VplotR

Spec sheet

Purpose

VplotR is an R package for generating two-dimensional paired-end fragment density plots called V-plots.Read 12 Oct 2026 · jserizay.com

Free plan

YesRead 24 Sep 2026 · jserizay.com

Support

The project invites bug reports and feature requests through GitHub issues and lists an email address for queries to J. Serizay.Read 12 Oct 2026 · jserizay.com

License

VplotR is licensed under GPL-3.Read 12 Oct 2026 · jserizay.com

Bioconductor integration

The package is integrated with the Bioconductor environment and can be installed from Bioconductor.Read 12 Oct 2026 · jserizay.com

Data sources

Genomic sequencing dataRead 24 Sep 2026 · jserizay.com

Footprints

The plotFootprint() function generates MNase-seq or ATAC-seq footprint profiles across genomic ranges.Read 12 Oct 2026 · jserizay.com

Fragment analyses

The package includes functions for fragment-size distributions and paired-end fragment profiles at individual loci.Read 12 Oct 2026 · jserizay.com

Included datasets

The package includes example ATAC-seq datasets from C. elegans, a yeast MNase-seq dataset, and a sample BAM file.Read 12 Oct 2026 · jserizay.com

Maintainer

Jacques Serizay is listed as the package author and maintainer.Read 12 Oct 2026 · jserizay.com

Normalization

V-plots support raw counts, library-depth and locus-count normalization, z-scores, and quantile scaling.Read 12 Oct 2026 · jserizay.com

Parallel plotting

Generation of multiple V-plots can be parallelized using a list of parameters and a cores setting.Read 12 Oct 2026 · jserizay.com

Platform

desktopRead 24 Sep 2026 · jserizay.com

Plotting integration

VplotR is designed around ggplot2 so plots can be combined with other plots to create publication-ready figures.Read 12 Oct 2026 · jserizay.com

Requirements

VplotR requires R >= 4.0 and has been tested on Mac OS >= 10.13, Ubuntu >= 18.04, and Windows Server 2012.Read 12 Oct 2026 · jserizay.com

Supported assays

It imports paired-end sequencing BAM files from DNA accessibility experiments including ATAC-seq, DNA-seq, and MNase-seq.Read 12 Oct 2026 · jserizay.com

V-plot generation

The plotVmat() function computes fragment density and generates V-plots over genomic loci of interest.Read 12 Oct 2026 · jserizay.com

Plans and prices

Every VplotR plan and price →

Where Specifiction places it

• Data Visualization Software#69 of 987.6