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pathway-enrichment

Run reproducible GO and KEGG enrichment from executed differential or module results, choosing ORA versus ranked GSEA, mapping IDs consistently, using the…

Skill by Sheldon-Bacchus

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Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.

npx agentmarket install skill/sheldon-bacchus-pathway-enrichment

Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.

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About

Run reproducible GO and KEGG enrichment from executed differential or module results, choosing ORA versus ranked GSEA, mapping IDs consistently, using the tested-gene universe, and separating up/down direction. Use for pathway analysis, GO/KEGG ORA, background selection, or enrichment interpretation. Do not use to invent a gene list or treat enrichment as validation of the same DE result.

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Permissions

What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.

Tools
No tools found
Secrets
None asked for
Install scripts
None found

Network hosts it talks to 1

  • codeload.github.com · found in install command

Files it touches

  • ~/.claude/skills/pathway-enrichment

What's inside

Skill name
pathway-enrichment
Description
Run reproducible GO and KEGG enrichment from executed differential or module results, choosing ORA versus ranked GSEA, mapping IDs consistently, using the tested-gene universe, and separating up/down direction. Use for pathway analysis, GO/KEGG ORA, background selection, or enrichment interpretation. Do not use to invent a gene list or treat enrichment as validation of the same DE result.
License
unknown
Metadata
role: tool-usage-and-result-interpretation · source: vendor/sources/bioSkills/pathway-analysis and vendor/sources/scientific-agent-skills/skills/pathway-enrichment · primary_tool: Rscript
Instructions
44 lines in SKILL.md · view on GitHub

Files (7)

  • SKILL.md
  • go_enrichment_basic.R · references/
  • kegg_enrichment.R · references/
  • upstream-expression-to-pathways.md · references/
  • upstream-go-enrichment.md · references/
  • upstream-kegg-pathways.md · references/
  • upstream-scientific-agent-pathway-enrichment.md · references/

The license isn't open source, so the instructions aren't shown here. Read SKILL.md on GitHub

More from Sheldon-Bacchus/bio-spec-mvp

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Last commit (this folder)
Sep 2, 2026 (1 month ago)

From GitHub (fetched Oct 24, 2026).

Details

License
License unknown
Repository
github.com/Sheldon-Bacchus/bio-spec-mvp
First seen
Oct 24, 2026
Last checked
Oct 24, 2026
Source
GitHubgithub-graphql

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Cite this page

pathway-enrichment skill. Agent Mart. https://agentmart.dev/skills/sheldon-bacchus-pathway-enrichment (last updated 2026-10-24)