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grst.bsky.social
Single Cell/Spatial. Cancer Immunology. Outdoor activities. Core developer @scverse.bsky.social. Working in Clinical Bioinformatics at Boehringer Ingelheim. Formerly PhD student at Medical University of Innsbruck. My private account. github.com/grst
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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

submitted 2 days ago • 0 comments

🎉 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:

submitted 13 days ago • 1 comment

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

submitted 18 days ago • 0 comments

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...

submitted 22 days ago • 1 comment

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...

submitted 22 days ago • 1 comment

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...

submitted 36 days ago • 1 comment

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)

submitted 39 days ago • 2 comments

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...

submitted 41 days ago • 0 comments

protein sequencing 👀

submitted 44 days ago • 0 comments

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⬇️

submitted 55 days ago • 8 comments

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-...

submitted 56 days ago • 1 comment

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.

submitted 73 days ago • 1 comment

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/

submitted 82 days ago • 1 comment

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/

submitted 82 days ago • 1 comment

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

submitted 107 days ago • 1 comment

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

submitted 103 days ago • 6 comments

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

submitted 378 days ago • 0 comments

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

submitted 398 days ago • 0 comments

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...

submitted 399 days ago • 1 comment

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...

submitted 401 days ago • 0 comments