Lightnews — Scholar-powered news

Gregor Sturm @grst.bsky.social · Aug 22

There's another scverse conference this year and it will be amazing!

Register now: www.eventbrite.com/e/scverse-co...

scverse @scverse.bsky.social · Aug 2

🎉 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

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Reposted by Gregor Sturm

scverse @scverse.bsky.social · Aug 2

🎉 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

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Gregor Sturm @grst.bsky.social · Aug 19

AFAIK, these differences are minor, numeric differences. I would consider them equivalent.

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Gregor Sturm @grst.bsky.social · Aug 13

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 · Aug 5

Register now for the best conference of the year!

scverse @scverse.bsky.social · Aug 2

🎉 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

Reposted by Gregor Sturm

scverse @scverse.bsky.social · May 12

📣 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

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Gregor Sturm @grst.bsky.social · Apr 2

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

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...

github.com

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Reposted by Gregor Sturm

Stephen Turner @stephenturner.us · Mar 14

rogue-scholar.org

Rogue Scholar

rogue-scholar.org

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Gregor Sturm @grst.bsky.social · Mar 14

Nice post!
How did you generate the doi-link for a blog post?

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Reposted by Gregor Sturm

Wolfgang Huber @wkhuber.bsky.social · Mar 4

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

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Gregor Sturm @grst.bsky.social · Feb 25

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

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Reposted by Gregor Sturm

scverse @scverse.bsky.social · Feb 14

🎉 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

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Reposted by Gregor Sturm

Edmund Miller @edmundmiller.dev · Feb 9

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

Gregor Sturm @grst.bsky.social · Feb 5

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

Bytesize: data science operations (DSO)

Gregor Sturm, Boehringer Ingelheim

nf-co.re

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Reposted by Gregor Sturm

Gregor Sturm @grst.bsky.social · Feb 5

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

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Gregor Sturm @grst.bsky.social · Feb 5

We try to avoid that by using this with preprocessed data only. All the heavy lifting is done with nextflow pipelines before. Datasets up to tens of GBs have worked well so far.

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Gregor Sturm @grst.bsky.social · Feb 5

Finally, many thanks to my colleagues @alexpeltzer.bsky.social, Daniel Schreyer and Tom Schwarzl for testing, adopting, and contributing to DSO.

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Gregor Sturm @grst.bsky.social · Feb 5

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

Bytesize: data science operations (DSO)

Gregor Sturm, Boehringer Ingelheim

nf-co.re

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Gregor Sturm @grst.bsky.social · Feb 5

We built this at @boehringerglobal.bsky.social to meet the quality standards required for biomarker analysis in clinical trials.

But I think this is useful for any kind of data analysis project.

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Gregor Sturm @grst.bsky.social · Feb 5

One of my favorite features: automated watermarking of all plots in a quarto report. Nobody gonna publish my plots anymore before I think they are ready.

An exemplary PCA plot with a "preliminary" watermark.

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Gregor Sturm @grst.bsky.social · Feb 5

It brings together the best tools:
- git, for code versioning
- dvc, for data versioning and tracking inputs and outputs
- jinja2, for templates
- uv, for Python dep mgmt
- quarto, for authoring reports
- hiyapyco, for hierarchical YAML config
- pre-commit, for linting

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Gregor Sturm @grst.bsky.social · Feb 5

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

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Reposted by Gregor Sturm

Stefano Mangiola @stemang.bsky.social · Jan 22

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 · Jan 19

(2) Finding the mistake, tracing it back to its origin, and fixing it was only possible because the data and scripts for building the atlas are publicly available and fully reproducible. github.com/icbi-lab/luca

GitHub - icbi-lab/luca: Single-cell Lung Cancer Atlas with 1.2M cells

Single-cell Lung Cancer Atlas with 1.2M cells. Contribute to icbi-lab/luca development by creating an account on GitHub.

github.com

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Gregor Sturm @grst.bsky.social · Jan 19

(1) Maintaining a data resource is very much like maintaining software. It is never "done" but constantly improving.

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Gregor Sturm @grst.bsky.social · Jan 19

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

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