#bioconductor — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #bioconductor, aggregated by home.social.
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Was seeing some very, very odd failures in multicore processing using `furrr` when `SummarizedExperiment` was loaded, when using R 4.4.1
I'm guessing there was a weird thing in the `BiocGenerics` package that wasn't playing nice.
So part of today's fun was upgrading to #RStats 4.6.0 (source on older fedora 39, and deb on Pop!OS) to get the latest version of #Bioconductor packages.
That seems to have fixed the bug I was seeing, at least.
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Was seeing some very, very odd failures in multicore processing using `furrr` when `SummarizedExperiment` was loaded, when using R 4.4.1
I'm guessing there was a weird thing in the `BiocGenerics` package that wasn't playing nice.
So part of today's fun was upgrading to #RStats 4.6.0 (source on older fedora 39, and deb on Pop!OS) to get the latest version of #Bioconductor packages.
That seems to have fixed the bug I was seeing, at least.
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Was seeing some very, very odd failures in multicore processing using `furrr` when `SummarizedExperiment` was loaded, when using R 4.4.1
I'm guessing there was a weird thing in the `BiocGenerics` package that wasn't playing nice.
So part of today's fun was upgrading to #RStats 4.6.0 (source on older fedora 39, and deb on Pop!OS) to get the latest version of #Bioconductor packages.
That seems to have fixed the bug I was seeing, at least.
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Was seeing some very, very odd failures in multicore processing using `furrr` when `SummarizedExperiment` was loaded, when using R 4.4.1
I'm guessing there was a weird thing in the `BiocGenerics` package that wasn't playing nice.
So part of today's fun was upgrading to #RStats 4.6.0 (source on older fedora 39, and deb on Pop!OS) to get the latest version of #Bioconductor packages.
That seems to have fixed the bug I was seeing, at least.
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Was seeing some very, very odd failures in multicore processing using `furrr` when `SummarizedExperiment` was loaded, when using R 4.4.1
I'm guessing there was a weird thing in the `BiocGenerics` package that wasn't playing nice.
So part of today's fun was upgrading to #RStats 4.6.0 (source on older fedora 39, and deb on Pop!OS) to get the latest version of #Bioconductor packages.
That seems to have fixed the bug I was seeing, at least.
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📅 Registration and schedule information for BioC2026 is now available.
The conference schedule is now live on the BioC2026 website, and registration is officially open for:
• the conference
• the Bioconductor-Carpentries Workshop
• the HackathonIf you’re planning to attend, now is a great time to explore the program and register. Early bird pricing ends on 15 June 2026.
🎟️ More details and registration: https://bioc2026.bioconductor.org
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📮You've got mail! 💌
We are thrilled to invite you to "Where do R packages live?" a discussion with folks from the #R foundation, #CRAN #Bioconductor #R-universe and @Posit
Let's learn from our panel about the ins-and-outs of where you might want to create a home for your R software 📦
Register today!
📆 Wed 20 May 2026
⏰ 5:00 PM AEST | 7:00 AM UTC
🔗 statsoc.org.au/event-6653060Looking forward to nerdy chats with @visnut Stevie P. @jeroenooms and Valerie B.
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📣 Meet Nicholas Cooley, Bioconductor’s new Developer Engagement Lead.
In his latest blog post, Nick reflects on stepping into this role and what he hopes to achieve for the Bioconductor community.
His focus is on strengthening developer support, improving onboarding, especially for early-career researchers, and creating better recognition for the many contributors who sustain the project.
Find out more here: https://blog.bioconductor.org/posts/2026-04-09-developer-engagement/
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📣 Call for Late-Breaking Poster Abstracts – EuroBioC2026
If you missed the earlier poster submission deadline, you can now submit your work as a late-breaking poster for EuroBioC2026.
📝 Submit by: Thursday, April 30, 2026
🔗Submit here: https://docs.google.com/forms/d/e/1FAIpQLSdBkwTH84uIzaMk5Zy5kxdQnSkoDbaUGdmcbFD007hpL8i-cg/viewform
Decisions will be shared within a week of the deadline. If you need an earlier notification (e.g., for funding or visa applications), feel free to reach out at [email protected].
