bio-pathway-reactome
Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Performs over-representation analysis and GSEA with visualization and pathway hierarchy exploration.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pathway-reactome --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: R stats (base), ReactomePA 1.46+, clusterProfiler 4.10+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Reactome Pathway Enrichment ## Core Pattern - Over-Representation Analysis **Goal:** Identify Reactome pathways over-represented in a gene list from differential expression or other analyses. **Approach:** Test for enrichment using the hypergeometric test via ReactomePA enrichPathway against curated peer-reviewed pathways. **"Run pathway enrichment against Reactome"** → Test whether genes in curated Reactome pathways are over-represented among significant genes. ```r library(ReactomePA) library(org.Hs.eg.db) pathway_result <- enrichPathway( gene = entrez_ids, # Character vector of Entrez IDs organism = 'human', # human, rat, mouse, celegans, yeast, zebrafish, fly pvalueCutoff = 0.05, pAdjustMethod = 'BH', readable = TRUE # Convert to gene symbols ) head(as.data
- Version Compatibility
- Core Pattern - Over-Representation Analysis
- Prepare Gene List from DE Results
- GSEA on Reactome Pathways
- With Background Universe
- Visualization
- View Pathway in Browser
- Export Results
- Different Organisms
- Compare Clusters
- Key Parameters
- Supported Organisms
- Related Skills
What does the bio-pathway-reactome skill do?
Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Performs over-representation analysis and GSEA with visualization and pathway hierarchy exploration.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pathway-reactome --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.