Generating fragment density plots in R/Bioconductor with VplotR

Serizay, Ahringer, Generating fragment density plots in R/Bioconductor with VplotR. Journal of Open Source Software 2021

Abstract

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 DNaseseq, MNase-seq or ATAC-seq. Plotting the size of the sequencing fragments generated by these assays relative to the center of regulatory regions produce two-dimensional fragment density plots called V-plots. Such plots can reveal nucleosome positioning or transcription factor binding sites at regulatory regions. 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.