean Davis (07:31:54): > https://www.nature.com/articles/d41586-025-00383-x - Attachment (Nature): ‘I was told to toughen up’: is academia getting resilience all wrong? > Being repeatedly told to bounce back and develop a thicker skin can mask a toxic lab culture.
Hiru (11:29:45): > @Hiru has joined the channel
MN (16:04:39): > @MN has joined the channel
Yanina Bellini Saibene (21:10:16): > :mega:The call for therOpenSci Champions Program 2025in Spanish edition is open. In this blogspot, you have all the details to participate::writing_hand:ESP:https://ropensci.org/es/blog/2025/03/10/campeones-america-latina/:memo:ENGhttps://ropensci.org/blog/2025/03/10/champeons-latin-america/We have also scheduled an event with champions and mentors who will share their experiences in previous cohorts for Wednesday, 12/03.:video_camera:https://ropensci.org/es/commcalls/champions-latino-2025/Share this info with your community!! > Help us spread the word by sharing our blog or these social media posts:pray:: > * Español, LinkedIn. > * English, LinkedIn. > * English, Mastodon > * Español, Mastodon > * English, BlueSky > * Español, BlueSky - Attachment (es.linkedin.com): #rse #datosabiertos #softwarelibre #cienciaabierta #cienciadedatos | rOpenSci > ¡Llegó el día! :tada: :tada: > Se abre el llamado al programa de campeon(a|e)s en español edición 2025. En este blogspot tenes todos los detalles para participar: > > :memo:…
Nicholas Medina (22:53:40): > @Nicholas Medina has joined the channel
2025-03-11
Sanika Menkudale (07:09:29): > @Sanika Menkudale has joined the channel
Sean Davis (11:31:35): > CZI starts the openRxiv nonprofit to support bioRxiv and medRxiv:https://openrxiv.org/ - Attachment (openRxiv): Homepage - openRxiv > openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.
Ying Lu (13:37:32): > @Ying Lu has joined the channel
Keshini (17:09:45): > @Keshini has joined the channel
2025-03-12
Rafael (09:21:18): > @Rafael has joined the channel
Joy Sung (17:13:27): > @Joy Sung has joined the channel
Joseph Rich (18:05:01): > @Joseph Rich has joined the channel
Sisi Wang (19:41:44): > @Sisi Wang has joined the channel
2025-03-13
Mihai Todor (06:58:15): > @Mihai Todor has joined the channel
Konstantinos Kardamiliotis (07:49:05): > @Konstantinos Kardamiliotis has joined the channel
Riya ann paul (16:55:33): > @Riya ann paul has joined the channel
2025-03-14
kli klei (11:49:18): > @kli klei has joined the channel
2025-03-15
Vish Nair (21:29:15): > @Vish Nair has joined the channel
2025-03-16
Noelle Teague (17:39:10): > @Noelle Teague has joined the channel
2025-03-17
Pedro Sanchez (07:25:39): > Hi! I’m trying to upgrade our file organization in the lab. The majority of raw files come from sequencing. What guidelines would you follow? Which resources can I read about it? > Many thanks and let me know if I can discuss about this in a proper channel !
Keenan (09:52:07): > @Keenan has joined the channel
Pariksheet Nanda (10:34:39) (in thread): > Is the status page down for anyone else?
Pariksheet Nanda (10:34:48) (in thread): > The server returned a "500 Internal Server Error".
Sean Davis (10:54:01) (in thread): > Down for me. It is a freemium service, so I suspect it will come back up soon.
