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数据与复现
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bio-pathway-reactome
维护者 FreedomIntelligence · 最近更新 2026年4月1日
bio-pathway-reactome：Reactome pathway enrichment ，使用 ReactomePA package。 执行 over-representation analysis 、 GSEA ，支持 visualization 、 pathway hierarchy exploration。 适合在analyzing gene lists against Reactome's curated peer-reviewed pathway database时使用。
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-reactome
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- 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)。
原始文档
SKILL.md 摘录
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.
适用场景
- 适合在analyzing gene lists against Reactome's curated peer-reviewed pathway database时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- 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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