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Bioconductor Africa is excited to kick off its Advanced Training Series with an introductory session on Bioconductor!
In this session, we will explore:
- The foundations of the Bioconductor project
- How it supports biological data analysis
- Opportunities to get involved in the global community📅 April 15, 2026
⏰ 4 PM EAT | 3 PM CAT | 2 PM WAT
👤 Speaker: Kevin Rue-Albrecht🔗 Register to attend: https://us06web.zoom.us/meeting/register/4iy904brRviPrFSBxIukdg#/registration
Coming up next: Microbiome data analysis (May 2026)
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April 2026 will bring a new #Ubuntu 26.04, a new #Rstats release 4.6.0 and a new #BioConductor 3.23. And ... as the "future is unevenly distributed" we already have #r2u running 26.04.
See 'zero to tidyverse' now under 26.04: 10 sec, 107 binary files, 1 command.
#r2u. Fast. East. Reliable. Pick All Three.
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April 2026 will bring a new #Ubuntu 26.04, a new #Rstats release 4.6.0 and a new #BioConductor 3.23. And ... as the "future is unevenly distributed" we already have #r2u running 26.04.
See 'zero to tidyverse' now under 26.04: 10 sec, 107 binary files, 1 command.
#r2u. Fast. East. Reliable. Pick All Three.
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April 2026 will bring a new #Ubuntu 26.04, a new #Rstats release 4.6.0 and a new #BioConductor 3.23. And ... as the "future is unevenly distributed" we already have #r2u running 26.04.
See 'zero to tidyverse' now under 26.04: 10 sec, 107 binary files, 1 command.
#r2u. Fast. East. Reliable. Pick All Three.
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April 2026 will bring a new #Ubuntu 26.04, a new #Rstats release 4.6.0 and a new #BioConductor 3.23. And ... as the "future is unevenly distributed" we already have #r2u running 26.04.
See 'zero to tidyverse' now under 26.04: 10 sec, 107 binary files, 1 command.
#r2u. Fast. East. Reliable. Pick All Three.
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April 2026 will bring a new #Ubuntu 26.04, a new #Rstats release 4.6.0 and a new #BioConductor 3.23. And ... as the "future is unevenly distributed" we already have #r2u running 26.04.
See 'zero to tidyverse' now under 26.04: 10 sec, 107 binary files, 1 command.
#r2u. Fast. East. Reliable. Pick All Three.
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🎉 Announcing the BioC2026 Sticker Design Winner: Kavya Vaddadi 🎉
Kavya's design celebrates Seattle as the host city of BioC 2026, featuring well-known
landmarks such as the Space Needle, the Seattle Great Wheel, Mount Rainier, and the surrounding evergreen forests. Puget Sound and a Washington State ferry reflect Seattle’s maritime landscape and the culture of connection across the region.👉 Register for BioC2026 here: https://ti.to/nf-projects/bioc2026
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🎉 Announcing the EuroBioC2026 Sticker Design Winner!
🏆 Winner: Rafael Romero Becerra, PhD
🎨 Rafael’s design captures Turku with the cathedral silhouette over the Aura River, Turku Castle in the background, and a playful nod to the iconic Posankka at the river’s edge. A Finnish–Scandinavian folk-art border ties it together, offering a warm regional welcome to the Bioconductor community.
👉 Register for EuroBioC2026 here: https://bit.ly/eurobioc2026-register
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📣 Final call! BioC2026 abstract submissions are closing soon.
Don't miss your chance to share your work and be part of the Bioconductor community at BioC2026. Submissions are welcome for workshops, posters, package demos, and short talks highlighting tools, research, and workflows in open-source bioinformatics.
⏰ Deadline: 20 March 2026
📍 BioC2026: 10–12 August 2026 | Seattle, WA, USA👉 Submit your abstract now:https://openreview.net/group?id=bioconductor.org/BioC/2026/Conference#tab-recent-activity
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📣 Call to Host EuroBioC2027
Interested in bringing the European Bioconductor Conference to your region? Applications are now open to host EuroBioC2027 or to join the planning committee to gain experience for future editions.
