#Bioconductor

Bioconductor📝 New blog post: Tagging Bioconductor packages with EDAM <a href="https://blog.bioconductor.org/posts/2025-07-18-edam/" rel="nofollow noopener" translate="no" target="_blank">https://blog.bioconductor.org/posts/2025-07-18-edam/</a> <a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#RStats</a> <a href="https://genomic.social/tags/EDAM" class="mention hashtag" rel="nofollow noopener" target="_blank">#EDAM</a> <a href="https://genomic.social/tags/Ontology" class="mention hashtag" rel="nofollow noopener" target="_blank">#Ontology</a>

Bioconductor💻🧬 Join the Bioconductor project at BioHackathon Europe 2025!We're excited to be part of BioHackathon Europe 2025 (Berlin, Nov 3–7) with a project focused on improving metadata and interoperability in bioinformatics.In-person registration closes Tuesday, July 15 - virtual participation stays open!🔗 Project details: <a href="https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/13.md" rel="nofollow noopener" translate="no" target="_blank">https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/13.md</a> 🔗 All projects: <a href="https://biohackathon-europe.org/projects/" rel="nofollow noopener" translate="no" target="_blank">https://biohackathon-europe.org/projects/</a>Join the discussion in the <a href="https://genomic.social/tags/edam" class="mention hashtag" rel="nofollow noopener" target="_blank">#edam</a>-collaboration channel on Bioconductor Zulip.<a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a>

Lluís RevillaIt is still 3 weeks away but there will be a developer session about <a href="https://fosstodon.org/tags/Rust" class="mention hashtag" rel="nofollow noopener" target="_blank">#Rust</a> and <a href="https://fosstodon.org/tags/rStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rStats</a> for <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> (and other interested developer) lead by Sun Wenji, and <a href="https://fosstodon.org/@josi" class="u-url mention" rel="nofollow noopener" target="_blank">@josi</a> among other :rust:-:rstats: developers 🚀 . I still don't know the link to the event but we know the date and hour, so mark your calendar 📆 July 28th at 17:00 to 18:00 CESTI'll share more details as soon as I know them<a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a>

Bioconductor📝 New blog post: Bioconductor and ggplot2 4.0.0 – What’s Changing and How to PrepareA major ggplot2 update (v4.0.0) is coming and may affect many Bioconductor packages. This post explains what’s changing, how to test your packages, and where to get help.📖 Read more: <a href="https://blog.bioconductor.org/posts/2025-07-07-ggplot2-update/" rel="nofollow noopener" translate="no" target="_blank">https://blog.bioconductor.org/posts/2025-07-07-ggplot2-update/</a><a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#RStats</a> <a href="https://genomic.social/tags/ggplot2" class="mention hashtag" rel="nofollow noopener" target="_blank">#ggplot2</a>

Bioconductor📝 New Bioconductor blog post!Written during <a href="https://genomic.social/tags/GBCC2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#GBCC2025</a> CoFest, this post highlights recent work to bring Bioconductor tools into Galaxy, featuring training materials, wrapper examples, and ideas for tool developers. Read more 👉 <a href="https://blog.bioconductor.org/posts/2025-07-03-bioc-to-galaxy/" rel="nofollow noopener" translate="no" target="_blank">https://blog.bioconductor.org/posts/2025-07-03-bioc-to-galaxy/</a><a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#RStats</a> <a href="https://genomic.social/tags/GalaxyProject" class="mention hashtag" rel="nofollow noopener" target="_blank">#GalaxyProject</a> <a href="https://genomic.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a>

BioconductorThank you to everyone who made <a href="https://genomic.social/tags/GBCC2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#GBCC2025</a> such a great week!From keynotes and technical talks to CoFest projects, it was a brilliant example of cross-community collaboration between Bioconductor and Galaxy 💻🧬<a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://genomic.social/tags/GalaxyProject" class="mention hashtag" rel="nofollow noopener" target="_blank">#GalaxyProject</a> <a href="https://genomic.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a>

Bioconductor📝 New blog post from the Bioconductor Training Committee!We’re collaborating with <a href="https://ecoevo.social/@physaliacourses2" class="u-url mention" rel="nofollow noopener" target="_blank">@physaliacourses2</a> to offer co-branded training in bioinformatics and computational biology.Read more 👉 <a href="https://blog.bioconductor.org/posts/2025-06-20-physalia-collaboration/" rel="nofollow noopener" translate="no" target="_blank">https://blog.bioconductor.org/posts/2025-06-20-physalia-collaboration/</a><a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://genomic.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a>

