igvR
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see igvR.
igvR: integrative genomics viewer
Bioconductor version: 3.17
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 "4.3") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GenomeBrowsers, Software, ThirdPartyClient, Visualization |
| Version | 1.20.0 |
| 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://paul-shannon.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_1.20.0.tar.gz |
| Windows Binary | igvR_1.20.0.zip (64-bit only) |
| macOS Binary (x86_64) | igvR_1.20.0.tgz |
| macOS Binary (arm64) | igvR_1.20.0.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 3.17 | Source Archive |