VplotR

DOI: 10.18129/B9.bioc.VplotR    

This is the development version of VplotR; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.12)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
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")

 

HTML R Script VplotR
PDF   Reference Manual
Text   NEWS

Details

biocViews ATACSeq, Alignment, BiologicalQuestion, Coverage, NucleosomePositioning, Sequencing, Software
Version 0.99.5
In Bioconductor since BioC 3.12 (R-4.0)
License GPL-3
Depends R (>= 4.0), GenomicRanges, IRanges, ggplot2
Imports cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats
LinkingTo
Suggests GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown
SystemRequirements
Enhances
URL https://github.com/js2264/VplotR
BugReports https://github.com/js2264/VplotR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package VplotR_0.99.5.tar.gz
Windows Binary VplotR_0.99.5.zip
macOS 10.13 (High Sierra) VplotR_0.99.5.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

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