VplotR
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see VplotR.
Set of tools to make V-plots and compute footprint profiles
Bioconductor version: 3.19
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("VplotR")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ATACSeq, Alignment, BiologicalQuestion, Coverage, NucleosomePositioning, Sequencing, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VplotR_1.14.0.tar.gz |
| Windows Binary (x86_64) | VplotR_1.14.0.zip |
| macOS Binary (x86_64) | VplotR_1.14.0.tgz |
| macOS Binary (arm64) | VplotR_1.14.0.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 |
| Old Source Packages for BioC 3.19 | Source Archive |