bio-pathway-gsea - Gene Set Enrichment Analysis with clusterProfiler
Performs Gene Set Enrichment Analysis using clusterProfiler to identify coordinated gene expression changes from ranked gene lists.
Tags
Updated: 2026-09-09Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Format ranked gene list vectors
- Convert gene symbols to Entrez IDs
- Execute GO gene set enrichment analysis
- Execute KEGG pathway GSEA analysis
- Perform MSigDB custom gene set GSEA
- Export GSEA analysis results to CSV
Inputs
- Differential expression results file
- Ranked gene list vector
- GMT gene set files
Outputs
- GSEA result CSV file
- GSEA result data frame
Requirements
- R environment
- clusterProfiler package
- org.Hs.eg.db package
- msigdbr package