Happy to announce the release of IggyTop, a metadatabase for immune receptor–epitope interactions. It's integrated with scirpy v0.24 so you can readily use it to annotate your single-cell TCR datasets. iggytop.readthedocs.io/en/latest/

This started as a collaboration with biocypher (@slobentanzer.bsky.social) at a @scverse.bsky.social hackathon, was then advanced by @valeriiadragan.bsky.social as a master thesis project and finally pushed over the finish line by Raphael De Gottardi

scverse conference 2026 will take place in Copenhagen, October 12–14. ✨ Three days of all-things-single-cell and open-source tooling and community in real life. More details soon but for now, mark your calendars. scverse.org/conference20... See you in Copenhagen 🇩🇰

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....

The main challenge was extending pandera-based schema validation to the complicated structure of SpatialData; Parquet and AnnData are easier! Blog: blog.lamin.ai/spatialdata Code: github.com/laminlabs/la... With @lukasheumos.bsky.social and many others!

Excited to share new preprint with NVIDIA on GPU-accelerated single-cell analysis 🚀 rapids-singlecell brings native GPU support to scverse/AnnData: hours → seconds (1M cells: ~52m → ~25s), scaling to 100M cells. Huge thanks to Severin Dicks 🙌 📄 arxiv.org/abs/2603.02402

We're excited to announce that registration for our upcoming Spatial Omics workshop has opened! Details in 🧵

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...

It's kind of insane that I need a firefox addon for every LLM chat interface to enforce usage of the (full) width of my screen

🚀 Interested in a postdoc in computational biology & AI for neuroscience? The NOMIS Synergy Fellowship offers a great opportunity to develop such a position in my lab within the interdisciplinary Synergy excellence cluster. 🔗 www.synergy-munich.de/news-events/...

Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social www.nature.com/articles/s41...

Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025

While we've been somewhat successful in spurring adoption of alevin-fry/simpleaf for scRNAseq processing, an impediment Dongze brought to our attention (now working directly w/ many experimentalists) was the need for a nice QC report for it's output; hence QCatch www.biorxiv.org/content/10.1... 1/x

We are looking for a Research Engineer (E13 TV-L) to work at the intersection of #ML and #compneuro! 🤖🧠 Help us build large-scale bio-inspired neural networks, write high-quality research code, and contribute to open-source tools like jaxley, sbi, and flyvis 🪰. More info: www.mackelab.org/jobs/

scverse conference 2025 done ✅ Really engaging week at Stanford with scPerturb-seq work, agentic models in biology, and strong interest in scaling software to millions of cells. Organizing alongside the rest of the @scverse.bsky.social team was a blast! Hope attendees found it productive 😄

Excited to see a home for MCP servers in bioinformatics emerge! The community needs a central hub for developing MCP servers for key bioinfo tools. At @scverse.bsky.social we're contributing to this effort - can't wait to share what we're building

Meet the keynote speakers for the 2025 scverse conference! Erika Alden DeBenedictis, Co-founder of The Align Foundation 🧵 @erika-alden.bsky.social @alignbio.bsky.social @pioneerlabs.bsky.social #scverse #scverse2025 #StructuralBiology #Biotech #Stanford

🌟 Thank You to Our Platinum Sponsor: 10x Genomics! 🌟 We're delighted to recognize 10x Genomics as a Platinum Sponsor of scverse conference 2025! 🏆 @10xgenomics.bsky.social #scverse2025 #ComputationalBiology #SingleCell #SpatialOmics #10xGenomics #Bioinformatics #Biotechnology

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

My favorite part of last-year #scverse conference was to finally meet in-person many developers that I only knew from their GitHub username! Submissions and travel grant applications close in 3 days. Find out more and apply at scverse.org/conference2025 @scverse.bsky.social

scVerse conference is at Stanford this year! Encourage folks (especially Bay Area/West coast folks) to sign up and attend. Cool workshops/talks and other events + great community of developers for one of the most widely used open source software for single cell data analysis!

It is pretty heart warming to see people start their really good pull request with "this is my first open source contribution. I hope that this is good.". Everyone starts somewhere and we're always happy to guide at @scverse.bsky.social .

