What is PEGS?

PEGS (Peak-set Enrichment of Gene-Sets) is a Python bioinformatics package for efficiently calculating enrichments of gene clusters in multiple genomic intervals data (e.g. ChIP-seq peak-sets) at different distances.

What it does

Given input BED file(s), containing genomic intervals, coming from ChIP-seq, ATAC-seq etc, and cluster(s) of genes for which user wants to calculate enrichment, PEGS will expand each interval in the BED file (from the centre, in both directions) for a given genomic distance, and extract overlapping gene TSSs.

Using these genes, input gene cluster(s), and total number of genes in the genome (RefSeq defined), PEGS will obtain the common genes (numbers shown in the output heatmap cells), and corresponding hypergeometric p-value (color in the output heatmap).

PEGS can very efficiently do this analysis for many peak-sets and gene clusters at multiple genomic distances simultaneously and outputs the result in a combined, easy to interpret heatmap.

Citing PEGS

If you use PEGS in your research then please cite:

• Briggs P, Hunter AL, Yang Sh et al. PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]. F1000Research 2021, 10:570 (https://doi.org/10.12688/f1000research.53926.2)