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gsva-analysis-and-visualization

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Use this skill to run GSVA or ssGSEA pathway-level differential analysis from a bulk expression matrix and a sample group file, then generate a heatmap from the saved GSVA result object. Trigger keywords: GSVA, ssGSEA, pathway enrichment, KEGG pathway analysis, MSigDB. NOT for: gene-level differential expression, single-cell analysis, methylation analysis, clinical diagnosis.

When to use

• 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
• "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"

When not to use

• Gene-level differential expression: use `differential-expression-analysis` instead
• Single-cell RNA-seq clustering or communication analysis: use `sc-clustering` or `cellchat`
• Immune infiltration scoring rather than pathway enrichment: use `ssgsea-r` or `ssgsea_immune`
• Clinical diagnosis, treatment selection, or patient-specific interpretation: do not use this skill; ask for a validated clinical workflow or human expert review

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