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bio-pathway-reactome
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-reactome
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- gene_list <- de_results$log2FoldChange names(gene_list) <- de_results$entrez_id gene_list <- sort(gene_list, decreasing = TRUE).
- gsea_result <- gsePathway( geneList = gene_list, organism = 'human', pvalueCutoff = 0.05, pAdjustMethod = 'BH', verbose = FALSE ).
- head(as.data.frame(gsea_result)).
- dotplot(pathway_result, showCategory = 15).
Source Doc
Excerpt From SKILL.md
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.
Prepare Gene List from DE Results
Goal: Extract significant Entrez gene IDs from differential expression results for Reactome enrichment.
Approach: Filter by significance and fold change, then convert symbols to Entrez IDs using bitr.
GSEA on Reactome Pathways
Goal: Detect coordinated expression changes in Reactome pathways using all genes ranked by a statistic.
Approach: Create a sorted named vector from DE results and run gsePathway for rank-based enrichment.
Use cases
- Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- go-enrichment - Gene Ontology enrichment
- kegg-pathways - KEGG pathway enrichment
- wikipathways - WikiPathways enrichment
- gsea - Gene Set Enrichment Analysis
- enrichment-visualization - Visualization functions
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