Pydeseq2

If you're doing differential gene expression analysis in Python instead of R, this handles the full DESeq2 workflow from count matrices through statistical testing. You get Wald tests with FDR correction, batch effect control through multi-factor designs, optional apeGLM shrinkage for cleaner fold changes, and straightforward pandas integration. The workflow is pretty standard: load your counts and metadata, specify a design formula, fit the model with dds.deseq2(), then run statistical tests with contrast specifications. Works well for moving R-based RNA-seq pipelines to Python or when you need differential expression as part of a larger computational biology workflow. The main thing is making sure your count matrix is in the right orientation (samples by genes) and your metadata aligns properly.

skills.sh installs: 217
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill pydeseq2 --agent claude-code

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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:

import pandas as pd
from pydeseq2.dds import DeseqDataSet
from pydeseq2.ds import DeseqStats

SKILL.md on GitHub

Details

Repository: github.com/davila7/claude-code-templates
Category: Python
First seen: Jun 3, 2026