🗓 Application deadline: 20 April 2026
📍 Event timing: September / early October 2027 (flexible)👉 Apply here: https://docs.google.com/forms/d/e/1FAIpQLScpwfbLq9inCJgmLbmdstqL96--0biCZGrnOi5QVmveSH1mHw/viewform
📩 Questions? Email [email protected]
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📣 The BioC2026 Call for Abstracts deadline has been extended.
Good news! There’s still time to submit your work and be part of BioC2026. We welcome submissions for workshops, posters, package demos, and short talks that showcase tools, research, and workflows advancing open-source bioinformatics.
⏰ New submission deadline: 20 March 2026
📍 BioC2026: 10-12 August 2026 | Seattle, WA, USA👉 Submit your abstract here: https://openreview.net/group?id=bioconductor.org/BioC/2026/Conference#tab-recent-activity
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🎉 We’re delighted to share that Ting Ye will be joining BioC2026 as a keynote speaker!
Ting Ye is an Assistant Professor in Biostatistics whose research advances human health through data-driven discovery and quantitative medical research.
📍 Join us in Seattle, 10–12 August 2026
🚨Have work to share? Abstract submissions are open!
Submit here: https://openreview.net/group?id=bioconductor.org/BioC/2026/Conference#tab-recent-activityLearn more about BioC2026: bioc2026.bioconductor.org
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🚀 Registration for EuroBioC2026 is open!
EuroBioC2026 will bring together the global Bioconductor community to showcase the latest cutting-edge developments in Bioconductor software packages and broader emerging technologies shaping computational biology.
📅 June 3–5, 2026
📍 BioCity, Turku, FinlandRegister by May 3 to secure your spot:
https://eurobioc2026.bioconductor.org/pages/registration.html -
🎨 Reminder: One week left to submit your sticker design! 🎨
The BioC2026 Sticker Design Contest is still open, but the deadline is fast approaching. This is your chance to design the official hex sticker for BioC2026, inspired by Seattle, WA.
🗓 Deadline: February 20, 2026
👉 Submit your design here:
https://docs.google.com/forms/d/e/1FAIpQLSd_1PdKpXEjw4Ky14T43N-3eQQ783oFkDiaR0_Vu_rJJZG8Hg/viewform -
Does anyone know if the code for generating all of the underlying bits for #recount3 (genome indices, exons, genes, etc) for a different genome organism (i.e. zebrafish) is available publicly?
I know of the monorail-external repo that helps someone running their own human or mouse samples in the same workflow, but I've got data from zebrafish that I'd love to run similarly.
#Bioinformatics #Bioconductor #RStats
Maybe @benlangmead (or another) knows of something I missed?
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📢 Deadline Extended: EuroBioC2026 Call for Abstracts
Great news! The submission deadline for EuroBioC2026 has been extended to February 13, 2026, to allow more time for submissions.
We welcome submissions for:
💡 Short talks (10 minutes + Q&A)
💡 Posters (A0 portrait)
💡 Workshops (1.5-hour hands-on sessions)👉 Submit your abstract here: https://openreview.net/group?id=bioconductor.org/EuroBioC/2026/Conference#tab-recent-activity
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🎨 Reminder: Only a few days left to submit your sticker design! 🎨
The EuroBioC2026 sticker design contest is still open, but the deadline is fast approaching. This is your chance to design the official sticker for the European Bioconductor Conference, happening in June 2026 in Turku, Finland.
🗓 Deadline: January 31st, 2026
👉 Submit your design here: https://docs.google.com/forms/d/e/1FAIpQLSe6RZlyUspUBZAYKzjX_ctHg3HO-3I1D2y5YTGOTwj8-z6R_Q/viewform🔗 Learn more: https://eurobioc2026.bioconductor.org/
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⏰ Reminder: Pre-conference Workshop Proposals for EuroBioC2026
EuroBioC2026 will host on-site pre-conference workshops on June 1–2, 2026, in Turku, Finland, ahead of the main conference.
