igvR
igvR: integrative genomics viewer
Bioconductor version: Release (3.19)
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 "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | GenomeBrowsers, Software, ThirdPartyClient, Visualization |
Version | 1.24.0 |
In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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/ |
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_1.24.0.tar.gz |
Windows Binary | igvR_1.24.0.zip |
macOS Binary (x86_64) | igvR_1.24.0.tgz |
macOS Binary (arm64) | igvR_1.24.0.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 |