igvR

This is the released version of igvR; for the devel version, see igvR.

igvR: integrative genomics viewer

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DOI: 10.18129/B9.bioc.igvR

Bioconductor version: Release (3.22)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GenomeBrowsers, Software, ThirdPartyClient, Visualization

Version 1.30.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 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

System Requirements

URL https://gladkia.github.io/igvR/

Suggests RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo

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Package Archives

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

Source Package igvR_1.30.0.tar.gz

Windows Binary (x86_64) igvR_1.30.0.zip

macOS Binary (x86_64) igvR_1.30.0.tgz

macOS Binary (arm64) igvR_1.30.0.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/

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