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igvR

igvR: integrative genomics viewer

Bioconductor version: Release (3.17)

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 "4.3") 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")
Explore CTCF ChIP-seq alignments, MACS2 narrowPeaks, Motif Matching and H3K4me3 methylation HTML R Script
GWAS Tracks HTML R Script
Introduction: a simple demo HTML R Script
Obtain and Display H3K27ac K562 track from the AnnotationHub HTML R Script
Obtain and Display H3K4Me3 K562 track from UCSC table browser HTML R Script
Paired-end Interaction Tracks HTML R Script
Use a Custom Genome HTML R Script
Use a Stock Genome HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GenomeBrowsers, Software, ThirdPartyClient, Visualization
Version 1.20.0
In Bioconductor since BioC 3.7 (R-3.5) (5.5 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz(>= 2.17.1)
Imports methods, BiocGenerics, httpuv, utils, rtracklayer, VariantAnnotation, RColorBrewer, httr
Linking To
Suggests RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo
System Requirements
Enhances
URL https://paul-shannon.github.io/igvR/
See More
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_1.20.0.tar.gz
Windows Binary igvR_1.20.0.zip (64-bit only)
macOS Binary (x86_64) igvR_1.20.0.tgz
macOS Binary (arm64) igvR_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/igvR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/igvR
Bioc Package Browser https://code.bioconductor.org/browse/igvR/
Package Short Url https://bioconductor.org/packages/igvR/
Package Downloads Report Download Stats