Our benchmark + guidelines for atlas-level differential gene expression of single cells is online: academic.oup.com/bib/article/... Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings. Collab w/ @leonhafner.bsky.social @itisalist.bsky.social

I hate reference limits of journals so much. I'm sitting here trying to find a few more references to remove despite me knowing that I'll either remove context & evidence for scientific conclusions or not mention tools that very much deserve to be mentioned and cited.

Preprint alert 🚨 Do you use chatbots in your work or even build MCP servers and agentic systems yourself? Or would you like to find a way to use biomedical tools using natural language? Then check out biocontext.ai, now out on bioRxiv: www.biorxiv.org/content/10.1...

We will have our next community meeting on Tuesday, 2025-06-24 at 18:00 CEST! Sneha Mitra (@snehamitra.bsky.social) will speak about SCARlink. (Zoom registration link and more information in thread!)

Happy to have this finally out! Check out the updated vignettes and if something is broken please open a GitHub issue and I'll have a look 😉👇

Happy to share CellAnnotator, a lightweight Python package to query OpenAI models for initial cell type annotations: github.com/quadbio/cell... Inspired by ideas in www.nature.com/articles/s41... and github.com/VPetukhov/GP..., implemented as an scVerse ecosystem package with docs and tutorials.

Tomorrow at 2025-04-15 18:00 CEST, we’ll have our next community meeting! Anastasia Litinetskaya will present “Multimodal integration and identification of disease-specific changes in single-cell atlases”. Check out the GitHub repo here: github.com/theislab/mul...

We are back 🔥

Best practices for single-cell analysis across modalities go.nature.com/4gJkk3c #ExpertRecommendation by @lukasheumos.bsky.social et al. (from the @fabiantheis.bsky.social lab) - now nearing 250k accesses! Free to read here: rdcu.be/eabUB

🎉 Scanpy 1.11.0 is out! 🎉 just after reaching 2000 stars on GitHub! - sc.pp.sample replaces subsample with many new features - Sparse Dask support pca - session-info2 package for more reproducible notebooks See the release notes:

We have additional available spots. Please consider joining! It will be a blast.

I keep being astonished at how terrible @microsoft.com Teams works on Firefox and I certainly don't blame Mozilla for it.

Ahhh finally I can use @nextflow.io to run doom! github.com/nextflow-io/...

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...

Why is there still no proper "thank you" emoji on @github.com ? I am grateful for other peoples time and feel like a thumbs up is kind of like a drive by reaction and a heart isn't always perfectly appropriate

I actually think that it' awesome that even fundamental packages like numpy, pandas, scipy, and others still develop rapidly and aren't afraid of making big API changes but it's quite time consuming to keep up when one maintains many packages. I can't imagine what e.g. the numba devs go through

I was just looking at our @scverse.bsky.social zulip chat statistics and am super happy about our steady and healthy growth. The two bursts are our official launch in May 2022 and the inaugural scverse conference in September of 2024. Please join us! scverse.zulipchat.com

Reminder!Today at 18:00 CET will be the last community meeting of the year! @lukasheumos.bsky.social will talk about about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. Zoom link can be found here: scverse.zulipchat.com#narrow/chann...

Next Tuesday at 2024-12-10 18:00 CET, we will hold the last community meeting of the year! @lukasheumos.bsky.social will talk about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. The GitHub repo: github.com/scverse/pertpy

Reminder! Today at 18:00 CET will be another community meeting! Malte Lücken will talk about about Open Problems in Single-Cell Analysis. Zoom link can be found here:

Next Tuesday at 2024-11-26 18:00 CET will be another community meeting! Malte Lücken will talk about about Open Problems in Single-Cell Analysis, a community-driven state-of-the-art benchmarking platform to facilitate development of single-cell methods. https://buff.ly/3CAGxSt

Explore the scverse Starter Pack! Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place. go.bsky.app/UvFMa8d

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

Thanks - really nice w these starter packs, did that. Meanwhile @scverse.bsky.social has also created one - really like that. bsky.app/starter-pack...

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...