scverse
Foundational tools for omics data (mostly in python).
- 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
- BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux
- @niklaskemp.bsky.social will present our new CREsted framework at the next scverse community meeting! CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...
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- 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...
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- 🔧 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/
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- 🧠 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
- 🔬 Whole slide histopathology images are a goldmine for tissue biology and diagnostics - but too often locked away in inaccessible formats or tools. In our new preprint, we introduce LazySlide: an open-source, modular, and interoperable framework. www.biorxiv.org/content/10.1...
- 🧠 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
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- It's happening! 🙌
- 📣 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!
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- 🎉 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 are back 🔥
- 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...
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- Awesome, congratulations! It was a pleasure to attend Yimin's talk at the @scverse.bsky.social 2024 conference and it's really nice to see that it was encouraging for Yimin.
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- 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...
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- The scverse ecosystem is one of the best things that could have ever happened to the single-cell and spatial fields. Smoother computational analyses mean faster and better research
- Closing 2024, scverse celebrates growth and collaboration! Huge thanks to everyone on this journey and our core team & board (@fabiantheis.bsky.social, @francescafinotello.bsky.social, @steglelab.bsky.social, Nir Yosef, @panosroussos.bsky.social, @robp.bsky.social). Here's to an inspiring 2025!
- 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
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- Thanks - really nice w these starter packs, did that. Meanwhile @scverse.bsky.social has also created one - really like that. bsky.app/starter-pack...at://did:plc:43xl2lpdbllhfdpa2cuwaw6m/app.bsky.graph.starterpack/3lb326xofwu2e
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