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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pathway-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 ## Core Pattern - Over-Representation Analysis **Goal:** Identify WikiPathways that are over-represented in a gene list. **Approach:** Test for enrichment using enrichWP against community-curated open-source pathway definitions. **"Run pathway enrichment against WikiPathways"** → Test whether genes from community-curated WikiPathways are over-represented among significant genes. ```r library(clusterProfiler) library(org.Hs.eg.db) wp_result <- enrichWP( gene = entrez_ids, # Character vector of Entrez IDs organism = 'Homo sapiens', # Full species name pvalueCutoff = 0.05, pAdjustMethod = 'BH' ) head(as.data.frame(wp_result)) ``` ## Prepare Gene List **Goal:** Extract significant Entrez gene IDs from DE results for WikiPathways enrichm
- Version Compatibility
- 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
- Common Organisms
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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pathway-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 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.