This time not bioinformatics, but geoinformatics: I created MapAnt Bayern, an automatically generated orienteering map of Bavaria: mapant.orienteering-allgaeu.de

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!

scverse conference 2025

Follow us on our channels to learn more details in the coming weeks

scverse.org

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

rogue-scholar.org

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...

LEMUR simplified | const-ae

A simplified implementation of the LEMUR algorithm.

const-ae.name

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

Working with >1M cells

Scirpy scales to millions of cells on a single workstation. This page is a work-in-progess collection with advice how to work with large datasets. Distance metrics: Computing pairwise sequence dist...

scirpy.scverse.org

🎉 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:

Release notes

Version 1.11: 1.11.0 2025-02-14: Release candidates: rc2 2025-01-24, rc1 2024-12-20. Features: rc1 sample() supports both upsampling and downsampling of observations and variables. subsample() is n...

buff.ly

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

Gregor Sturm@grst.bsky.social · last yr.

If you want to learn more, I'll be presenting this at a @nf-co.re bytesize talk: nf-co.re/events/2025/...

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...

GitHub - Boehringer-Ingelheim/dso: Data Science Operations (dso) command line tool

Data Science Operations (dso) command line tool. Contribute to Boehringer-Ingelheim/dso development by creating an account on GitHub.

github.com

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...

GitHub - Boehringer-Ingelheim/dso: Data Science Operations (dso) command line tool

Data Science Operations (dso) command line tool. Contribute to Boehringer-Ingelheim/dso development by creating an account on GitHub.

github.com

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)

Cellxgene Data Portal

Find, download, and visually explore curated and standardized single cell datasets.

cellxgene.cziscience.com

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...

Scverse x Owkin Hackathon in Paris

We're pleased to announce the next Scverse Hackathon will take place in the Owkin offices in Paris from 17/03/2025 9am to 19/03/2025 1:30pm. This hackathon is a joint initiative between the scverse c...

docs.google.com

protein sequencing 👀

Oxford Nanopore@nanoporetech.com · 2y ago

1/ We’re excited to announce our first speaker of London Calling 2025 Jeff Nivala will share their groundbreaking ‘proof-of-concept' method showcasing the capability of #nanopore sequencing to read #polypeptide strands. Register here: nanoporetech.com/about/events... #nanoporeconf

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

Adaptive immune receptor repertoire analysis - Nature Reviews Methods Primers

The adaptive immune receptor repertoire (AIRR) drives adaptive immune responses, which could determine disease outcomes, infectious disease and cancer. Mhanna, Bashour et al. outline the approaches an...

nature.com

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...