📢 Join BioC2026 online! Although in-person registration for BioC2026 is now closed, you can still join the conference virtually from anywhere in the world. 💻 Virtual registration closes: August 12 Secure your virtual ticket today: 🎟️ ti.to/nf-projects/...

Excited that the {anndataR} 📦 publication is out academic.oup.com/bioinformati... 🎉! I hope this makes it easier to move single-cell data between R and Python and encourages people to take advantage of both languages. Check it out on @bioconductor.bsky.social bioconductor.org/packages/ann....

My quick wrap up of the recent @bioconductor.bsky.social 3.23 release focusing on single-cell and other things I'm interested in lazappi.id.au/posts/2026-0...

My quick wrap up of the recent @bioconductor.bsky.social 3.23 release focusing on single-cell and other things I'm interested in lazappi.id.au/posts/2026-0...

#rstats SSA SCV section is excited to bring a panel discussion on “where do R packages live?” May 20, 5pm AEST Sign up to join at statsoc.org.au/event-6653060 @fontikar.bsky.social

Last week I attended a SpatialData hackathon with members of the @scverse.bsky.social, @bioconductor.bsky.social and @openmicroscopy.org communities in Padua, Italy. Here is a short blog post about the experience www.data-intuitive.com/insights/blo....

2nd SpatialData Hackathon – Data Intuitive

Frameworks, formats and Interoperability

data-intuitive.com

New in Git, ✨ git history ✨ (I don't mean the Git history 🫠 ) 😰 Oh shit, that old commit's message had a typo! 😌 git history reword <commit-id> 😰 Oh shit, that old commit is too big! 😌 git history split <commit-id> (to split it into two commits) github.blog/open-source/... (h/t Hugo Gruson)

Highlights from Git 2.54

The open source Git project just released Git 2.54. Here is GitHub’s look at some of the most interesting features and changes introduced since last time.

github.blog

Agents for comp bio are advancing rapidly, but evals are lagging. Current benchmarks can be overly prescriptive. Full analysis vignettes are hard to verify. We introduce CompBioBench: 100 diverse, challenging, verifiable tasks. We benchmark Codex and Claude Code. biorxiv.org/content/10.6... 1/9

LaminR 📦 has been officially announced! This is a project @rcannood.bsky.social and I have worked on to create an R client for @laminlabs.bsky.social. 📦 Repo github.com/laminlabs/la... Announcement blog blog.lamin.ai/intro-to-lam... DI blog www.data-intuitive.com/insights/blo...

We previously showed how changing training data alone can improve deep learning prediction of spatial transcriptomics gene expression from histology images by +38% (without any changes to model architecture). We've now updated our preprint w/ expanded results: www.biorxiv.org/content/10.1... 🧵1/n

Nice blog post from @thomas-sandmann.genomic.social.ap.brid.gy testing out {anndataR} 📦 tomsing1.github.io/blog/posts/a... 🎉! Cool to see people trying it out, find it on @bioconductor.bsky.social if you want to give it a go bioconductor.org/packages//re...

If you work with Docker a lot, here is your friendly reminder to occasionally run `docker system prune`. I just freed up 417 GB so I have space to work again 🗑️.

I'll been at #FOG2026 in London next week 🧬. If you are attending and want to have a chat feel free to get in touch 🗣️.

This was fun! I just posted all the links and resources we talked about at www.andrewheiss.com/blog/2026/01... - check it out to learn more about Raycast, Espanso, and neat Positron/VS Code extensions like Peacock and Pastum and Project Manager #rstats #databs

How to make your data analysis life easier using Positron, Raycast, and Espanso | Andrew Heiss

Links and resources from my time on Posit’s Data Science Lab in January 2026

andrewheiss.com

Libby Heeren@libbyheeren.bsky.social · 7mo ago

TOMORROW! (Tuesday) @andrew.heiss.phd is gonna be on the DS Lab showing us how he makes his life easier: #Positron extensions he loves, OS tools he uses, and #duckdb + Connections pane 👀 Bonus, we'll def share the "moving the activity bar" thing live, too 👏🏻 Register: pos.it/dslab #rstats #databs

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

anndataR enables seamless R-Python interoperability for single-cell RNA-seq by reading, writing, and converting H5AD files, supporting Seurat and SingleCellExperiment formats www.biorxiv.org/content/10.1... 🧬🖥️🧪 #Rstats github.com/scverse/annd...

