# Deseq2 Differential Expression

> DESeq2 differential expression analysis skill with normalization, statistical modeling, and visualization

- Skill: `a5c-ai/deseq2-differential-expression` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/deseq2-differential-expression`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/deseq2-differential-expression/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/deseq2-differential-expression

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# DESeq2 Differential Expression Skill

## Purpose
Provide DESeq2 differential expression analysis with normalization, statistical modeling, and visualization.

## Capabilities
- Size factor normalization
- Negative binomial modeling
- Shrinkage estimation
- Batch effect modeling
- Multi-factor designs
- Result visualization (MA plots, volcano plots)

## Usage Guidelines
- Design experiments with appropriate replication
- Include batch effects in model when present
- Apply appropriate shrinkage estimators
- Use multiple testing correction
- Generate publication-quality visualizations
- Document analysis parameters and thresholds

## Dependencies
- DESeq2
- edgeR
- limma-voom

## Process Integration
- RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
- Single-Cell RNA-seq Analysis (scrnaseq-analysis)
- CRISPR Screen Analysis (crispr-screen-analysis)