igvR

DOI: 10.18129/B9.bioc.igvR    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see igvR.

igvR: integrative genomics viewer

Bioconductor version: 3.14

Access to igv.js, the Integrative Genomics Viewer running in a web browser.

Author: Paul Shannon

Maintainer: Paul Shannon <paul.thurmond.shannon at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("igvR")

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("igvR")

 

HTML	R Script	Choose a Stock or Custom Genome
HTML	R Script	Explore ChIP-seq alignments from a bam file, MACS2 narrowPeaks, conservation, H3K4me3 methylation and motif matching
HTML	R Script	Explore VCF variants, GWAS snps, promoters and histone marks around the MEF2C gene in Alzheimers Disease
HTML	R Script	Introduction: a simple demo
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GenomeBrowsers, Software, ThirdPartyClient, Visualization
Version	1.14.0
In Bioconductor since	BioC 3.7 (R-3.5) (4 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz(>= 2.9.1)
Imports	methods, BiocGenerics, httpuv, utils, MotifDb, seqLogo, rtracklayer, VariantAnnotation, RColorBrewer
LinkingTo
Suggests	RUnit, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://paul-shannon.github.io/igvR/
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	igvR_1.14.0.tar.gz
Windows Binary	igvR_1.14.0.zip
macOS 10.13 (High Sierra)	igvR_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/igvR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/igvR
Package Short Url	https://bioconductor.org/packages/igvR/
Package Downloads Report	Download Stats