Agboola Abimbola (11:57:01): > @Agboola Abimbola has joined the channel
Shade Akinremi (12:04:33): > @Shade Akinremi has joined the channel
thebluevirtue (12:12:34): > @thebluevirtue has joined the channel
Jesulolufemi Adelanke (12:14:44): > @Jesulolufemi Adelanke has joined the channel
Eseoghene Cynthia Princewill-Ukot (12:22:59): > @Eseoghene Cynthia Princewill-Ukot has joined the channel
progress olaoye (12:28:23): > @progress olaoye has joined the channel
Precious Chijioke (12:42:11): > @Precious Chijioke has joined the channel
Daberechi Okorie (12:53:33): > @Daberechi Okorie has joined the channel
Dorcas Odetayo (13:11:23): > @Dorcas Odetayo has joined the channel
Anne-Marie Sharp (13:14:33): > @Anne-Marie Sharp has joined the channel
Chidimma Ekenedu (13:28:21): > @Chidimma Ekenedu has joined the channel
Yvette Odionye (13:37:53): > @Yvette Odionye has joined the channel
Jane Ezeala (Jannyblink’s) (14:08:11): > @Jane Ezeala (Jannyblink’s) has joined the channel
Emily Chima (14:20:52): > @Emily Chima has joined the channel
Ambogo (14:30:08): > @Ambogo has joined the channel
Utibe Ita (14:49:55): > @Utibe Ita has joined the channel
Igber Nicholas (15:19:09): > @Igber Nicholas has joined the channel
Adelaide (16:32:34): > @Adelaide has joined the channel
Halima Momoh (16:34:34): > @Halima Momoh has joined the channel
Lois Omonaiye (16:42:05): > @Lois Omonaiye has joined the channel
Richard Akintola (17:09:53): > @Richard Akintola has joined the channel
Francisca Gundu (17:20:08): > @Francisca Gundu has joined the channel
chumarjay (18:43:14): > @chumarjay has joined the channel
isaac imitini (19:09:18): > @isaac imitini has joined the channel
Divya Karlapudi (22:27:13): > @Divya Karlapudi has joined the channel
Fik (22:44:00): > @Fik has joined the channel
2025-03-18
Krisha Jada (00:01:03): > @Krisha Jada has joined the channel
NIDHI SINGH (01:05:07): > @NIDHI SINGH has joined the channel
Star Chukwunyerenwa (Ozi) (05:20:11): > @Star Chukwunyerenwa (Ozi) has joined the channel
Marjorie Bourgoin (05:47:24): > @Marjorie Bourgoin has joined the channel
chiamaka Uche (06:00:54): > @chiamaka Uche has joined the channel
Oladipo Abolanle (07:20:40): > @Oladipo Abolanle has joined the channel
emmanuel adeitan (08:38:03): > @emmanuel adeitan has joined the channel
Munachi Elekwa (10:11:51): > @Munachi Elekwa has joined the channel
Marvellous Jayesimi (10:48:10): > @Marvellous Jayesimi has joined the channel
Kafayat Azeez-Fashola (10:49:13): > @Kafayat Azeez-Fashola has joined the channel
Adebisi Adeyemi (11:28:52): > @Adebisi Adeyemi has joined the channel
Anthony (13:07:57): > @Anthony has joined the channel
Jennifer Slotnick (13:09:06): > @Jennifer Slotnick has joined the channel
Muraina Boluwatife (13:42:50): > @Muraina Boluwatife has joined the channel
Preethi grace Manthena (14:07:30): > @Preethi grace Manthena has joined the channel
Kehinde Kilanko (14:23:08): > @Kehinde Kilanko has joined the channel
Álvaro Sánchez Hernández (14:53:27): > @Álvaro Sánchez Hernández has joined the channel
Nicolo (14:57:55): > @Nicolo has joined the channel
Mariam Omiteru (15:18:55): > @Mariam Omiteru has joined the channel
Roman Iureniev (18:27:33): > @Roman Iureniev has joined the channel
Axel (19:41:30): > @Axel has joined the channel
Kibe Ume (20:33:01): > @Kibe Ume has joined the channel
Sivaranjani Balachander (22:27:59): > @Sivaranjani Balachander has joined the channel
2025-03-19
Amaka (03:48:02): > @Amaka has joined the channel
Ifunanya Benita Obiaku (03:54:17): > @Ifunanya Benita Obiaku has joined the channel
Oriade Adeola (09:42:50): > @Oriade Adeola has joined the channel
iniobong simeon (10:10:26): > @iniobong simeon has joined the channel
Ayomide Olugbenga Ojo (11:16:53): > @Ayomide Olugbenga Ojo has joined the channel
Ndukauba Oluchi (12:32:06): > @Ndukauba Oluchi has left the channel
Sophiane Bouirdene (14:28:24): > @Sophiane Bouirdene has joined the channel
D-coder111 (16:23:12): > @D-coder111 has joined the channel
2025-03-20
Chinenye Aroh (09:14:54): > @Chinenye Aroh has joined the channel
Tina Hsieh (10:21:12): > @Tina Hsieh has joined the channel
Armand Bankhead (15:47:34): > @Armand Bankhead has joined the channel
2025-03-22
Vanisha Garg (07:56:31): > @Vanisha Garg has joined the channel
2025-03-24
Lama Salem (17:29:31): > @Lama Salem has joined the channel
2025-03-25
Montana-D (06:47:09): > @Montana-D has joined the channel
Yunyi Cheng (15:54:47): > @Yunyi Cheng has joined the channel
2025-03-26
nithya (11:41:34): > @nithya has joined the channel
GiuliaGuidu (12:13:22): > @GiuliaGuidu has joined the channel
Ameenat Oloko (13:15:42): > @Ameenat Oloko has joined the channel
2025-03-27
Jacqueline Murphy (05:41:05): > @Jacqueline Murphy has joined the channel
Yanina Bellini Saibene (09:41:04): > rOpenSci March news!:envelope_with_arrow:#RStats:mega:rOpenSci Champions Program 2025 In Spanish: Apply before April 30th!:tada:New rOpenSci Champion(a|e)s Program cohort:rocket:Better documentation for R-universe!:handshake:rOpenSci Participation at NumFOCUS’ DISC Unconf 2025:video_camera:Community Call “Fomentando la Ciencia Abierta en América Latina - Programa de rOpenSci” Resources:spiral_calendar_pad:Coworking:world_map:New packages {pangoling}, {mbquartR}, {mapmetadata}, {geotargets}, {saperlipopette}:sparkles:3 use cases, of {osmextract} and {babelquarto}:memo:Blog posts:raised_back_of_hand:Calls for contributions:toolbox:Package development cornerhttps://ropensci.org/blog/2025/03/27/news-march-2025/ - Attachment (ropensci.org): rOpenSci News Digest, March 2025 > Call for
