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#Bioconductor

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Bioconductor<p>Bioconductor 3.21 is released!</p><p>A huge thank you to all developers and community members for your contributions.<br>Explore what’s new in the full release announcement:<br><a href="https://bioconductor.org/news/bioc_3_21_release/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">bioconductor.org/news/bioc_3_2</span><span class="invisible">1_release/</span></a></p><p><a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RStats</span></a></p>
Lluís Revilla<p>Some <a href="https://fosstodon.org/tags/R" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>R</span></a> <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rstats</span></a> about the packages on the repositories: <a href="https://fosstodon.org/tags/CRAN" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CRAN</span></a> has 722 packages that use Bioconductor (3%), <a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> has 2802 packages that use CRAN's packages (77%). </p><p>1.3% CRAN and 0.6% Bioconductor respectively use package outside these two repositories. But 91% and 93% use packages on their respective repos. 8% and 3% do not have any dependency on external packages (but could depend on system dependencies).</p>
Bioconductor<p>🎓🌍 Bioconductor Kenya Course Kickoff! 🎉 Our first Bioconductor course in Africa started in Nairobi! Day 1 featured learning and collaboration with Laurent Gatto, and Michael Landi. Sessions later this week by Fabricio Almeida-Silva, Laurah Ondari, and Zedias Chikwambi. Thanks to CZI and UL Global for funding. <br><a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a> <a href="https://genomic.social/tags/RProgramming" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RProgramming</span></a> <a href="https://genomic.social/tags/Carpentries" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Carpentries</span></a> <a href="https://genomic.social/tags/Africa" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Africa</span></a></p>
Posit<p>We’re pleased to announce that Posit Package Manager 2024.08.0 is now available! 📦 </p><p>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 noreferrer" target="_blank">#<span>logging</span></a>, improvements to <a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> performance, and more. </p><p>Learn more on our blog: <a href="https://posit.co/blog/posit-package-manager-2024-08-0/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">posit.co/blog/posit-package-ma</span><span class="invisible">nager-2024-08-0/</span></a></p><p><a href="https://fosstodon.org/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RStats</span></a> <a href="https://fosstodon.org/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Python</span></a></p>
Ludovic Courtès<p>Wanna contribute to the future of <a href="https://toot.aquilenet.fr/tags/Rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Rstats</span></a> and <a href="https://toot.aquilenet.fr/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> packages in <a href="https://toot.aquilenet.fr/tags/Guix" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Guix</span></a>?</p><p>Ricardo Wurmus is looking for successors to take care of the ‘guix-cran’ and ‘guix-bioc’ channels and explains the machinery that automatically keeps them up-to-date:<br><a href="https://lists.gnu.org/archive/html/guix-devel/2024-06/msg00169.html" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">lists.gnu.org/archive/html/gui</span><span class="invisible">x-devel/2024-06/msg00169.html</span></a></p><p><a href="https://toot.aquilenet.fr/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleResearch</span></a></p>
Ludovic Courtès<p>Fellow hacker Ricardo Wurmus takes a break, maybe that’s an opportunity for you to help <a href="https://toot.aquilenet.fr/tags/Guix" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Guix</span></a>?<br><a href="https://lists.gnu.org/archive/html/guix-devel/2024-05/msg00227.html" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">lists.gnu.org/archive/html/gui</span><span class="invisible">x-devel/2024-05/msg00227.html</span></a></p><p>If you’d like to give a hand on <a href="https://toot.aquilenet.fr/tags/CRAN" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CRAN</span></a> and <a href="https://toot.aquilenet.fr/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> packaging, on mentoring, <a href="https://toot.aquilenet.fr/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Python</span></a> packaging, or Cuirass CSS+JS, get in touch with Ricardo!</p>
Ludovic Courtès<p>All* of <a href="https://toot.aquilenet.fr/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> in a <a href="https://toot.aquilenet.fr/tags/Guix" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Guix</span></a> channel, thanks to the incredible Ricardo Wurmus:<br><a href="https://hpc.guix.info/channel/guix-bioc" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">hpc.guix.info/channel/guix-bio</span><span class="invisible">c</span></a></p><p>* Actually everything not already in Guix, minus a few big data packages.</p>
Ludovic Courtès<p><a href="https://toot.aquilenet.fr/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> source code tarballs tend to quickly vanish from bioconductor.org, which hampers reproducibility.</p><p>So far, those referred to by <a href="https://toot.aquilenet.fr/tags/Guix" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Guix</span></a> were not being archived by <a href="https://toot.aquilenet.fr/tags/SoftwareHeritage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SoftwareHeritage</span></a>, but the good news is that the good people at <span class="h-card"><a href="https://mstdn.social/@swheritage" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>swheritage</span></a></span> are already addressing it:<br><a href="https://issues.guix.gnu.org/39885#15" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="">issues.guix.gnu.org/39885#15</span><span class="invisible"></span></a></p><p><a href="https://toot.aquilenet.fr/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleResearch</span></a> <a href="https://toot.aquilenet.fr/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a></p>
Aidan :rna:<p>Been here for a little bit but still haven’t done a <a href="https://genomic.social/tags/introduction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>introduction</span></a> :mastodon: — I’m a PhD candidate at Pitt working on <a href="https://genomic.social/tags/phylogenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenomics</span></a>, specifically using <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>genomics</span></a> <a href="https://genomic.social/tags/bigdata" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bigdata</span></a> to predict gene function de novo by looking at how genetic regions have evolved together over time. <br>I write lots of code in <a href="https://genomic.social/tags/R" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>R</span></a> and <a href="https://genomic.social/tags/C" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>C</span></a> for <a href="https://genomic.social/tags/bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioconductor</span></a>, feel free to tag me on anything related to this post! I also write tutorials based on the work I do and have a blog (both linked on my profile page) :rna: :rna:<br><a href="https://genomic.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rstats</span></a></p>
Laurent Gatto<p>Hello, here's my fediverse <a href="https://fosstodon.org/tags/introduction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>introduction</span></a>:</p><p>I'm a computational biologist/bioinformatician, professor at UCLouvain in Brussels. I work with various types of omics data, with a special interest in <a href="https://fosstodon.org/tags/MassSpectrometry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MassSpectrometry</span></a> and <a href="https://fosstodon.org/tags/proteomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>proteomics</span></a>. I (co-)develop and maintain several <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rstats</span></a> and <a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> packages. In addition to R, I use <a href="https://fosstodon.org/tags/emacs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>emacs</span></a> quite a bit, and run.</p><p>Thanks for reading!</p>
Johannes Rainer<p>Hi there! </p><p>I'm developing open source software for <a href="https://fosstodon.org/tags/metabolomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>metabolomics</span></a> and <a href="https://fosstodon.org/tags/massspectrometry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>massspectrometry</span></a> data (👉 <a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a>) and doing <a href="https://fosstodon.org/tags/metabolomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>metabolomics</span></a> and <a href="https://fosstodon.org/tags/proteomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>proteomics</span></a> research. </p><p>Happy to be here now :blobcatcheer:</p>
Susan Holmes<p>Hello there.<br>I moved from mastodon.social to fosstodon.org to keep nerding out about <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rstats</span></a> (:rstats:) and <a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a>, <a href="https://fosstodon.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a>, Immunology and <a href="https://fosstodon.org/tags/Microbiome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Microbiome</span></a>, as well as general science and Maths. Sorry for the double posting, still trying to get to know the ropes of our new digs. I love it that the community just up and moved so quickly...talk to you soon.🤓</p>
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