Stefan Peidli (@SPeidli)

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Stefan Peidli @SPeidli Jan 26, 2024

Check out scPerturb, out now in Nature Methods!

Among other things: new datasets in our database, and a lot more information per dataset (e.g. mean No. of counts, cells per perturbation) in the interactive data table. You can find it on our website, link in thread!

Tessa Green @the_tessallator Jan 26, 2024

"scPerturb: harmonized single-cell perturbation data" is out now in Nature Methods!

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Stefan Peidli @SPeidli Jul 21, 2024

Are you developing or benchmarking methods for single-cell perturbation data?
I've written a very simple example pipeline in snakemake that auto downloads all (/selected) datasets from scperturb and applies your custom script to each of them in parallel: github.com/stefanpeidli/s…

github.com GitHub - stefanpeidli/scperturb_snakemake_example: Example repository for analyzing many datasets... Example repository for analyzing many datasets at once from scperturb.org using snakemake - stefanpeidli/scperturb_snakemake_example

Stefan Peidli @SPeidli Jul 11, 2024

Check out datavzrd, super useful tool for making tables pretty for showing on the web. I used it to make a simple metadata table for a database, see here: projects.sanderlab.org/scperturb/data…

Johannes Köster (@johanneskoester.bsky.social) @johanneskoester Jul 11, 2024

#datavzrd, our tool for rendering modern interactive, visual, server-free, tabular scientific HTML reports with zero/low-code (datavzrd.github.io), now has a tutorial (1-2h): datavzrd.github.io/docs/tutorial.….
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Stefan Peidli @SPeidli Sep 18, 2023

Very unique data with mutliple doses and time points after infection. We had lots of opportunity for data analysis. And go check out the amazing diffusion map we got for the endothelials!

Emanuel Wyler @ewyler Sep 18, 2023

What drives severe COVID-19? In our new preprint, we explore this question using and interspecies comparison of lung single-cell RNA-seq data – summary in the thread below, lead by @SPeidli and Samantha Praktiknjo! … (1/7)

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Stefan Peidli @SPeidli Jul 10, 2023

Cluster analysis is the first thing most PhD students do when working with scRNAseq data because it's simple and part of scanpy/seurat's tutorials. But often enough data does not actually allow clustering because it is too homogeneous (e.g. cell lines)!

Rafael Irizarry @rafalab Jul 10, 2023

Clustering algorithms report clusters even when none exist. In single-cell RNA-Seq pipelines, novel cell types are often identified by clustering algorithms. Expanding on Kimes et al.'s work, we introduce significance analysis for single-cell RNA-Seq data: nature.com/articles/s4159…

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Stefan Peidli

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