pydeseq2

SUMMARY

What it does

This skill provides a complete workflow for differential gene expression analysis of bulk RNA-seq data using PyDESeq2. It covers data loading and validation, design specification with formulaic strings, DESeq2 fitting (size factors, dispersions, GLM), Wald tests with multiple testing correction, optional LFC shrinkage, result interpretation, and visualization (volcano and MA plots). It includes a command-line script for standard analyses and references for detailed API and workflow guidance. The skill requires Python >=3.11 and PyDESeq2 0.5.4-compatible dependencies.