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

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.

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

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 🧵👇

Do any #rstats reticulate experts have examples of using register_module_help_handler() or register_help_topics()? I feel like these should be able to let a package provide access to help information but there isn't much documentation on how to use them.

Thought for computational biologists choosing projects: If you’re interested in method development, one counterintuitive strategy can be to dive deep into biology.

I just uploaded the first version of {{exactplot}} to github.com/const-ae/exa... 🎉 It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility. #rstats

Check out our speakers for #ozsinglecell25. May 21-23, Sydney Registrations opening soon www.ozsinglecell.com

I am Stoked about our upcoming @scverse.bsky.social and @owkin.bsky.social hackathon, focused on spatial omics data analysis. 📅 March 17-19, 2025 📍 Owkin office, Paris Apply now: docs.google.com/forms/d/e/1F...

Our paper on nurturing a #PositiveResearchCulture within your #research #team published by @wellcometrust.bsky.social gives useful tips for your lab. As well as making you a good team leader, nurturing culture pays off in building your science: 1/11 wellcomeopenresearch.org/articles/9-3...

We are here 🦋. Save the date for Oz Single Cell 2025, 23-25 May in Sydney

Save the Date for Cancer Bioinformatics Australia '25! The 2nd CBA will be in Sydney on June 18th 2025. Planning is well under way, with invited speakers including but not limited to @jwhwong.bsky.social and @nadia-davidson.bsky.social See cancerbioinformatics.au for info and updates.

1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.

To bring to light data science topics that usually don’t make it into publications I started a blog on this topic: hrovatin.github.io By interviewing different researchers, I plan to find out what is going on in the community.

Have you been thinking hard about statistical modelling of scATAC-seq data? (No.) Luckily for you, @aaronkwc.bsky.social has! Aaron will help you grok: What's going on? What is TF-IDF? Is there really single-cell level chromatin information? Check it out 👇 www.biorxiv.org/content/10.1... 🧪🧬💻

Biology is *spatiotemporal* Processes such as cancer, wound healing, & embryonic development occur in both time AND space. @shazanfar.bsky.social 5/

You need to be careful with how you approach library size normalisation in spatial txomics, or what you could end up eliminating organs / meaningful structures. -- Dharmesh Bhuva 2/

My #pyconau talk on those side project(s) that keep on giving is up! As I (almost) end with, contributions to fastqe.com and biomojify are always welcome! 🥑 🧀 🍇 🍅 💀 💩 🚨 🙂 😍 www.youtube.com/watch?v=E3-A...

Super excited to share our Human Neural Organoid Atlas, now out in Nature! Led by @zhisonghe.bsky.social @josch1.bsky.social, and myself, this resource was created from 36 scRNA-seq datasets—totalling over 1.7 million cells! 🔬✨
 www.nature.com/articles/s41...
 Find out how it can serve you ⏬
 🧵1/8

Hive mind of 🧬 🖥️ - I am looking for one or two small data sets/repo that has a nice collection of bioinformatics file formats, e.g. a sample FASTA, FASTQ, VCF , GFF etc. They can be related experiments/organisms or disparate.

I am stoked to see our EHR framework ehrapy (github.com/theislab/ehr...) being the cover of the most recent Nature Medicine issue. We consider ehrapy a MVP for a much grander ecosystem for EHR analysis like we have for single-cell data (@scverse). Read more: www.nature.com/articles/s41...

Interested in predicting transcriptomic effects of perturbations? Check out our @NeurIPS24 D&B spotlight living perturbation prediction benchmark & new drug perturbation dataset: - paper: openreview.net/forum?id=WTI... ! - benchmarking platform: openproblems.bio/results/pert... 🧵1/8

I made a bot that posts pre-prints of single cell papers: @prepub-singlecell.bsky.social (I posted about it a little while ago when no one was here, so posting again now :D) It's pretty dumb so very open to suggestions for improvements!

And I made one for single cell which is needs more people, but is still a starting point 😅 go.bsky.app/U57Mar8

Really hoping the Bioconductor community will keep growing on here so I thought I'd try a starter pack. Please let me know if you'd like to be added or removed. go.bsky.app/8CieMWu

A delight to talk about the not-as-silly-as-they-sound emoji bioinformatics tools FASTQE and Biomojify at #AGTA24 Education is a pillar of research, and education thrives on engagement. Contributions and examples of use in the wild always welcome! fastqe.com

Quick blog post with my #sketchnotes from the #scverse #SingleCell conference lazappi.id.au/posts/2024-0...

I'm excited to share the next version of patchwork with the world, available on CRAN now. First class support for gt tables and even more freedom with `free()` #rstats #ggplot2

Final #scverse conference keynote Fabian Theis "From scanpy to the virtual cell: the coming-of-age of single cell analysis" #sketchnotes

#scverse conference keynote Maria Brbic "Towards AI-driven discoveries in Single-Cell genomics" #sketchnotes

#scverse conference keynote Alex Wolf "Many anecdotes make a novel? Study-centered analysis & training models" #sketchnotes

#scverse conference keynote Christina Leslie "Machine learning for regulatory genomics at single-cell resolution" #sketchnotes

Love to see it: communities of scientists are forming on Bluesky. This is a nice network analysis, complete with a leaderboard mikeyoungacademy.dk/communities-...