igvR

DOI: 10.18129/B9.bioc.igvR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see igvR.

igvR: integrative genomics viewer

Bioconductor version: 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>

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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

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
LinkingTo
Suggests	RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo
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_1.20.0.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 [email protected]:packages/igvR
Bioc Package Browser	https://code.bioconductor.org/browse/igvR/
Package Short Url	https://bioconductor.org/packages/igvR/
Package Downloads Report	Download Stats