Skill UI

Query the Reactome Content and Analysis Services (or the reactome2py client) to fetch pathway hierarchies, map genes, run overrepresentation/expression analyses, and explore disease interactions for systems biology research.

This skill performs advanced pathway and gene-set enrichment analysis crucial for interpreting gene lists (e.g., DE genes, screen hits). It distinguishes between Over-Representation Analysis (ORA) for thresholded lists and Gene Set Enrichment Analysis (GSEA) for full ranked lists. Supports scoring pathway activity (ssGSEA/GSVA) and utilizes major databases like GO, KEGG, Reactome, and MSigDB for comprehensive biological interpretation, ensuring publication-ready results.