Data & ReproScientific DatabasesFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-pathway-kegg-pathways

Maintainer FreedomIntelligence · Last updated April 1, 2026

KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.

OpenClawNanoClawDiscoveryDataset Buildingbio-pathway-kegg-pathways🧬 bioinformatics (gptomics bio-* suite)bioinformatics — pathway & network analysiskegg

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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').

Source Doc

Excerpt From SKILL.md

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