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VplotR

Set of tools to make V-plots and compute footprint profiles


Bioconductor version: Release (3.18)

The pattern of digestion and protection from DNA nucleases such as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to infer the location of associated proteins. This package contains useful functions to analyze patterns of paired-end sequencing fragment density. VplotR facilitates the generation of V-plots and footprint profiles over single or aggregated genomic loci of interest.

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

Citation (from within R, enter citation("VplotR")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("VplotR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VplotR")
VplotR HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ATACSeq, Alignment, BiologicalQuestion, Coverage, NucleosomePositioning, Sequencing, Software
Version 1.12.1
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL (>= 3)
Depends R (>= 4.0), GenomicRanges, IRanges, ggplot2
Imports cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats
System Requirements
URL https://github.com/js2264/VplotR
Bug Reports https://github.com/js2264/VplotR/issues
See More
Suggests GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package VplotR_1.12.1.tar.gz
Windows Binary VplotR_1.12.1.zip
macOS Binary (x86_64) VplotR_1.12.1.tgz
macOS Binary (arm64) VplotR_1.12.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/VplotR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VplotR
Bioc Package Browser https://code.bioconductor.org/browse/VplotR/
Package Short Url https://bioconductor.org/packages/VplotR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive