Quickly install tooluniverse-gene-enrichment AI skill to your development environment via command line
Open Terminal: Open your terminal or command line tool (Terminal, iTerm, Windows Terminal, etc.)
Run Installation Command: Copy and run this command: npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-gene-enrichment
Verify Installation: Once installed, the skill will be automatically configured in your AI coding environment and ready to use in Claude Code, Cursor, or OpenClaw
Perform comprehensive gene enrichment analysis including Gene Ontology (GO), KEGG, Reactome, WikiPathways, and MSigDB enrichment using both Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA). Integrates local computation via gseapy with ToolUniverse pathway databases for cross-validated, publication-ready results.
IMPORTANT: Always use English terms in tool calls (gene names, pathway names, organism names), even if the user writes in another language. Only try original-language terms as a fallback if English returns no results. Respond in the user's language.
| genelist | Yes | List of gene symbols, Ensembl IDs, or Entrez IDs | ["TP53", "BRCA1", "EGFR"] | | organism | No | Organism (default: human). Supported: human, mouse, rat, fly, worm, yeast, zebrafish | human | | analysistype | No | ORA (default) or GSEA | ORA |
Facts (cite-ready)
Stable fields and commands for AI/search citations.
Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supports GO enrichment (BP, MF, CC), KEGG, Reactome, WikiPathways, MSigDB Hallmark, and 220+ Enrichr libraries. Handles multiple ID types (gene symbols, Ensembl, Entrez, UniProt), multiple organisms (human, mouse, rat, fly, worm, yeast), customizable backgrounds, and multiple testing correction (BH, Bonferroni). Use when users ask about gene enrichment, pathway analysis, GO term enrichment, KEGG pathway analysis, GSEA, over-representation analysis, functional annotation, or gene set analysis. Source: mims-harvard/tooluniverse.
How do I install tooluniverse-gene-enrichment?
Open your terminal or command line tool (Terminal, iTerm, Windows Terminal, etc.) Copy and run this command: npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-gene-enrichment Once installed, the skill will be automatically configured in your AI coding environment and ready to use in Claude Code, Cursor, or OpenClaw