数据与复现科研数据库FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-pathway-kegg-pathways

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

bio-pathway-kegg-pathways：KEGG pathway 、 module enrichment analysis ，使用 clusterProfiler enrichKEGG 、 enrichMKEGG。支持 4000+ organisms ，通过 KEGG online database。适合在identifying metabolic 、 signaling pathways over-represented in gene list时使用。

OpenClawNanoClaw选题发现数据建库bio-pathway-kegg-pathways🧬 bioinformatics (gptomics bio-* suite)bioinformatics — pathway & network analysiskegg

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

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_ids <- bitr(sig_genes，fromType = 'SYMBOL'，toType = 'ENTREZID'，OrgDb = org.Hs.eg.db) gene_list <- gene_ids$ENTREZID。
kegg_ids <- bitr_kegg(gene_list，fromType = 'ncbi-geneid'，toType = 'kegg'，organism = 'hsa')。

原始文档

SKILL.md 摘录

Core Pattern

Goal: Identify KEGG metabolic and signaling pathways over-represented in a gene list.

Approach: Test for enrichment using the hypergeometric test via clusterProfiler enrichKEGG against the KEGG online database.

"Find enriched KEGG pathways in my gene list" → Test whether KEGG pathway gene sets are over-represented among significant genes.

Prepare Gene List

Goal: Extract significant Entrez gene IDs from DE results in the format required by enrichKEGG.

Approach: Filter by significance thresholds and convert gene symbols to Entrez IDs (KEGG requires NCBI Entrez).

library(org.Hs.eg.db)

de_results <- read.csv('de_results.csv')
sig_genes <- de_results$gene_id[de_results$padj < 0.05 & abs(de_results$log2FoldChange) > 1]

## KEGG ID Conversion

**Goal:** Convert between KEGG-specific identifiers and other gene ID formats.

**Approach:** Use bitr_kegg to map between kegg, ncbi-geneid, ncbi-proteinid, and uniprot ID types.

```r