On the recordRead 12 Oct 202617 facts
VplotR
Plans and prices
VplotR
Free
GPL-3 licensed R package · Requires R >= 4.0 · Available from Bioconductor release > 3.12
Read 12 Oct 2026 · jserizay.com
On the record
- Bioconductor integration
- The package is integrated with the Bioconductor environment and can be installed from Bioconductor.jserizay.com · read 12 Oct 2026
- Data sources
- Genomic sequencing datajserizay.com · read 24 Sep 2026
- Footprints
- The plotFootprint() function generates MNase-seq or ATAC-seq footprint profiles across genomic ranges.jserizay.com · read 12 Oct 2026
- Fragment analyses
- The package includes functions for fragment-size distributions and paired-end fragment profiles at individual loci.jserizay.com · read 12 Oct 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 · read 12 Oct 2026
- License
- VplotR is licensed under GPL-3.jserizay.com · read 12 Oct 2026
- Maintainer
- Jacques Serizay is listed as the package author and maintainer.jserizay.com · read 12 Oct 2026
- Normalization
- V-plots support raw counts, library-depth and locus-count normalization, z-scores, and quantile scaling.jserizay.com · read 12 Oct 2026
- Parallel plotting
- Generation of multiple V-plots can be parallelized using a list of parameters and a cores setting.jserizay.com · read 12 Oct 2026
- Platform
- desktopjserizay.com · read 24 Sep 2026
- Plotting integration
- VplotR is designed around ggplot2 so plots can be combined with other plots to create publication-ready figures.jserizay.com · read 12 Oct 2026
- Purpose
- VplotR is an R package for generating two-dimensional paired-end fragment density plots called V-plots.jserizay.com · read 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 · read 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 · read 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 · read 12 Oct 2026
- V-plot generation
- The plotVmat() function computes fragment density and generates V-plots over genomic loci of interest.jserizay.com · read 12 Oct 2026
