Agent Skills Index

Directory / Scientific Agent Skills (K-Dense) / pathway-enrichment

pathway-enrichment

skill Science, research & learning

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".
Description from the SKILL.md front matter.

Install

GitHub CLI v2.90+ (Copilot by default)
gh skill install K-Dense-AI/scientific-agent-skills pathway-enrichment
For Claude Code
gh skill install K-Dense-AI/scientific-agent-skills pathway-enrichment --agent claude-code
For Codex
gh skill install K-Dense-AI/scientific-agent-skills pathway-enrichment --agent codex

Commands follow each host's documentation (Any Agent Skills host (Claude Code, Codex, Cursor, Gemini CLI, Copilot…) docs). gh skill needs GitHub CLI 2.90 or later and is in public preview.

Listed from K-Dense Inc.'s catalog, not reviewed by us. Read the source before installing.

Catalog
Scientific Agent Skills (K-Dense)
Author
K-Dense Inc.
Source code
K-Dense-AI/scientific-agent-skills
License
MIT
Repository stars
52,795 for K-Dense-AI/scientific-agent-skills (the whole catalog repo)
Version
1.3
Added to catalog
Not tracked for this source
Last change
2026-10-19 (last push to the repo)

What it contains

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