peakCombiner: An R package to curate and merge enriched genomic regions into consensus peak sets

Author(s): Markus Muckenhuber, Michael Stadler, Kathleen Sprouffske

Affiliation(s): NIBR, Oncology Data Science



Genome-wide epigenomic data sets like ChIP-seq or ATAC-seq typically use peak calling tools to identify genomic regions of interest, called peaks, usually for multiple sample replicates and across experimental conditions. Many downstream analyses require a consensus set of genomic regions relevant to the experiment, but current tools within the R ecosystem to create combined peak sets easily and flexibly from conditions and replicates are limited. Here, we describe peakCombiner, a fully R based, user-friendly, transparent, and customisable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimise input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses. We are planning to make peakCombiner available as a Bioconductor package.