functional-enrichment

GO and KEGG functional enrichment from BED files is performed by mapping genomic regions to genes using HOMER, then calculating enrichment to produce result tables and R visualization plots. It accepts BED, narrowPeak, or broadPeak region formats.

The best way to visualize HOMER enrichment results in R is to use ggplot2 to generate barplots and dotplots. This approach takes the tidy enrichment output from HOMER and creates quick visual summaries for biological interpretation.

Yes, you can use HOMER for functional enrichment directly from a plain gene list. The workflow supports direct gene-list inputs to run GO and KEGG enrichment, bypassing the need for prior genomic region annotation.

Yes, you need to install and configure HOMER before running GO and KEGG enrichment. The workflow relies on HOMER's annotatePeaks.pl and findGO.pl scripts to map genomic regions and calculate the enrichment results.

To handle chromosome naming and genome version checks for HOMER enrichment, the workflow includes built-in QC checks. These validate your input formats and genome version parameters before running the annotation and enrichment steps.

You should not use HOMER for genomic region enrichment if your input data lacks a compatible genome version for annotation, or if you cannot meet the requirement to install and configure the HOMER software environment locally.