bio-pathway-wikipathways
WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Performs over-representation analysis and GSEA for 30+ species.
npx skills add BioTender-max/awesome-bio-agent-skills --skill wikipathways --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: ReactomePA 1.46+, clusterProfiler 4.10+, rWikiPathways 1.24+ 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. # WikiPathways Enrichment ## When to Use WikiPathways WikiPathways is community-curated (wiki model), not expert or peer-reviewed like KEGG/Reactome. This means: - **Strengths**: disease-specific and drug-related pathways not found in KEGG/Reactome; fully open (CC0 license); newer pathways contributed by active researchers; 30+ species - **Limitations**: quality varies by pathway -- some are meticulously curated by domain experts, others may be incomplete or contributed by non-specialists - **Best use**: complement to KEGG/Reactome, not a standalone primary database. Run WikiPathways alongside KEGG or Reactome to catch pathways unique to the WikiPathways collection. Check the "Last edited" date and contributor for specific pathways before relying on them for
- Version Compatibility
- When to Use WikiPathways
- Core Pattern - Over-Representation Analysis
- Prepare Gene List
- GSEA on WikiPathways
- With Background Universe
- Make Results Readable
- Visualization
- Using rWikiPathways Directly
- Custom GMT-Based Analysis
- Different Organisms
- Compare Clusters
- Export Results
- Key Parameters
What does the bio-pathway-wikipathways skill do?
WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Performs over-representation analysis and GSEA for 30+ species.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill wikipathways --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.