igvShiny

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

igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

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DOI: 10.18129/B9.bioc.igvShiny

Bioconductor version: Release (3.22)

This package is a wrapper of Integrative Genomics Viewer (IGV). It comprises an htmlwidget version of IGV. It can be used as a module in Shiny apps.

Author: Paul Shannon [aut], Arkadiusz Gladki [aut, cre] ORCID iD ORCID: 0000-0002-7059-6378 , Karolina Scigocka [aut]

Maintainer: Arkadiusz Gladki <gladki.arkadiusz at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("igvShiny")

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("igvShiny")

igvShiny Overview HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, Sequencing, ShinyApps, Software

Version 1.6.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

License MIT + file LICENSE

Depends R (>= 3.5.0), GenomicRanges, methods, shiny

Imports BiocGenerics, checkmate, futile.logger, GenomeInfoDbData, htmlwidgets, httr, jsonlite, randomcoloR, utils

System Requirements

URL https://github.com/gladkia/igvShiny https://gladkia.github.io/igvShiny/

Bug Reports https://github.com/gladkia/igvShiny/issues

Suggests BiocStyle, GenomicAlignments, knitr, Rsamtools, rtracklayer, RUnit, shinytest2, VariantAnnotation

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Package Archives

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

Source Package igvShiny_1.6.0.tar.gz

Windows Binary (x86_64) igvShiny_1.5.0.zip (64-bit only)

macOS Binary (x86_64) igvShiny_1.6.0.tgz

macOS Binary (arm64) igvShiny_1.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/igvShiny

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/igvShiny

Bioc Package Browser https://code.bioconductor.org/browse/igvShiny/

Package Short Url https://bioconductor.org/packages/igvShiny/

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