Generating fragment density plots in R/Bioconductor with VplotR
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.
Software
Cite
Serizay J, Ahringer J. Generating fragment density plots in R/Bioconductor with VplotR. Journal of Open Source Software. 2021;6(59):3009. doi:10.21105/joss.03009
@article{serizay_joss_2021,
author = {Serizay, Jacques and Ahringer, Julie},
title = {{Generating fragment density plots in R/Bioconductor with VplotR}},
journal = {Journal of Open Source Software},
year = {2021},
volume = {6},
number = {59},
pages = {3009},
doi = {10.21105/joss.03009},
url = {https://doi.org/10.21105/joss.03009}
}