If you’re interested in hosting a workshop, please submit your interest here: https://docs.google.com/forms/d/e/1FAIpQLScYOBMs0JsmoZY21mCSnWSBObm-OX7NtZi6NEjY9zNdhsqL5w/viewform
🗓 Deadline: 30 January 2026
Selections will be based on relevance and alignment with the workshop and conference themes.
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In this lab, we try to cite our software tools. Hopefully they won't get removed by the primary author. But at least they are there to start.
Each comment here is a citation (I don't have Endnote, and I'm not sure how they are managing the citations, so it seemed easier to add them all as comments). There are more on the next page, but I figured this page was illustrative of what we should strive for as #academics citing our tools.
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🚀 EuroBioC2026 – Call for Abstracts is Now Open!
We invite submissions for short talks, posters, and workshops for EuroBioC2026.
🗓️ Important Dates
• 30 January 2026: Call closes👉 Submit your abstract here: https://openreview.net/group?id=bioconductor.org/EuroBioC/2026/Conference
⚠️ Note: The OpenReview submission system requires all submitters to create an account at least two weeks before the abstract deadline. Please register early to avoid issues
For any questions, contact [email protected]
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🚨 Last chance to register!
Registration for BioCAsia closes this Friday, 21 November, at 5 PM (Australia time) and this is your final opportunity to secure your spot.
BioCAsia will run in parallel with the ABACBS 2025 Workshops at Flinders University, Adelaide, on Thu 27 & Fri 28 November 2025. With both events hosted in the same venue, you can move seamlessly between sessions for a rich mix of topics and hands-on learning.
👉 Register now: https://www.abacbs.org/abacbs-2025-workshops
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We’re live at GBioS, University of Abomey-Calavi in Benin! 5 days of learning, coding & collaboration began yesterday at #BiocInBenin.
C’est parti! Une semaine d’apprentissage et de collaboration a commencé à GBioS hier.
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📣 Calling all Bioconductor users and developers! 🧬 ✨
We’re launching a new online quarterly seminar series showcasing contributor innovations and sparking conversations about how packages work together. Expect 30 minutes of insight, 15 minutes of guided discussion, and 15 minutes of open Q&A.
📅 Date: Dec 2, 2025
🕒 Time: 9 PM CET / 3 PM EST / 12 PM PST
➡️ Register: https://dfci.zoom.us/webinar/register/WN_0nAabJt1Qeyd8QsJjvEzOQ
📑 Paper: https://pmc.ncbi.nlm.nih.gov/articles/PMC12328236/ -
#r2u for #Rstats now also includes #BioConductor on arm64 and not only on standard amd64. Following the upgrade to #BioConductor 3.22 we added this hardware platform.
`zlibbioc` was removed so a few packages we have for amd64 could not be built. Should I backfill it (and them)?
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🌟 Sponsor Spotlight 🌟
The Chan Zuckerberg Initiative (CZI) supports the science and technology that will make it possible to cure, prevent, and manage all diseases within this century.
A huge thank you to CZI for being a Silver Sponsor of EuroBioC2025!
Interested in partnering with EuroBioC2026? Please contact [email protected]
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🌟 Sponsor Spotlight 🌟
ISGlobal is a consolidated hub of excellence in research that brings together the efforts of leading institutions in health care and academia. Through this collaboration, ISGlobal advances global health through cutting-edge research, policy, and training.
A huge thank you to ISGlobal for being a Silver Sponsor of EuroBioC2025!
