ClaudSkills / Science & Research / math-stats

Bio Pathway Enrichment Foundations

Q: What is a Claude Code skill and how does the Bio Pathway Enrichment Foundations 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. Bio Pathway Enrichment Foundations is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at https://claudskills.com/learn/what-is-skill-md/.

Category: Science & Research · Sub-category: math-stats · Last updated: 2026-07-11

Chooses the enrichment generation before any tool runs, mapping the input shape to a method class - a pre-selected gene list plus a background to over-representation analysis (ORA, hypergeometric), a ranked statistic for all genes to gene set enrichment (GSEA), a signed signaling topology to pathway-topology (SPIA) - then making the null explicit (competitive vs self-contained, gene vs subject sampling) and running a trustworthiness checklist (testable-gene universe, FDR, redundancy collapse, leading-edge check, version reporting). Covers why every clusterProfiler GSEA is the inter-gene-correlation-uncorrected competitive null, why the background not the gene list decides ORA significance, and why no method is universally best. Use when deciding ORA vs GSEA vs topology, which gene-set DB, whether a result is trustworthy, or which null a tool computes. For ORA see go-enrichment, GSEA see gsea, databases kegg-pathways/reactome-pathways/wikipathways; the ranking comes from differential-expression/de-results.

Security AStatic scan found no risk patternsHow grading works ›

What this skill does

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

When to invoke it: Use when deciding ORA vs GSEA vs topology, which gene-set DB, whether a result is trustworthy, or which null a tool computes. For ORA see go-enrichment, GSEA see gsea, databases kegg-pathways/reactome-pathways/wikipathways; the ranking comes from differential-expression/de-results.

Who uses this skill

The Bio Pathway Enrichment Foundations Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 161,000+ 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/bio-pathway-enrichment-foundations
curl -L https://claudskills.com/skills/bio-pathway-enrichment-foundations/SKILL.md \
  -o ~/.claude/skills/bio-pathway-enrichment-foundations/SKILL.md

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

Skills live at ~/.claude/skills/bio-pathway-enrichment-foundations/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bio-pathway-enrichment-foundations\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 Bio Pathway Enrichment Foundations Claude Code skill?

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

What does the Bio Pathway Enrichment Foundations 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 Bio Pathway Enrichment Foundations skill?

Use Bio Pathway Enrichment Foundations when your Claude Code task falls under the Science & Research category — specifically in the math stats 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 Bio Pathway Enrichment Foundations" or describe the task and let Claude pick). Browse related skills at /category/science/.

What is a Claude Code skill and how does the Bio Pathway Enrichment Foundations 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. Bio Pathway Enrichment Foundations is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at /learn/what-is-a-claude-skill/.

Attribution & license

Source: https://github.com/bg-szy/TOP-SKILLS/blob/HEAD/skills/awesome-skills/bio-pathway-enrichment-foundations/SKILL.md
Author: bg-szy
Website: https://bg-szy.github.io/TOP-SKILLS/

Cite this skill

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

APA

bg-szy. (2026). Bio Pathway Enrichment Foundations [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/bio-pathway-enrichment-foundations/

BibTeX

@misc{bio-pathway-enrichment-foundations-2026,
  author    = {bg-szy},
  title     = {Bio Pathway Enrichment Foundations [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/bio-pathway-enrichment-foundations/}
}

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Badge

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Security scan

Grade A · scanned 2026-07-26 — free static scan against the OWASP Agentic Skills Top 10.

No risk patterns were found in any of the ten OWASP-aligned categories. How grading works ›

✓ Prompt injection
✓ Data exfiltration
✓ Supply chain
✓ Reverse shell
✓ Credentials
✓ Execution
✓ Filesystem
✓ Persistence
✓ Obfuscation
✓ Network

Show this grade on your repo (click to copy):

[![Security: A](https://img.shields.io/badge/Security-A-2e7d32)](https://claudskills.com/skills/bio-pathway-enrichment-foundations/#security)

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