Freedom251 › Data Visualization Software
VplotR
What VplotR is
VplotR is a free desktop R package for analyzing paired-end genomic sequencing data as two-dimensional fragment-density V-plots. It imports BAM files from DNA-accessibility experiments such as ATAC-seq, DNA-seq, and MNase-seq. The plotVmat() function calculates fragment density over selected genomic loci, while plotFootprint() creates MNase-seq or ATAC-seq footprint profiles across genomic ranges. Other functions examine fragment-size distributions and paired-end fragment profiles at individual loci. Built around ggplot2, VplotR lets users combine its graphics with other plots for publication-ready figures. V-plots can use raw counts, library-depth or locus-count normalization, z-scores, and quantile scaling. Multiple plots can run in parallel using a parameter list and cores setting. Example data include C. elegans ATAC-seq, yeast MNase-seq, and a sample BAM file. The package integrates with Bioconductor, requires R 4.0 or later, and is licensed under GPL-3.
Who it suits
VplotR is suited to researchers working with paired-end accessibility sequencing data. It also fits users who need ggplot2-compatible figures, footprint profiles, normalization choices, or parallel plot generation.
What it does well
- Imports ATAC-seq, DNA-seq, and MNase-seq BAM files
- Creates V-plots and footprint profiles
- Supports several normalization methods
- Works with ggplot2 and Bioconductor
- Includes example sequencing datasets
What to know first
- Requires R version 4.0 or later
- It is a desktop R package, not a hosted service
- Parallel plotting requires configuring parameters and cores
Plans
| Plan | Billed and limits | Price |
|---|---|---|
| VplotR | GPL-3 licensed R package · Requires R >= 4.0 · Available from Bioconductor release > 3.12 | Free |
As jserizay.com lists them, read 12 Oct 2026. The maker's own page has the final word.
Verdict
VplotR focuses on specialized visualization and fragment analysis for DNA-accessibility sequencing. Its Bioconductor and ggplot2 integration, example data, and normalization options support research workflows, provided the R requirement is met.
Facts from VplotR's own pages
- Bioconductor integration
- The package is integrated with the Bioconductor environment and can be installed from Bioconductor. · jserizay.com, 12 Oct 2026
- Data sources
- Genomic sequencing data · jserizay.com, 24 Sept 2026
- Footprints
- The plotFootprint() function generates MNase-seq or ATAC-seq footprint profiles across genomic ranges. · jserizay.com, 12 Oct 2026
- Fragment analyses
- The package includes functions for fragment-size distributions and paired-end fragment profiles at individual loci. · jserizay.com, 12 Oct 2026
- Free plan
- Yes · jserizay.com, 24 Sept 2026
- Included datasets
- The package includes example ATAC-seq datasets from C. elegans, a yeast MNase-seq dataset, and a sample BAM file. · jserizay.com, 12 Oct 2026
- License
- VplotR is licensed under GPL-3. · jserizay.com, 12 Oct 2026
- Maintainer
- Jacques Serizay is listed as the package author and maintainer. · jserizay.com, 12 Oct 2026
- Normalization
- V-plots support raw counts, library-depth and locus-count normalization, z-scores, and quantile scaling. · jserizay.com, 12 Oct 2026
- Parallel plotting
- Generation of multiple V-plots can be parallelized using a list of parameters and a cores setting. · jserizay.com, 12 Oct 2026
- Platform
- desktop · jserizay.com, 24 Sept 2026
- Plotting integration
- VplotR is designed around ggplot2 so plots can be combined with other plots to create publication-ready figures. · jserizay.com, 12 Oct 2026
- Purpose
- VplotR is an R package for generating two-dimensional paired-end fragment density plots called V-plots. · jserizay.com, 12 Oct 2026
- Requirements
- VplotR requires R >= 4.0 and has been tested on Mac OS >= 10.13, Ubuntu >= 18.04, and Windows Server 2012. · jserizay.com, 12 Oct 2026
- Support
- The project invites bug reports and feature requests through GitHub issues and lists an email address for queries to J. Serizay. · jserizay.com, 12 Oct 2026
- Supported assays
- It imports paired-end sequencing BAM files from DNA accessibility experiments including ATAC-seq, DNA-seq, and MNase-seq. · jserizay.com, 12 Oct 2026
- V-plot generation
- The plotVmat() function computes fragment density and generates V-plots over genomic loci of interest. · jserizay.com, 12 Oct 2026
Where VplotR stands on Freedom251
- Data Visualization Software#53 of 98