Bioconductor🎉 Two weeks in, and our move from Slack to Zulip is going great. Thanks to everyone in the Bioconductor community for helping make the switch smooth and getting involved in the new space.If you haven’t joined yet, come take a look: ➡️ <a href="https://chat.bioconductor.org" rel="nofollow noopener" translate="no" target="_blank">https://chat.bioconductor.org</a> 📖 <a href="https://blog.bioconductor.org/posts/2025-05-29-slack-to-zulip/" rel="nofollow noopener" translate="no" target="_blank">https://blog.bioconductor.org/posts/2025-05-29-slack-to-zulip/</a>Big thanks to the <a href="https://fosstodon.org/@zulip" rel="nofollow noopener" translate="no" target="_blank">https://fosstodon.org/@zulip</a> team for supporting open-source communities. <a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#RStats</a> <a href="https://genomic.social/tags/OpenSource" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenSource</a>

Bioconductor📝 New Bioconductor Blog Post!We’ve just launched the first in a new series by Vince Carey, founding contributor to Bioconductor and core developer, exploring the evolving complexity and value of the Bioconductor ecosystem.Check it out 👉 <a href="https://blog.bioconductor.org/posts/2025-05-26-ask" rel="nofollow noopener" translate="no" target="_blank">https://blog.bioconductor.org/posts/2025-05-26-ask</a><a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#RStats</a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://genomic.social/tags/DataScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#DataScience</a> <a href="https://genomic.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a>

Bioconductor🔔 In case you missed it: NEW scholarship opportunities to attend GBCC2025 are now open! We are thrilled to offer this opportunity to our community and hope to see you there!Apply now: <a href="https://forms.gle/WKoLb5NUR6FVmeRM9" rel="nofollow noopener" translate="no" target="_blank">https://forms.gle/WKoLb5NUR6FVmeRM9</a> <a href="https://genomic.social/tags/GBCC2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#GBCC2025</a> <a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://genomic.social/tags/UseGalaxy" class="mention hashtag" rel="nofollow noopener" target="_blank">#UseGalaxy</a> <a href="https://genomic.social/tags/DataScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#DataScience</a>

galaxyproject📣 GBCC2025 Poster Abstracts Deadline ExtendedGood news! The deadline for submitting your abstract for a poster presentation at GBCC2025 has been extended to May 9th. Join us at Cold Spring Harbor, June 23–26.We’re looking forward to seeing your work!🔗 Submit here: <a href="https://gxy.io/GBCC-abstracts" rel="nofollow noopener" translate="no" target="_blank">https://gxy.io/GBCC-abstracts</a><a href="https://mstdn.science/tags/GBCC2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#GBCC2025</a> <a href="https://mstdn.science/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://mstdn.science/tags/DataScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#DataScience</a> <a href="https://mstdn.science/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a> <a href="https://mstdn.science/tags/UseGalaxy" class="mention hashtag" rel="nofollow noopener" target="_blank">#UseGalaxy</a>

galaxyproject🎓 GBCC2025 Training Topics 🌟GBCC2025 is coming soon! We want to hear from you:- Topics you're interested in learning about - Interest in leading a sessionFill out the form by March 21st to help shape our training schedule!🔗 <a href="https://forms.gle/i34Ag8SHMtBAmpPh7" rel="nofollow noopener" translate="no" target="_blank">https://forms.gle/i34Ag8SHMtBAmpPh7</a> Thanks! 🙏 For more information about the Galaxy Bioconductor Community Conference (June 23 - 26, 2025), see the GBCC2025 website: <a href="https://gbcc2025.org" rel="nofollow noopener" translate="no" target="_blank">https://gbcc2025.org</a><a href="https://mstdn.science/tags/GBCC2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#GBCC2025</a> <a href="https://mstdn.science/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://mstdn.science/tags/DataScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#DataScience</a> <a href="https://mstdn.science/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a> <a href="https://mstdn.science/tags/UseGalaxy" class="mention hashtag" rel="nofollow noopener" target="_blank">#UseGalaxy</a>

kupac^ESC:wqDesperate bioinformatician looking for a function to calculate coverage based on a list of intervals. Something like summarising genomicranges to coverage values. Do you know something like that?UPDATE: `GenomicRanges::coverage` is a good candidate.<a href="https://functional.cafe/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://functional.cafe/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a> <a href="https://functional.cafe/tags/bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioconductor</a>

