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Reactome pathway analysis starter

Skill ma-compbio-lab/SkillFoundry/skills/systems-biology/reactome-pathway-analysis-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill reactome-pathway-analysis-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.1 KB, 256 tokens by cl100k_base, as published. Nobody here has run it

Reactome Pathway Analysis Starter

Use this skill to submit a short identifier list to the official Reactome Analysis Service and return a compact ranked pathway table.

What it does

  • Sends a small gene or protein identifier list to Reactome's official analysis endpoint.
  • Summarizes the top enriched pathways, the best FDR observed, and the number of pathways under a chosen threshold.
  • Emits deterministic JSON that is easier to route into reports or downstream agent workflows than the full raw service payload.

When to use it

  • You need a verified starter for pathway analysis.
  • You want a lightweight ranked pathway summary rather than a full enrichment payload dump.

Example

python3 skills/systems-biology/reactome-pathway-analysis-starter/scripts/run_reactome_pathway_analysis.py \
  --identifiers BRCA1,TP53,EGFR \
  --top-n 5 \
  --out scratch/reactome-pathway-analysis/top_pathways.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/systems-biology/reactome-pathway-analysis-starter/tests -p 'test_*.py'
  • Repository smoke target: make smoke-reactome-pathway-analysis

Keep looking

Skills are one crate of 328,083. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.