PyDESeq2 documentation

This package is a python implementation of the DESeq2 method [LHA14] for differential expression analysis (DEA) with bulk RNA-seq data, originally in R. It aims to facilitate DEA experiments for python users.

As PyDESeq2 is a re-implementation of DESeq2 from scratch, you may experience some differences in terms of retrieved values or available features.

Currently, available features broadly correspond to the default settings of DESeq2 (v1.34.0) for single-factor and paired multi-factor analysis (with n-level categorical factors), with an optional apeGLM LFC shrinkage step [ZIL19]. We plan to implement more in the near future. In case there is a feature you would particularly like to be implemented, feel free to open an issue on GitHub.

Citing this work

title={PyDESeq2: a python package for bulk RNA-seq differential expression analysis},
author={Muzellec, Boris and Telenczuk, Maria and Cabeli, Vincent and Andreux, Mathieu},
doi = {10.1101/2022.12.14.520412},


PyDESeq2 is released under an MIT license.