Interested in partnering with EuroBioC2026? Please contact [email protected]
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@jeremy-data.bsky.social biology based on #bioconductor (and I’m a BioJava contributor) - also model building in health informatics (I’d use #tidymodels and #vetiver now) vs Python
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@jeremy-data.bsky.social biology based on #bioconductor (and I’m a BioJava contributor) - also model building in health informatics (I’d use #tidymodels and #vetiver now) vs Python
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@jeremy-data.bsky.social biology based on #bioconductor (and I’m a BioJava contributor) - also model building in health informatics (I’d use #tidymodels and #vetiver now) vs Python
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@jeremy-data.bsky.social biology based on #bioconductor (and I’m a BioJava contributor) - also model building in health informatics (I’d use #tidymodels and #vetiver now) vs Python
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@jeremy-data.bsky.social biology based on #bioconductor (and I’m a BioJava contributor) - also model building in health informatics (I’d use #tidymodels and #vetiver now) vs Python
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🌟 Sponsor Spotlight 🌟
Seqera centralizes data, streamlines pipelines, and brings mission-critical infrastructure under one secure, compliant umbrella.
A huge thank you to Seqera for being a Silver Sponsor of EuroBioC2025!
Interested in partnering with EuroBioC2026? Please contact [email protected]
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🌟 Sponsor Spotlight 🌟
The Department of Medicine and Life Sciences at Universitat Pompeu Fabra (MELIS-UPF) is a María de Maeztu Centre of Excellence advancing science with real social impact and strengthening Spain’s global visibility in life sciences.
A huge thank you to MELIS-UPF for being a Silver Sponsor of EuroBioC2025!
Interested in partnering with EuroBioC2026? Please contact [email protected]
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🧬Mark Your Calendars – EuroBioC2026 in Turku!
EuroBioC2026 will take place June 3 - 5, 2026, in beautiful Turku, Finland!
Expect three exciting days of the Bioconductor community highlighting the latest advances in Bioconductor software and emerging technologies shaping computational biology.More details coming soon.
Keep an eye on 👉 https://eurobioc2026.bioconductor.org/ -
Thank you to all our sponsors, organizers, speakers, and attendees for making #EuroBioC2025 in Barcelona such a success!
From inspiring keynote talks and engaging workshops to interactive poster sessions and community discussions, this year’s event highlighted the creativity and innovation driving the Bioconductor community.
Read the full recap blog post here 👉 https://blog.bioconductor.org/posts/2025-10-24-EuroBioC2025-recap/
See you next year at #EuroBioC2026! 🎉
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🚀 New on the Bioconductor Blog: GPU Support in Bioconductor
📝 Written by Andres Wokaty
Bioconductor is building stronger support for GPU-accelerated package development, enabling faster and more scalable analysis workflows.
Learn how package maintainers can take advantage of this new GPU infrastructure: https://blog.bioconductor.org/posts/2025-10-10-gpus/
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🌟 Save the Date! BioC2026 is Coming! 🌟
Mark your calendars! 🗓️ The Bioconductor Conference, BioC2026, will be at Fred Hutch Cancer Center, Seattle, WA, from August 10-12, 2026.
Join top experts in bioinformatics, data science, and computational biology to share insights and explore Bioconductor's latest advancements.
Stay tuned for registration, speakers, and program details. Visit: https://bioc2026.bioconductor.org/. 🎉
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Learned RNA-seq workflow using C. diff data from a study 🧬. Processed raw reads thru fastp → kallisto → DESeq2 pipeline. Results matched the original paper’s findings, with clear differential expression between mucus and control conditions 📊.
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Thanks to our EuroBioC2025 sponsors!
We’re grateful to our Silver and Bronze sponsors for helping make EuroBioC2025 in Barcelona possible. Your support brought the Bioconductor community together and made a real difference. 💙Silver: Seqera, UPF–María de Maeztu, Chan Zuckerberg Initiative, ISGlobal–Severo Ochoa
Bronze: R Consortium, BigOmics Analytics, MedBio Informatics, Physalia Courses -
EuroBioC2025 is in full swing here in Barcelona!
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!
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⏳ Last chance to register!
EuroBioC2025 and Bioconductor Carpentry Workshops close registration tomorrow!Secure your spot now and be part of the Bioconductor community in Barcelona.
🔗 https://eurobioc2025.bioconductor.org/#EuroBioC2025 #Bioconductor #Bioinformatics #Carpentries #FinalCall