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数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现
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bio-pathway-wikipathways

维护者 FreedomIntelligence · 最近更新 2026年4月1日

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.

OpenClawNanoClaw分析处理复现实验bio-pathway-wikipathways🧬 bioinformatics (gptomics bio-* suite)bioinformatics — pathway & network analysiswikipathways

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-wikipathways

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

2 min

核心说明

  • gene_list <- de_results$log2FoldChange names(gene_list) <- de_results$entrez_id gene_list <- sort(gene_list，decreasing = TRUE)。
  • gsea_wp <- gseWP( geneList = gene_list，organism = 'Homo sapiens'，pvalueCutoff = 0.05，pAdjustMethod = 'BH' )。
  • head(as.data.frame(gsea_wp))。
  • wp_readable <- setReadable(wp_result，OrgDb = org.Hs.eg.db，keyType = 'ENTREZID')。

原始文档

SKILL.md 摘录

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.

Prepare Gene List

Goal: Extract significant Entrez gene IDs from DE results for WikiPathways enrichment.

Approach: Filter by significance thresholds and convert gene symbols to Entrez IDs with bitr.

GSEA on WikiPathways

Goal: Detect coordinated expression changes in WikiPathways using a ranked gene list.

Approach: Sort genes by fold change and run gseWP for rank-based enrichment testing.

适用场景

  • 适合在analyzing gene lists against community-curated open-source pathways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
  • reactome-pathways - Reactome pathway enrichment
  • gsea - Gene Set Enrichment Analysis
  • enrichment-visualization - Visualization functions

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