We will have our next community meeting on Tuesday, 2025-09-16 at 18:00 CEST! Niklas Kempynck will be presenting on CREsted, a package for training enhancer models on scATAC-seq data. (Zoom registration link and more information in thread!) 🧵

🎉 scverse conference 2025 Abstracts DEADLINE IN LESS THAN 48 HOURS! 🎉 The deadline to submit abstracts for the scverse Conference 2025 is 11:59PM PST, September 15, 2025! More information in thread 🧵 #scverse #scverse2025 #SingleCell #Conference

We will have our next community meeting on Tuesday, 2025-09-16 at 18:00 CEST! Niklas Kempynck will be presenting on CREsted, a package for training enhancer models on scATAC-seq data. (Zoom registration link and more information in thread!) 🧵

🧠 Arc Workshop at the upcoming scverse conference 2025 🧠 Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning 🧵 @arcinstitute.org #scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells

🔬 CZI Workshop at scverse 2025 🔬 Multimodal And Spatial Single Cell Data: From Data APIs to AI-driven Biological Discovery 🧵 @chanzuckerberg.bsky.social #scverse2025 #SingleCell #SpatialOmics #CELLxGENE #VirtualCells #AIBiology

🧬 Tahoe Workshop at scverse conference 2025 🧬 Disease Biology and Therapeutics in the Age of Frontier Datasets 🧵 @tahoetherapeutics.bsky.social #scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology

🎉scverse conference 2025 Call for Abstracts DEADLINE EXTENDED! 🎉 We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025! 🧵 #scverse #scverse2025 #SingleCell #Conference

We will have our next community meeting on Tuesday, 2025-09-02 at 18:00 CEST! Emma Dann will be presenting on "Mapping genetic effects on complex traits with single-cell perturbation data". Zoom registration link: lnkd.in/dZpbKKsY

Super excited for the 2nd edition of the #scverse conference! A fantastic opportunity to showcase and discover innovative data frameworks for #singlecell analysis, and to meet the developers behind the scverse ecosystem. Looking forward to connecting with the community! Register now! 👇

Meet the keynote speakers for the 2025 scverse conference! Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University 🧵 @elhamazizi.bsky.social @columbiauniversity.bsky.social #scverse #scverse2025 #machinelearning #genomics #cancerimmunology

We will have our next community meeting on Tuesday, 2025-09-02 at 18:00 CEST! Emma Dann will be presenting on "Mapping genetic effects on complex traits with single-cell perturbation data". 🧵

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

💰 Travel Grants Available for scverse conference 2025! 💰 Did you know we are offering grants to help anyone in financial need attend our annual conference? 🌍 🧵 #scverse #scverse2025 #SingleCell #Conference #StanfordUniversity #TravelGrant

Meet the keynote speakers for the 2025 scverse conference! John Marioni, Head of Computation at Genentech Research and Early Development 🧵 @genentech.bsky.social #scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Genentech #Stanford

🧠 Meet the keynote speakers for the 2025 scverse conference! Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai 🧵 @panosroussos.bsky.social #scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote

Want to contribute to the scverse omics ecosystem? Join the NVIDIA and scverse Hackathon: Accelerate Omics Workflows! Collaborate with NVIDIA experts, GPU-accelerated tools, and the scverse community. Apply by Aug 27, 2025. #Omics #DataScience #Hackathon #GPU LINK: buff.ly/OCUdlks

anndata 0.12 is out now! We have lots of great features that we hope address some persistent needs. Here are some of the highlights!

🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉 We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025! Details in thread! 🧵 1/3

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...

Working on this project has been a great privilege, thanks to the many contributions from all team members, including members from the @scverse.bsky.social and BioCypher communities.

If you are interested in building out the biomedical MCP ecosystem, we invite you to share your work through BioContextAI and to connect via GitHub (github.com/biocontext-ai) or through the @scverse.bsky.social Zulip (scverse.zulipchat.com), were you can find us in the "[wg] biocontext-ai" channel.

🔗 Ecosystem CORNETO is powering LIANA+ (liana-py.readthedocs.io), linking cell–cell communication events to intracellular signaling (@scverse.bsky.social). It’s also at the core of NetworkCommons (networkcommons.readthedocs.io), our community-driven platform for network methods.

We will have our next community meeting on Tuesday, 2025-07-08 at 18:00 CEST! Ilan will be speaking about the new upcoming anndata release. (Zoom registration link and more information in thread!)

We will have our next community meeting on Tuesday, 2025-07-08 at 18:00 CEST! Ilan will be speaking about the new upcoming anndata release. (Zoom registration link and more information in thread!)

🔧 decoupler 2.0.6 is out thanks to @paubadiam.bsky.social‬, now as a core @scverse.bsky.social package scverse.org This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇 decoupler.readthedocs.io/en/latest/

Great open-source QC reporting tool from @robp.bsky.social Rob Patro’s group, member of our management committee!

