GSVA Analysis And Visualization

When to Use

Use this skill when the user wants one of the following:

• Pathway-level GSVA or ssGSEA analysis from a bulk expression matrix plus a sample group file
• Case-vs-control or treatment-vs-control pathway enrichment comparison using GSVA plus limma
• KEGG or MSigDB pathway analysis for bulk RNA-seq or microarray-like expression data
• Heatmap generation from an existing data/GSVA_list.rda result object
• A reproducible CLI-backed GSVA workflow with saved tables, an .rda object, and a PDF heatmap

Typical request patterns:

• "Run GSVA on my bulk RNA-seq matrix and compare case vs control"
• "Use ssGSEA to score pathways and save the pathway differential results"
• "Generate a KEGG pathway heatmap from my saved GSVA result"
• "Do pathway enrichment with GSVA for these grouped bulk samples"