pydeseq

Source: https://github.com/aipoch/medical-research-skills

When to Use

Use this skill when you need to run DESeq2-style differential expression in Python, especially in these scenarios:

1. Case vs control bulk RNA-seq from a raw integer count matrix (e.g., treated vs control).
2. Multi-factor designs to adjust for batch effects or covariates (e.g., ~ batch + condition, ~ age + condition).
3. DESeq2 migration when converting an R DESeq2 workflow into a Python pipeline.
4. Pipeline integration where results must stay in Python objects (pandas/AnnData) for downstream QC, plots, or reporting.
5. Requests mentioning “DESeq2”, “differential expression”, “Wald test”, “FDR/padj”, “volcano plot”, “MA plot”, or “PyDESeq2”.

Key Features