DOI: 10.18129/B9.bioc.VplotR  

This package is for version 3.16 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: 3.16

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>

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biocViews ATACSeq, Alignment, BiologicalQuestion, Coverage, NucleosomePositioning, Sequencing, Software
Version 1.8.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 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
Suggests GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown
URL https://github.com/js2264/VplotR
BugReports https://github.com/js2264/VplotR/issues
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Source Package VplotR_1.8.0.tar.gz
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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/
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