> ## Documentation Index
> Fetch the complete documentation index at: https://docs.kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# pydeseq2 — AI agent skill for life sciences

> Runs differential expression analysis on bulk RNA-seq count data with PyDESeq2, the Python port of DESeq2.

# `pydeseq2`

> Runs differential expression analysis on bulk RNA-seq count data with PyDESeq2, the Python port of DESeq2. Covers formulaic single- and multi-factor designs, contrasts, Wald tests, Benjamini-Hochberg FDR correction, optional apeGLM LFC shrinkage, pandas and AnnData (H5AD) integration, CSV export, volcano and MA plots, and a command-line script. Use when comparing gene expression between conditions such as treated vs control, adjusting for batch or covariates, porting an R DESeq2 workflow to Python, or building a Python pipeline for differential expression from raw integer counts. Not for single-cell data or for R-based DESeq2 itself.

**Category:** [life-sciences](/research-agent-skills/skills#life-sciences) · **License:** MIT · **Version:** 1.4

## Install

```bash theme={null}
npx research-agent-skills install pydeseq2
npx skills add KalarisLabs/research-agent-skills --skill pydeseq2
```

## When to use it

Runs differential expression analysis on bulk RNA-seq count data with PyDESeq2, the Python port of DESeq2. Covers formulaic single- and multi-factor designs, contrasts, Wald tests, Benjamini-Hochberg FDR correction, optional apeGLM LFC shrinkage, pandas and AnnData (H5AD) integration, CSV export, volcano and MA plots, and a command-line script. Use when comparing gene expression between conditions such as treated vs control, adjusting for batch or covariates, porting an R DESeq2 workflow to Python, or building a Python pipeline for differential expression from raw integer counts. Not for single-cell data or for R-based DESeq2 itself.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/pydeseq2/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.


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