Functional Enrichment Analysis

关于

Streamlines the biological interpretation of genomic data by performing functional enrichment analysis using HOMER and R. It handles the entire workflow from input validation and coordinate-to-gene mapping to running Gene Ontology (Biological Process, Molecular Function, Cellular Component) and KEGG enrichment. The skill automatically generates standardized tidy tables and publication-ready visualizations like barplots and dotplots using ggplot2. It is particularly useful for researchers working with BED, narrowPeak, or broadPeak files who need to link genomic regions to biological functions while ensuring data quality through chromosome standardization and assembly checks.

主要功能

• Supports custom background gene sets for statistical accuracy
• Maps genomic coordinates (BED/narrowPeak) to unique gene sets
• 2 GitHub stars
• Executes GO (BP/MF/CC) and KEGG enrichment using HOMER
• Generates publication-quality R barplots and dotplots
• Standardizes chromosome naming and validates genome assemblies

使用场景

• Visualizing functional profiles of genomic regions for research publications
• Annotating ChIP-seq or ATAC-seq peaks with biological functions
• Analyzing differentially expressed gene lists for pathway enrichment