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/

There's another scverse conference this year and it will be amazing! Register now: www.eventbrite.com/e/scverse-co...

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

Register now for the best conference of the year!

📣 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

Blog post by @const-ae.bsky.social with a simple explanation of the manifold regression algorithm & code that underlies our paper “Analysis of multi-condition single-cell data with latent embedding multivariate regression” (doi.org/10.1002/eji....). const-ae.name/post/2025-01...

Just released scirpy v0.21 -- Now with GPU Support for Hamming sequence distance and a brand new tutorial for working with scTCR datasets >1M cells: scirpy.scverse.org/en/latest/tu... @scverse.bsky.social

🎉 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:

Been looking forward to this talk since @alexpeltzer.bsky.social told me about DSO in October!

I'd like to share DSO, a command line helper to build reproducible data science projects with ease. It is an opinionated way to organize data science projects, built around data version control (DVC). github.com/Boehringer-I...

I'd like to share DSO, a command line helper to build reproducible data science projects with ease. It is an opinionated way to organize data science projects, built around data version control (DVC). github.com/Boehringer-I...

We (Chen Zhan!) just launched #sccomp for #Python! Testing for differences in cell-type proportion in #singlecell #spatial data? #sccomp is a mixed-effect Bayesian model - Use sum-constrained BetaBinomial distribution - Outliers detect. - Remove unwanted effects github.com/MangiolaLabo...

Two years after publication of our single-cell lung cancer atlas, a user found a mistake in the annotation of the EGFR-status of some patients. We fixed the issue and the atlas is now updated on cell-x-gene: cellxgene.cziscience.com/collections/... What are the takeaways from that? (1/3)

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...

protein sequencing 👀

After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳 www.nature.com/articles/s41... LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space. Some highlights⬇️

Dynamic electricity tariffs are an incentive to use energy when it's abundant and emits little CO2. But are they also cheaper? ✅ For 2024, we would have saved 10-13% compared to our current fixed price tariff. Without any optimization. Full post (in German): grst.github.io/dynamischer-...

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.

Formulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint. To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline". To make this easier, we developed "formulaic-contrasts": formulaic-contrasts.readthedocs.io/en/latest/

Formulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint. To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline". To make this easier, we developed "formulaic-contrasts": formulaic-contrasts.readthedocs.io/en/latest/

📢 Preprint alert: #Benchmarking second-generation methods for cell-type #deconvolution of #transcriptomic data t.co/MhLf5Eo3yY A thread 🧵👇 1/

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

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

Confused by Neutrophils in Cancer? Check out our latest review! www.cell.com/trends/cance...

Nice fresh review on immune repertoire analysis from @victorgreiff.bsky.social

We released scirpy v0.15 with a focus on performance improvements. "alignment" distance to find similar clonotypes is now 2-3x faster by default. Additionally there's an (approximate) "fastalignment" metric that is up to 20x faster. scirpy.scverse.org/en/latest/ch...

For anyone who is working with Personalis data: We made an R package that automates loading the data into a MultiAssayExperiment: github.com/Boehringer-I...