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functional-analysis

Review a bounded human gene set with Reactome pathway overrepresentation and STRING identifier mapping, enrichment, functional association networks, and PPI…

Skill by phenixace

IndexedMIT★ 2
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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.

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About

Review a bounded human gene set with Reactome pathway overrepresentation and STRING identifier mapping, enrichment, functional association networks, and PPI enrichment. Use preflight to confirm mappings and parameters; persist the full analysis only after researcher approval.

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

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Runs as
Python package

Network hosts it talks to 1

  • codeload.github.com · found in install command

Files it touches

  • ~/.claude/skills/functional-analysis

What's inside

Skill name
functional-analysis
Description
Review a bounded human gene set with Reactome pathway overrepresentation and STRING identifier mapping, enrichment, functional association networks, and PPI enrichment. Use preflight to confirm mappings and parameters; persist the full analysis only after researcher approval.
License
MIT
Instructions
9 lines in SKILL.md · view on GitHub

Before installing

  • Ships executable scripts

Files (4)

  • SKILL.md
  • openai.yaml · agents/
  • handler.py · scripts/
  • skill.json

SKILL.md (first lines)

# Gene-set Functional Analysis

Use `functional_analysis_preflight` for two to fifty human gene or protein identifiers. Confirm every STRING mapping, unmapped identifier, the STRING confidence threshold, FDR threshold, reported-term limit, and whether disease pathways are included.

Use `functional_analysis_run` only through a researcher-approved workflow. Keep Reactome and STRING results separate in the evidence record; do not merge their statistics into an invented score. Preserve official source links, STRING version, retrieval time, parameters, input identifiers, mappings, output tables, and the run manifest.

Reactome overrepresentation depends on list construction and reference coverage. FDR is a multiple-testing correction, not the probability that a pathway is true. STRING edges are functional associations and do not necessarily represent direct physical interactions. Database enrichment is a hypothesis-generating result, not causal or replicate-level evidence.

From phenixace/Molemo_WorkBench, MIT.

More from phenixace/Molemo_WorkBench

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Last commit (this folder)
Aug 29, 2026 (1 month ago)

From GitHub (fetched Oct 24, 2026).

Details

License
MIT
Repository
github.com/phenixace/Molemo_WorkBench
First seen
Oct 24, 2026
Last checked
Oct 24, 2026
Source
GitHubgithub-graphql

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Cite this page

functional-analysis skill. Agent Mart. https://agentmart.dev/skills/phenixace-functional-analysis (last updated 2026-10-24)