pydeseq2

PyDESeq2 Overview PyDESeq2 is a Python implementation of DESeq2 for differential expression analysis with bulk RNA-seq data. Design and execute complete workflows from data loading through result interpretation, including single-factor and multi-factor designs, Wald tests with multiple testing correction, optional apeGLM shrinkage, and integration with pandas and AnnData. When to Use This Skill This skill should be used when: Analyzing bulk RNA-seq count data for differential expression Comparing gene expression between experimental conditions (e.g., treated vs control) Performing multi-factor designs accounting for batch effects or covariates Converting R-based DESeq2 workflows to Python Integrating differential expression analysis into Python-based pipelines Users mention "DESeq2", "differential expression", "RNA-seq analysis", or "PyDESeq2" Quick Start Workflow For users who want to perform a standard differential expression analysis: Show more