iiinova — where your digital self keeps evolving

Gregor Sturm @grst.bsky.social · 05/08/2026

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

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Gregor Sturm @grst.bsky.social · 29/05/2026

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/

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Gregor Sturm @grst.bsky.social · 22/08/2025

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

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Gregor Sturm @grst.bsky.social · 13/08/2025

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

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Gregor Sturm @grst.bsky.social · 05/08/2025

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scverse @scverse.bsky.social · 12/05/2025

📣 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.org

scverse conference 2025

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Gregor Sturm @grst.bsky.social · 02/04/2025

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

github.com

Release v0.5.0 · scverse/cookiecutter-scverse

New template sync We re-implemented template sync from scratch instead on relying on cruft. This allows us to create real merge conflicts that show up as such on GitHub instead of .rej files. Gene...

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Wolfgang Huber @wkhuber.bsky.social · 04/03/2025

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...

const-ae.name

LEMUR simplified | const-ae

A simplified implementation of the LEMUR algorithm.

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scverse @scverse.bsky.social · 14/02/2025

🎉 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:

buff.ly

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...

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Edmund Miller @edmundmiller.dev · 09/02/2025

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

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Gregor Sturm @grst.bsky.social · 05/02/2025

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.com

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.

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Gregor Sturm @grst.bsky.social · 05/02/2025

github.com

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.

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Stefano Mangiola @stemang.bsky.social · 22/01/2025

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...

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Gregor Sturm @grst.bsky.social · 19/01/2025

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.cziscience.com

Cellxgene Data Portal

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

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Constantin Ahlmann-Eltze @const-ae.bsky.social · 03/01/2025

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⬇️

Overview of the LEMUR steps: (1) subspace alignment, (2) differential expression, (3) DE neighborhoods, (4) pseudobulking.

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Gregor Sturm @grst.bsky.social · 02/01/2025

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-...

Monthly comparison of fixed price tariff (AÜW) with dynamic tariff (tado).

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khrovatin.bsky.social @khrovatin.bsky.social · 16/12/2024

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.

hrovatin.github.io

Karin Hrovatin

Data science blog on topics that don’t get published.

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Gregor Sturm @grst.bsky.social · 07/12/2024

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/

# Define model with interaction term
model = MyModel(data, "~ treatment * timepoint")

# compare timepoints
contrast = model.cond(timepoint="on_treatment") - model.cond(timepoint="baseline")

# compare timepoints within drugA only
contrast = (
model.cond(treatment="drugA", timepoint="on_treatment") -
model.cond(treatment="drugA", timepoint="baseline")
)

# compare interaction of timepoint with treatment
# (= difference of changes between both treatments)
contrast = (
mod.cond(treatment="drugB", timepoint="on_treatment")
- mod.cond(treatment="drugB", timepoint="baseline")
) - (
mod.cond(treatment="drugA", timepoint="on_treatment")
- mod.cond(treatment="drugA", timepoint="baseline")
)

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Gregor Sturm @grst.bsky.social · 07/12/2024

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

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

t.co

https://doi.org/10.1101/2024.06.10.598226

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scverse @scverse.bsky.social · 16/11/2024

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

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Will Macnair @willmacnair.bsky.social · 11/11/2024

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

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Gregor Sturm @grst.bsky.social · 25/01/2024

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...

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