GenVisR

DOI: 10.18129/B9.bioc.GenVisR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GenVisR.

Genomic Visualizations in R

Bioconductor version: 3.8

Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.

Author: Zachary Skidmore [aut, cre], Alex Wagner [aut], Robert Lesurf [aut], Katie Campbell [aut], Jason Kunisaki [aut], Obi Griffith [aut], Malachi Griffith [aut]

Maintainer: Zachary Skidmore <zlskidmore at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

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

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("GenVisR")

 

HTML	R Script	GenVisR: An introduction
HTML	R Script	Visualizing Small Variants
HTML	R Script	waterfall: function introduction
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, DNASeq, DataRepresentation, Infrastructure, Software
Version	1.14.2
In Bioconductor since	BioC 3.3 (R-3.3) (3 years)
License	GPL-3 + file LICENSE
Depends	R (>= 3.3.0), methods
Imports	AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField, GenomicFeatures, GenomicRanges(>= 1.25.4), ggplot2 (>= 2.1.0), grid, gridExtra (>= 2.0.0), gtable, gtools, IRanges(>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, stats, utils, viridis, data.table, BSgenome, grDevices, GenomeInfoDb, VariantAnnotation
LinkingTo
Suggests	BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38
SystemRequirements
Enhances
URL
BugReports	https://github.com/griffithlab/GenVisR/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	GenVisR_1.14.2.tar.gz
Windows Binary	GenVisR_1.14.2.zip
Mac OS X 10.11 (El Capitan)	GenVisR_1.14.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenVisR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenVisR
Package Short Url	http://bioconductor.org/packages/GenVisR/
Package Downloads Report	Download Stats