GO/KEGG Enrichment

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/

# Python dependencies
pip install -r requirements.txt