# Gsea Pathway Analyzer

> Gene Set Enrichment Analysis skill for functional annotation and pathway interpretation

- Skill: `a5c-ai/gsea-pathway-analyzer` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/gsea-pathway-analyzer`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/gsea-pathway-analyzer/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/gsea-pathway-analyzer

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# GSEA Pathway Analyzer Skill

## Purpose
Enable Gene Set Enrichment Analysis for functional annotation and pathway interpretation.

## Capabilities
- Preranked GSEA execution
- Gene ontology enrichment
- KEGG/Reactome pathway analysis
- Custom gene set support
- Leading edge analysis
- Publication-ready visualizations

## Usage Guidelines
- Rank genes appropriately for analysis type
- Select relevant gene set collections
- Apply multiple testing correction
- Identify leading edge genes for interpretation
- Generate clear visualizations
- Document gene set versions

## Dependencies
- GSEA
- clusterProfiler
- g:Profiler
- Enrichr

## Process Integration
- RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
- Single-Cell RNA-seq Analysis (scrnaseq-analysis)
- Multi-Omics Data Integration (multi-omics-integration)