This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

VplotR

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

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

Bioconductor version: Development (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")

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

Details

biocViews ATACSeq, Alignment, BiologicalQuestion, Coverage, NucleosomePositioning, Sequencing, Software
Version 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 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
Linking To
Suggests GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown
System Requirements
Enhances
URL https://github.com/js2264/VplotR
Bug Reports https://github.com/js2264/VplotR/issues
See More
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_1.11.0.tar.gz
Windows Binary VplotR_1.11.0.zip
macOS Binary (x86_64) VplotR_1.11.0.tgz
macOS Binary (arm64) VplotR_1.11.0.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