WARNING: This repo is unmaintained. If you are interested in pure-python differential expression analysis, please look at PyDESeq2_ .

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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.

.. _scanpy: https://github.com/theislab/scanpy .. _documentation: https://diffxpy.rtfd.io/en/latest .. _tutorials: https://diffxpy.rtfd.io/en/latest/tutorials.html .. _PyDESeq2: https://pydeseq2.readthedocs.io/en/stable/