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 BioTender-max/awesome-bio-agent-skills --skill reactome-pathways --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 ## When to Use Reactome | Scenario | Reactome? | Alternative | |----------|-----------|-------------| | Signaling pathway detail (reaction-level) | Yes -- best choice | KEGG (pathway-level only) | | Metabolic pathway focus | Supplement | KEGG has stronger metabolic coverage | | Reproducibility / open license required | Yes (CC0) | WikiPathways (CC0) | | Non-model organism (bacteria, plants) | No (7 species only) | KEGG (8,000+ species) | | Non-human model organism (mouse, rat, fly) | Caution | Annotations are computationally inferred via orthology from human; may contain errors | Reactome pathways are curated by PhD-level biologists and externally peer-reviewed, making them the highest-quality curated pathway database. Human is the p
- Version Compatibility
- When to Use Reactome
- 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
- Interpretation Notes
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 BioTender-max/awesome-bio-agent-skills --skill reactome-pathways --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.