September 5, 2023

PyDESeq2: a python package for bulk RNA-seq differential expression analysis


We present PyDESeq2, a python implementation of the DESeq2 workflow for differential expression analysis on bulk RNA-seq data. This implementation achieves better precision, allows speed improvements on large datasets, as shown in experiments on TCGA data, and can be more easily interfaced with modern python-based data science tools.

Availability and Implementation

PyDESeq2 is released as an open-source software under the MIT license. The source code is available on GitHub at

Boris Muzellec
Maria Telenczuk
Vincent Cabeli
Mathieu Andreux