VplotR

This is the development version of VplotR; for the stable release version, see VplotR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

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

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-4295-0624

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

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

Jacques Serizay. VplotR: Set of tools to make V-plots and compute footprint profiles. doi:10.18129/B9.bioc.VplotR, R package version 1.23.0, https://bioconductor.org/packages/VplotR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, Alignment, BiologicalQuestion, Coverage, NucleosomePositioning, Sequencing, Software
Version	1.23.0
In Bioconductor since	BioC 3.12 (R-4.0) (6 years)
License	GPL (>= 3)
Depends	R (>= 4.0), GenomicRanges, IRanges, ggplot2
Imports	cowplot, magrittr, Seqinfo, 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

Suggests	GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	VplotR_1.23.0.tar.gz
Windows Binary (x86_64)	VplotR_1.23.0.zip
macOS Binary (big-sur-x86_64)	VplotR_1.23.0.tgz
macOS Binary (sonoma-arm64)	VplotR_1.23.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VplotR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VplotR
Package Short Url	https://bioconductor.org/packages/VplotR/
Package Downloads Report	Download Stats