igvR

DOI: 10.18129/B9.bioc.igvR    

igvR: integrative genomics viewer

Bioconductor version: Release (3.10)

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>

Citation (from within R, enter citation("igvR")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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 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 1.6.1
In Bioconductor since BioC 3.7 (R-3.5) (1.5 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz(>= 2.7.20)
Imports methods, BiocGenerics, httpuv, utils, MotifDb, seqLogo, rtracklayer, VariantAnnotation, randomcoloR
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_1.6.1.tar.gz
Windows Binary igvR_1.6.1.zip
Mac OS X 10.11 (El Capitan) igvR_1.6.1.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
Old Source Packages for BioC 3.10 Source Archive

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