A very big thank you to all co-authors and collaborators! @lazappi.bsky.social @rcannood.bsky.social Martin Morgan @scverse.bsky.social @ivirshup.bsky.social Chananchida Sang-aram Danila Bredikhin Brian Schilder Ruth Seurinck @yvansaeys.bsky.social @saeyslab.bsky.social

It's taken more than 2 years but we can officially announce anndataR! There's still a lot of features to add but we hope a robust, "official", R-native H5AD reader/writer will unlock the defacto single-cell storage format for R users by avoiding issues with current solutions like zellkonverter.

Louise Deconinck@louisedck.bsky.social · 12mo ago

We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉 🔗 Read the paper: www.biorxiv.org/content/10.1... 💻 Check the package in action: anndatar.data-intuitive.com

We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉 🔗 Read the paper: www.biorxiv.org/content/10.1... 💻 Check the package in action: anndatar.data-intuitive.com

This week in my graduate-level Science Communication course, we are discussing communicating science to the public through public speaking (i.e., museum "evening with a scientist" nights, Nerd Nite lectures, speaking at community events, etc). What advice do you have to share with my students? 🧪

Bioconductor moving to Zulip for community chat stat.ethz.ch/pipermail/bi...

www.wehi.edu.au/careers/make... WEHI is looking for new lab heads! New and experienced lab heads welcome. Check out the ad, consider applying and share. We’re a collaborative bunch, in Australia, with fabulous technology, great colleagues at a values-driven organisation. @wehi-research.bsky.social

Analyzing your single-cell data by mapping to a reference atlas? Then how do you know the mapping actually worked, and you’re not analyzing mapping-induced artifacts? We developed mapQC, a mapping evaluation tool www.biorxiv.org/content/10.1... from the ‪@fabiantheis lab. Let’s dive in🧵

We digitized the AfD report of the Federal Office for the Protection of the Constitution. This (secret) document was created to deliver proofs for the party‘s extreme right nature. Now you can explore it interactively. ➡️ 🎁 🇩🇪 www.spiegel.de/politik/deut...

🔥 Just published! Thrilled to share that our work on funkyheatmap has just been published in the Journal of Open Source Software 🎉

There is no reason to stay bound to one programming language. I discussed ways to ease R-Python interoperability with Luke Zappia, Philipp Angerer, Tomasz Kalinowski. Their tips and tricks are collected in this blog: hrovatin.github.io/posts/r_pyth... @lazappi.bsky.social @t-kalinowski.bsky.social

From R to Python with minimal baggage

Getting the best of both worlds.

hrovatin.github.io

Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...! Keep reading for more about how we did the study and what we found out 🧵 👇 1/16

We're hiring for a bioinformatics lead at the OceanOmics Centre! L7, come work with all of the cool genomics data! HiFi, HiC, Illumina, a PromethION, it's all there. Sequence *all* of the marine vertebrates! #bioinformatics external.jobs.uwa.edu.au/cw/en/job/51...

Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...! Keep reading for more about how we did the study and what we found out 🧵 👇 1/16

🚨🧠 New paper alert: Stress alters neuronal balance in the developing brain 🧠🚨 Our latest study in @science.orgAdvances explores how glucocorticoid exposure—a key environmental risk factor—shapes early human brain development using #organoids. @mpi-psychiatry.bsky.social @drcricru.bsky.social 🧵👇

Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids

Chronic exposure to glucocorticoids during brain development leads to priming of the inhibitory neuron lineages in organoids.

science.org