gsea-pathway-analyzer

name	gsea-pathway-analyzer
description	Gene Set Enrichment Analysis skill for functional annotation and pathway interpretation
allowed-tools	["Read","Write","Glob","Grep","Edit","WebFetch","WebSearch","Bash"]
metadata	{"version":"1.0","category":"bioinformatics","tags":["transcriptomics","pathway-analysis","gsea","functional"]}
graph	{"domains":["domain:bioinformatics"],"specializations":["specialization:biomedical-informatics"],"skillAreas":["skill-area:statistical-analysis","skill-area:graph-algorithms","skill-area:data-analysis"],"workflows":["workflow:experiment-design"],"roles":["role:research-scientist","role:biomedical-engineer"]}

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)