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!)

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!)

🧠 Built on the @scverse.bsky.social ‬ecosystem 🐍, LazySlide makes advanced histopathology analysis accessible with minimal code. Segment tissue, classify cells, run vision-language queries or integrate with omics data - all these without training, and in an already familiar API. lazyslide.rtfd.io

We will have our next community meeting on Tuesday, 2025-06-10 at 18:00 CEST! Sergei Rybakov will speak about MappedCollection. (Zoom registration link and more information in thread!)

We will have our next community meeting on Tuesday, 2025-06-10 at 18:00 CEST! @Sergei will speak about MappedCollection. (Zoom registration link and more information in thread!)

Tuesday, 2025-05-27 at 18:00 CEST, we will have our next community meeting! Yuan Gao will speak about Forseti and introduce the Patro lab's upcoming tool, QCatch. (Zoom registration link in thread!)

This Tuesday, 2025-05-27 at 18:00 CEST, we will have our next community meeting! Yuan Gao will speak about Forseti and introduce the Patro lab's upcoming tool, QCatch. (Zoom registration link in thread!)

scverse turns 3! What started as a shared vision for interoperable single-cell analysis has become a vibrant, global community. From AnnData to full multimodal pipelines, we’re building the future of everything single-cell and spatial omics, together. Here’s to what’s next!

This Tuesday, 2025-05-13 at 18:00 CEST, we will have our next community meeting! Gregor Sturm will present on scirpy! Check out more information here: scirpy.scverse.org/en/latest/ , and register for the zoom link below:

📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20... Call for abstracts and registrations coming soon!

Just released a new version of the @scverse.bsky.social cookiecutter template: github.com/scverse/cook... Some highlights: 🔃 improved template sync (merge conflicts now show up as such) 🚀 use hatch as project manager 🔧 lots of fixes and documentation updates

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...

I put together a VS Code extension to help launch these notebooks bsky.app/profile/manz...

7/ "Speed and usability first"! #Segger is built on @scverse.bsky.social, @pytorch.org, @PyG, @lightningai.bsky.social, @geopandas & @RAPIDSai to zip through big ST datasets smoothly.

9/ #Segger grew from conferences, hackathons, & community efforts. Huge thanks to the co-lead Andrew Moorman, co-authors and colleagues, and supervisors @moritzgerstung.bsky.social and @danapeer.bsky.social . More contributions of any kind are always welcomed! & Big thanks to @scverse.bsky.social

Join us at 18:00 CET, March 4, Benjamin Rombaut will speak about Harpy, a spatial proteomics tool, as well as other tools from the Saeys lab! For more information, check out the Github: buff.ly/3XnViQl , and lab website: buff.ly/3XlL6HX ! Find the zoom link here: buff.ly/3CArAjJ !

Today, 2025-03-04 18:00 CET, Benjamin Rombaut will speak about Harpy, a spatial proteomics tool, as well as other tools from the Saeys lab! For more information, check out the Github: buff.ly/3XnViQl , and lab website: buff.ly/3XlL6HX ! Find the zoom link here: buff.ly/3CArAjJ !

This Tuesday at 2025-03-04 18:00 CET, Benjamin Rombaut @berombau.bsky.social will speak about Harpy, a spatial proteomics tool, as well as other tools from the Saeys lab @saeyslab.bsky.social ! For more information, check out the Github: buff.ly/3XnViQl , and lab website: buff.ly/3XlL6HX !

Join us Tuesday at 2025-03-04 18:00 CET! @berombau.bsky.social from @saeyslab.bsky.social will speak about Harpy, a tool to analyze spatial proteomics data . For more information, check out the GitHub:buff.ly/MUT81ar & lab website : buff.ly/RJUDHJZ - Zoom link can be found here: buff.ly/y0MmT65

Join us Tuesday at 2025-02-18 18:00 CET! Marius Lange will speak about Moslin, a new algorithm to map cells across time and lineage. For more information, check out the GitHub: https://buff.ly/4hTO522 & publication: https://buff.ly/41gcQzZ

🎉 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 just released simpleaf v0.19.0 (github.com/COMBINE-lab/...). Make sure to pair it with piscem v0.12 for faster scATAC-seq processing. The other big feature & first explicit @scverse.bsky.social integration point is AnnData format output with the new `--anndata-out` flag!

Don't forget to apply to the upcoming @scverse.bsky.social x @owkin.bsky.social hackathon - applications due this Friday, February 7th! 📆March 17-19, 2025 📍Owkin Office, Paris docs.google.com/forms/d/e/1F...

On Tuesday at 2025-02-04 18:00 CET, @jkobject will talk about scPrint, a transformer model that infers gene networks from scRNA-seq data, at our 2nd community meeting of 2025! For more information, check out the GitHub: https://buff.ly/40RJ3gT & pre-print https://buff.ly/4hwK4Av