Functional Enrichment (HOMER + R)

Overview

• Validate input: Accept BED/peak files with genomic coordinates or gene lists; check format and genome assembly.
• Map regions to genes: Convert regions to a unique gene set using HOMER annotatePeaks.pl.
• Run GO enrichment: Use HOMER findGO.pl (or annotatePeaks.pl -go) for BP/MF/CC.
• Run KEGG enrichment: Use HOMER findGO.pl -kegg (or annotatePeaks.pl -kegg).
• Collect outputs: Save tidy tables for downstream plotting and a compact summary of top terms.
• Visualize in R: Create barplots and dotplots (GO/KEGG) with ggplot2 from standardized outputs.
• QC & troubleshooting: Provide checks for genome mismatch, chromosome naming, and low-signal inputs.

Inputs & Outputs