go-kegg-enrichment
Performs GO (Gene Ontology) and KEGG pathway enrichment analysis on gene lists. Trigger when: - User provides a list of genes (symbols or IDs) and asks for enrichment analysis - User mentions "GO enrichment", "KEGG enrichment", "pathway analysis" - User wants to understand biological functions of gene sets - User provides differentially expressed genes (DEGs) and asks for interpretation - Input: gene list (file or inline), organism (human/mouse/rat), background gene set (optional) - Output: enriched terms, statistics, visualizations (barplot, dotplot, enrichment map)
Install via CLI (Recommended)
clawhub install openclaw/skills/skills/aipoch-ai/go-kegg-enrichmentGO/KEGG Enrichment Analysis
Automated pipeline for Gene Ontology and KEGG pathway enrichment analysis with result interpretation and visualization.
Features
- GO Enrichment: Biological Process (BP), Molecular Function (MF), Cellular Component (CC)
- KEGG Pathway: Pathway enrichment with organism-specific mapping
- Multiple ID Support: Gene symbols, Entrez IDs, Ensembl IDs, RefSeq
- Statistical Methods: Hypergeometric test, Fisher's exact test, GSEA support
- Visualizations: Bar plots, dot plots, enrichment maps, cnet plots
- Result Interpretation: Automatic biological significance summary
Supported Organisms
| Common Name | Scientific Name | KEGG Code | OrgDB Package |
|---|---|---|---|
| Human | Homo sapiens | hsa | org.Hs.eg.db |
| Mouse | Mus musculus | mmu | org.Mm.eg.db |
| Rat | Rattus norvegicus | rno | org.Rn.eg.db |
| Zebrafish | Danio rerio | dre | org.Dr.eg.db |
| Fly | Drosophila melanogaster | dme | org.Dm.eg.db |
| Yeast | Saccharomyces cerevisiae | sce | org.Sc.sgd.db |
Usage
Basic Usage
# Run enrichment analysis with gene list
python scripts/main.py --genes gene_list.txt --organism human --output results/
Parameters
| Parameter | Description | Default | Required |
|---|---|---|---|
--genes | Path to gene list file (one gene per line) | - | Yes |
--organism | Organism code (human/mouse/rat/zebrafish/fly/yeast) | human | No |
--id-type | Gene ID type (symbol/entrez/ensembl/refseq) | symbol | No |
--background | Background gene list file | all genes | No |
--pvalue-cutoff | P-value cutoff for significance | 0.05 | No |
--qvalue-cutoff | Adjusted p-value (q-value) cutoff | 0.2 | No |
--analysis | Analysis type (go/kegg/all) | all | No |
--output | Output directory | ./enrichment_results | No |
--format | Output format (csv/tsv/excel/all) | all | No |
Advanced Usage
# GO enrichment only with specific ontology
python scripts/main.py \
--genes deg_upregulated.txt \
--organism mouse \
--analysis go \
--go-ontologies BP,MF \
--pvalue-cutoff 0.01 \
--output go_results/
# KEGG enrichment with custom background
python scripts/main.py \
--genes treatment_genes.txt \
--background all_expressed_genes.txt \
--organism human \
--analysis kegg \
--qvalue-cutoff 0.05 \
--output kegg_results/
Input Format
Gene List File
TP53
BRCA1
EGFR
MYC
KRAS
PTEN
With Expression Values (for GSEA)
gene,log2FoldChange
TP53,2.5
BRCA1,-1.8
EGFR,3.2
Output Files
Metadata
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Find the right skillPaste this into your clawhub.json to enable this plugin.
{
"plugins": {
"official-aipoch-ai-go-kegg-enrichment": {
"enabled": true,
"auto_update": true
}
}
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