Jonathan CarrollMy very first <a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> package is now in the devel release <a href="https://bioconductor.org/packages/DFplyr" rel="nofollow noopener" translate="no" target="_blank">https://bioconductor.org/packages/DFplyr</a>🎉 This package brings {dplyr} verbs to S4 DataFrames ({S4Vectors}) so no need to detour your data through a tibble to slice, dice, and transform it. This also means that S4 columns (e.g. GRanges, NumericList, ...) are supported.<a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a> :rstats: 🧬

Dr. Robert M FlightThat means start *again*. But now {Rsamtools} won't compile! $#%&Finally got <a href="https://mastodon.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> version set properly, and {renv} respects it nicely, and finds everything properly using `renv::install("bioc::...").{Rsamtools} will compile if it's installed via {renv}, but not via {BiocManager}?? Whatever, it seems like it's all back finally, and just the manuscript itself is out of date, and all important packages are off by minor versions. Ugh.Almost makes me want to use docker images. / end

Dr. Robert M FlightBut I forgot about the manuscript revision we are still working on! 🙃 Which really shouldn't work with an updated R version and packages (especially {targets} due to new storage format!).OK, let's finally try out {rig}! And at worst case, all packages are listed in `renv.lock`, we can do this. 💪But many package versions listed in `renv.lock` don't match the <a href="https://mastodon.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> version recorded, those two somehow got out of sync. 😭 But I trusted the Bioconductor version listed initially. /2

Dr. Robert M FlightWas banging my head trying to figure out why an <a href="https://mastodon.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#RStats</a> package didn't want to install but kept segfaulting. {renv} still had the old version of <a href="https://mastodon.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> listed, so the incorrect version of package wasn't being downloaded to install. 🤦‍♂️Easiest thing was to wipe out {renv}, and start fresh.

PositWe’re pleased to announce that Posit Package Manager 2024.08.0 is now available! 📦 This release provides support for remote administration of Package Manager, more advanced configurable <a href="https://fosstodon.org/tags/logging" class="mention hashtag" rel="nofollow noopener" target="_blank">#logging</a>, improvements to <a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> performance, and more. Learn more on our blog: <a href="https://posit.co/blog/posit-package-manager-2024-08-0/" rel="nofollow noopener" translate="no" target="_blank">https://posit.co/blog/posit-package-manager-2024-08-0/</a><a href="https://fosstodon.org/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#RStats</a> <a href="https://fosstodon.org/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#Python</a>

galaxyproject🚀Announcing GBCC 2025: The first joint conference between Bioconductor & Galaxy!Join us June 23-26 at Cold Spring Harbor for workshops, talks, and more. Stay tuned for updates, including a logo contest!Read more in our blog post: <a href="https://galaxyproject.org/news/2024-09-03-gbc-c2025/" rel="nofollow noopener" translate="no" target="_blank">https://galaxyproject.org/news/2024-09-03-gbc-c2025/</a> <a href="https://mstdn.science/tags/GBCC2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#GBCC2025</a> <a href="https://mstdn.science/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://mstdn.science/tags/Galaxy" class="mention hashtag" rel="nofollow noopener" target="_blank">#Galaxy</a> <a href="https://mstdn.science/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://mstdn.science/tags/Genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genomics</a> <a href="https://mstdn.science/tags/DataScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#DataScience</a>

Jonathan CarrollA bigger post than usual this time, but I wanted to cover as much of the background as I could... <a href="https://jcarroll.com.au/2024/08/11/tidy-dataframes-but-not-tibbles/" rel="nofollow noopener" translate="no" target="_blank">https://jcarroll.com.au/2024/08/11/tidy-dataframes-but-not-tibbles/</a>{DFplyr} - use {dplyr} functions on an S4Vectors::DataFrame<a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a> <a href="https://fosstodon.org/tags/bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioconductor</a> <a href="https://fosstodon.org/tags/tidyomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#tidyomics</a>

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