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owkin / PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
https://pydeseq2.readthedocs.io/en/latest/
MIT License
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single cell dataset #248

Open wangjiawen2013 opened 8 months ago

wangjiawen2013 commented 8 months ago

Hi, Does pydeseq2 support single cell data now? such get the differential expressing genes of each cluster/cell_type?

BorisMuzellec commented 8 months ago

Hi @wangjiawen2013! Yes, it's possible to analyse single-cell data with pydeseq2 + decoupleR and/or scanpy.

See this decoupleR vignette or this youtube tutorial.