The Bioconductor 3.22 release is now available. It includes 2,361 software packages, 435 experiment data packages, 926 annotation packages, 29 workflows, and 6 books. This cycle adds 59 new software packages, 6 new experiment data packages, 2 new annotation packages, and 1 new book, along with many updates across the existing ecosystem. A few themes stand out for people working in genomics, single-cell transcriptomics, and spatial omics.
MIT Technology Review : Biodiversity: A missing link in combating climate change Science : At futuristic meeting, AIs took the lead in producing and reviewing all the studies . Nextflow plugin registry: registry.nextflow.io . posit::conf(2025) Quarto workshop materials . At posit::conf(2025), Posit hosted two Quarto workshops: Branded Websites, Presentations,
Bruno Rodrigues: A Polyglot Data Science Pipeline with rixpress . This post demonstrates the power of the rixpress R package to build, orchestrate, and execute a fully reproducible, polyglot data science pipeline.
I used Google Docs in a recent paper I led because I had collaborators across the US, UK, Jersey, Denmark, and Mauritius, and Google Docs is infinitely better than Word online / O365 at collaborative real-time editing. I’ve used Zotero for over a decade for reference management, and I used it for this paper.
GPU Support in Bioconductor . GPU acceleration enables faster and more scalable analysis workflows, especially for tasks like deep learning, image processing, and large-scale genomics. Bioconductor is developing better support for maintainers authoring GPU-capable packages, including adding a new Nvidia GPU build machine, new release and devel (Nvidia) GPU software builds, GPU-aware containers, and a biocViews GPU term.
I recommend subscribing to Claus Wilke’s newsletter, Genes, Minds, Machines. I’ve linked to many of his essays in recent weeks. This one was a good read. Now that I’m back in academia and will be taking on Ph.D. students in my lab, this was good advice for me to read, as a future mentor.
In cybersecurity, defenders have to get everything right. Cyber defense must patch every vulnerability, secure every endpoint, anticipate every exploit. Attackers, by contrast, only need to find one overlooked flaw. That imbalance, which has shaped decades of cyber conflict, has a biological analogue.
The most recent release of Positron (2025.10.0 build 199) has a few updates to the data explorer. Among other things, the actions you take in the data explorer like filtering and sorting can be converted to code: dplyr code for data frames, and SQL for DuckDB datasets.
Happy Friday, colleagues. It’s the end of the week and once again I’m going through my long list of idle browser tabs trying to catch up where I can. Lots of R and AI-related news this week. Subscribe now Strengthening nucleic acid biosecurity screening against generative protein design tools. This was a really cool paper published in Science this week from a team at Microsoft, Battelle, IDT, Twist, and others.
Over the weekend I stumbled across an interesting conference paper: Evaluating and Improving Navigability of Wikipedia . The article shows if you follow the first link in the main text of an English Wikipedia article, and then repeat the process for subsequent articles, it’ll lead you to Philosophy 97% of the time. I had my doubts, so I gave this a try with a few topics close to me. From Data science
Happy Friday, colleagues. It’s the end of the week and once again I’m going through my long list of idle browser tabs trying to catch up where I can. Lots of R and AI-related news this week. Subscribe now Emil Hvitfeldt: Slidecrafting (slidecrafting-book.com) . This is a really wonderful one-stop shop for tips on making beautiful slides with reveal.js and Quarto.