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igvR

igvR: integrative genomics viewer


Bioconductor version: Release (3.18)

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

Author: Paul Shannon

Maintainer: Arkadiusz Gladki <gladki.arkadiusz 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 1.22.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
URL https://gladkia.github.io/igvR/
See More
Suggests RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package igvR_1.22.0.tar.gz
Windows Binary igvR_1.22.0.zip (64-bit only)
macOS Binary (x86_64) igvR_1.22.0.tgz
macOS Binary (arm64) igvR_1.22.0.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