Claire Rioualen (09:56:10) (in thread): > Hi! Not sure about internal organisation, but if you’re interested in data management and deposition: > * In France there is a national repository for data deposition, and “thematic reference centres” that can help or orientate people depending on their research Focus > * In Europe there are also some useful resources provided or recomended by the ELIXIR network, such as theResearch Data Management community, a list ofdatabases for data deposition, or maybe theData Stewardship Wizardresources - Attachment (recherche.data.gouv.fr): Recherche Data Gouv > To share or open up research data, these need to be deposited in a trustworthy data repository that promotes the FAIR (Findable, Accessible, Interoperable,… - Attachment (elixir-europe.org): ELIXIR Deposition Databases for Biomolecular Data | ELIXIR > ELIXIR has compiled a list of resources that it recommends for the deposition of experimental data. The scientific community has a shared responsibility to ensure long-term data preservation and accessibility. The purpose of this Deposition Databases list is to provide guidance to those who formulate policy and working practices about the appropriate repositories for publishing open data in the life sciences. - Attachment (ds-wizard.org): Data Stewardship Wizard > Leading open-source platform for collaborative and living data management plans trusted worldwide from data management pioneers to international research institutes.
skruettn (10:43:19): > @skruettn has joined the channel
Tiia Freeman (18:43:24): > @Tiia Freeman has joined the channel
2025-03-28
Khadija Juma (07:17:39): > @Khadija Juma has joined the channel
Mitch Kitoi (07:20:20): > @Mitch Kitoi has joined the channel
Noel Okumu (07:24:41): > @Noel Okumu has joined the channel
Bridget Imarhia (09:40:20): > @Bridget Imarhia has joined the channel
Eren Ada (19:56:37): > @Eren Ada has joined the channel
2025-03-29
Hashaam Khan (18:22:12): > @Hashaam Khan has joined the channel
2025-03-30
Amarachi Ordor (03:41:29): > @Amarachi Ordor has joined the channel
aw (13:00:56): > @aw has joined the channel
2025-03-31
Bola (09:19:24): > @Bola has joined the channel
Sophia Mogere (15:38:40): > @Sophia Mogere has joined the channel
David M. (16:23:19): > @David M. has joined the channel
2025-04-01
Proffagelle (10:42:27): > @Proffagelle has joined the channel
2025-04-02
Krittiyabhorn Kongtanawanich (00:35:31): > @Krittiyabhorn Kongtanawanich has joined the channel
Hugo Gruson (03:54:00): > @Hugo Gruson has joined the channel
2025-04-03
Adrienne (09:25:50): > @Adrienne has joined the channel
2025-04-04
Adriana Flores (10:21:44): > @Adriana Flores has joined the channel
Dan Ngugi (15:03:00): > @Dan Ngugi has joined the channel
2025-04-07
Felix Lisso (05:43:43): > @Felix Lisso has joined the channel
Precious (10:45:33): > @Precious has joined the channel
Bianca Boisvert (10:59:52): > @Bianca Boisvert has joined the channel
Pedro Sanchez (12:05:33) (in thread): > Thanks very much, Claire! I totally missed your message
2025-04-08
Austin Morrissey (00:51:37): > @Austin Morrissey has joined the channel
Pedro Madrigal (12:02:32): > @Pedro Madrigal has joined the channel
Xinyi Jiang (12:43:06): > @Xinyi Jiang has joined the channel
Ahmed Hamid Awan (14:37:38): > @Ahmed Hamid Awan has joined the channel
2025-04-09
Guannan Yang (04:04:09): > @Guannan Yang has joined the channel
İrem Işıkoğlu (15:41:04): > @İrem Işıkoğlu has joined the channel
2025-04-10
Hossein Moosavi (05:30:55): > @Hossein Moosavi has joined the channel
2025-04-11
Feargal Ryan (03:49:30): > @Feargal Ryan has joined the channel
Antonia Beatriz Soler Riera (09:09:54): > @Antonia Beatriz Soler Riera has joined the channel
Gonza Gertrude (10:30:44): > @Gonza Gertrude has left the channel
Cristopher Fierro (11:42:26): > @Cristopher Fierro has joined the channel
Kayleigh Lawson-Michod (11:58:23): > @Kayleigh Lawson-Michod has joined the channel
2025-04-13
Jhulimar Doerl (20:55:27): > @Jhulimar Doerl has joined the channel
2025-04-14
Saad Farooq (07:06:20): > @Saad Farooq has joined the channel
Danielle_Hunt (11:02:44): > @Danielle_Hunt has joined the channel
Joseph Okoye (17:28:20): > @Joseph Okoye has joined the channel
2025-04-16
Lori Shepherd (15:21:24): > 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
Kevin Rue-Albrecht (11:16:49): > In the current funding environment , if Bioconductor needs to diversify funding sources, I found myself a water bottle on Amazon in just the right colour scheme:innocent:would have bought it from the Bioconductor store if there was one:stuck_out_tongue_winking_eye: - File (JPEG): IMG_3926
Fabricio Almeida-Silva (12:20:45) (in thread): > We would all love a Bioconductor store. Should we start a petition?
