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)
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...
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Adapting to all the constant new features in the Python package led us to come up with a flexible wrapping approach via reticulate.
This lets us expose new functionality automatically while adapting or replacing when needed to work nicely in R.
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...
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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 🗑️.
Festival of genomics social media banner showing I am attending
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
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
Hopefully coming soon to @bioconductor.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.
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? 🧪
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
If they don't agree then it depends which you find more convincing I guess. I think there are lots of reasons two benchmarks might not after without either if them being "wrong" though.
Very on brand 😹. I guess I missed a space 🤦🏻. At least the mystery is solved.
Yeah, it surprised me a bit as well. This wasn't the main aim of the paper though so it's a fairly limited comparison. There is a lot more you could do if you wanted to properly compare them.
Thanks!
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 🧵 👇
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Thanks!
Thanks!
Hmmm...It's broken for me too 😿. I'm not sure what happened there but this is working www.nature.com/articles/s41.... Thanks for letting me know!