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...