igvR
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see igvR.
igvR: integrative genomics viewer
Bioconductor version: 3.13
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 "4.1") 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")| Choose a Stock or Custom Genome | HTML | R Script |
| Explore ChIP-seq alignments from a bam file, MACS2 narrowPeaks, conservation, H3K4me3 methylation and motif matching | HTML | R Script |
| Explore VCF variants, GWAS snps, promoters and histone marks around the MEF2C gene in Alzheimers Disease | HTML | R Script |
| Introduction: a simple demo | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GenomeBrowsers, Software, ThirdPartyClient, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz(>= 2.9.1) |
| Imports | methods, BiocGenerics, httpuv, utils, MotifDb, seqLogo, rtracklayer, VariantAnnotation, RColorBrewer |
| System Requirements | |
| URL | https://paul-shannon.github.io/igvR/ |
See More
| Suggests | RUnit, BiocStyle, knitr, rmarkdown |
| 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_1.12.0.tar.gz |
| Windows Binary | igvR_1.12.0.zip |
| macOS 10.13 (High Sierra) | igvR_1.12.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |