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immune-pathway-analysis

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Run immune pathway GSVA or ssGSEA analysis from a bulk expression matrix, a sample group file, and a local immune Reactome gene-set table, then export differential pathway results and a heatmap for two-group comparison.

When to use

• "Run immune pathway GSVA for these samples."
• "Score immune Reactome pathways and compare case versus control."
• "Generate an immune pathway heatmap from a saved result."
• "Use a local immune gene-set table for pathway scoring."
• Bulk RNA-seq or microarray-like expression matrices
• Local immune Reactome gene-set tables prepared in advance
• Two-group pathway differential analysis with `limma`
• Reproducible CLI execution with append-only provenance files

When not to use

• Immune cell fraction estimation or deconvolution
• Gene-level differential expression without pathway scoring
• Single-cell clustering, annotation, or communication analysis
• Clinical diagnosis or treatment selection

Skill page

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