Generating fragment density plots in R/Bioconductor with VplotR

A multitude of proteins bind to DNA at regulatory regions to control the expression of neighbouring genes. Their binding can be revealed by chromatin accessibility assays such as DNase-seq, MNase-seq or ATAC-seq. The size of the sequencing fragments generated by these assays, as well as their location relative to the center of regulatory regions, can be used to produce two-dimensional fragment density plots called V-plots. Such plots have successfully been used in the past to reveal nucleosome positioning or transcription factor binding sites at regulatory regions in different genomes. Here, we present VplotR, an R package to easily generate V-plots and one-dimensional footprint profiles over single or aggregated genomic loci of interest. The use of VplotR will improve our understanding of molecular organization at regulatory regions.