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)