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

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)