WARNING: This repo is unmaintained. If you are interested in pure-python differential expression analysis, please look at PyDESeq2 .

Fast and scalable differential expression analysis on single-cell RNA-seq data

diffxpy covers a wide range of differential expression analysis scenarios encountered in single-cell RNA-seq scenarios and integrates into scanpy workflows. Import diffxpy as import diffxpy.api as de to access the following differential expression analysis-related tools:

1. differential expression analysis in the module de.test.*
2. gene set enrichment analysis based on differential expression calls in the module de.enrich.*

Refer to the documentation and the tutorials for details of these modules.