Pathway Enrichment

Q: What is a Claude Code skill and how does the Pathway Enrichment skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Pathway Enrichment is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Engineering category. Learn more at https://claudskills.com/learn/what-is-skill-md/.

Category: Engineering · Sub-category: testing · Last updated: 2026-05-29

Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever 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".

About this skill (catalog notes)

Pathway Enrichment includes a dedicated installation section; pricing or quota commentary; 5 code blocks for direct copy-paste. At roughly 1,536 words the SKILL.md is on the longer end of the catalog distribution.

Source: k-dense.ai
License: MIT
Original author: K-Dense-AI
Indexed lastmod: 2026-05-29
Catalog position: Engineering · testing
Indexed related skills: 10

How Pathway Enrichment fits the catalog

Pathway Enrichment sits in the Engineering category under the testing sub-topic in the ClaudSkills catalog. There are 10 related skills indexed alongside it; comparing a few before installing usually reveals which fits your workflow best.

These notes are auto-generated from features detected in the SKILL.md file and from this catalog's structure — they aren't part of the source repository.

What this skill does

Pathway Enrichment is a community-contributed Claude Code skill in the testing sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/pathway-enrichment/ and loads when your prompt matches the skill's trigger.

When to invoke it: Use whenever 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.

Who uses this skill

The Pathway Enrichment Claude Code skill is built for software engineers, backend developers, full-stack teams, and technical leads building and maintaining production systems. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 93,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).

How to install

Free

Manual install (2 steps)

mkdir -p ~/.claude/skills/pathway-enrichment
curl -L https://claudskills.com/skills/pathway-enrichment/SKILL.md \
  -o ~/.claude/skills/pathway-enrichment/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/pathway-enrichment/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/pathway-enrichment/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\pathway-enrichment\SKILL.md on Windows. See the full install guide for step-by-step instructions.

📱 Install from your phone or desktop Telegram

Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →

Pro

One-click install via the desktop app

The ClaudSkills desktop app installs any skill directly into ~/.claude/skills/ with one click — no terminal required. Pro starts at $9/mo or $149 lifetime.

Pro

For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.

See pricing → Download desktop app

Frequently asked questions

How do I install the Pathway Enrichment Claude Code skill?

Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/pathway-enrichment/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.

What does the Pathway Enrichment skill do?

Is this skill free to install?

Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.

When should I use the Pathway Enrichment skill?

Use Pathway Enrichment when your Claude Code task falls under the Engineering category — specifically in the testing area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use Pathway Enrichment" or describe the task and let Claude pick). Browse related skills at /category/engineering/.

What is a Claude Code skill and how does the Pathway Enrichment skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Pathway Enrichment is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Engineering category. Learn more at /learn/what-is-a-claude-skill/.

Attribution & license

Source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/HEAD/skills/pathway-enrichment/SKILL.md
License: MIT
Author: K-Dense-AI
Website: https://k-dense.ai

Cite this skill

If you reference this skill in a blog post, paper, or documentation, you can cite it as:

APA

K-Dense-AI. (2026). Pathway Enrichment [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/pathway-enrichment/

BibTeX

@misc{pathway-enrichment-2026,
  author    = {K-Dense-AI},
  title     = {Pathway Enrichment [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/pathway-enrichment/}
}

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