dhvani solanki (16:07:35): > @dhvani solanki has joined the channel
Khanh (16:36:07): > @Khanh has joined the channel
2025-04-18
D. Taylor (10:29:29): > @D. Taylor has joined the channel
Shashwati (15:23:48): > @Shashwati has joined the channel
2025-04-19
Kevin Rue-Albrecht (17:11:52): > Fun fact,it’sreal:https://pypi.org/project/tariff/ - Attachment (PyPI): tariff > Make importing great again! A parody package that imposes tariffs on Python imports. - File (JPEG): Image from iOS
2025-04-20
Laurent Gatto (00:41:23) (in thread): > It is funny, but maybe not totally useless to avoid too many dependencies - every additional (non-core) package you depend on costs you 5%.
Dr. ZUBAIDA KHATOON (06:08:58): > @Dr. ZUBAIDA KHATOON has joined the channel
2025-04-21
Promita (09:25:55): > @Promita has joined the channel
Yue-Chen Liu (15:11:16): > @Yue-Chen Liu has joined the channel
2025-04-22
Silvia González (10:19:50): > @Silvia González has joined the channel
pedro silva lerena (13:47:32): > @pedro silva lerena has joined the channel
2025-04-23
Emma Sharp (00:08:37): > @Emma Sharp has joined the channel
Anika Jaswal (07:11:50): > @Anika Jaswal has joined the channel
Dafne (12:11:46): > @Dafne has joined the channel
Jessica (12:17:57): > @Jessica has joined the channel
MWorks (12:20:06): > @MWorks has joined the channel
2025-04-24
Ali Hajj (03:24:50): > @Ali Hajj has joined the channel
Maria Eleni Fafouti (11:10:21): > @Maria Eleni Fafouti has joined the channel
Amaan (13:38:27): > @Amaan has joined the channel
2025-04-25
Marisa Loach (04:56:56): > @Marisa Loach has joined the channel
Pedro Sodrzeieski (15:11:32): > @Pedro Sodrzeieski has joined the channel
Eduarda Guimarães Sousa (15:27:38): > @Eduarda Guimarães Sousa has joined the channel
Carlos Mata-Machado (21:21:13): > @Carlos Mata-Machado has joined the channel
2025-04-27
vaishnavi (00:31:04): > @vaishnavi has joined the channel
2025-04-28
Yanina Bellini Saibene (14:03:49): > rOpenSci April news!:envelope_with_arrow:#RStats:mega:Event: Career Paths for U.S. Federal Data Scientists:trophy:rOpenSci Champions Program 2025 In Spanish: Apply before April 30th!:newspaper:Noam RossandYanina Bellini Saibenein the News:capital_abcd:More Languages, More Access: Discover rOpenSci in Spanish:spiral_calendar_pad:Coworking:package:New packages {gtexr}, {c3dr}:memo:Blog posts:computer:Calls for contributions:toolbox:Package development cornerhttps://ropensci.org/blog/2025/04/28/news-april-2025/ - Attachment (ropensci.org): rOpenSci News Digest, April 2025 > Career Paths for U.S. Federal Data Scientists, Website in Spanish
seigi (14:04:54): > @seigi has joined the channel
Brian Repko (16:09:10): > @Brian Repko has left the channel
2025-04-29
Esme Phillips (09:19:15): > @Esme Phillips has joined the channel
Yi-Chi Chu (10:58:35): > @Yi-Chi Chu has joined the channel
2025-04-30
George Kemboi (07:55:38): > @George Kemboi has joined the channel
MARTA SEVILLA PORRAS (12:12:32): > @MARTA SEVILLA PORRAS has joined the channel
So Yoen Choi (15:04:45): > @So Yoen Choi has joined the channel
Haroon (23:42:00): > @Haroon has joined the channel