igvR
This is the released version of igvR; for the devel version, see igvR.
igvR: integrative genomics viewer
Bioconductor version: Release (3.23)
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("igvR")):Paul Shannon. igvR: igvR: integrative genomics viewer. doi:10.18129/B9.bioc.igvR, R package version 1.32.0, https://bioconductor.org/packages/igvR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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")| "Introduction: a simple demo" | HTML | R Script |
| "Use a Stock Genome" | HTML | R Script |
| "Use a Custom Genome" | HTML | R Script |
| "Explore CTCF ChIP-seq alignments, MACS2 narrowPeaks, Motif Matching and H3K4me3 methylation" | HTML | R Script |
| "Paired-end Interaction Tracks" | HTML | R Script |
| "Obtain and Display H3K4Me3 K562 track from UCSC table browser" | HTML | R Script |
| "Obtain and Display H3K27ac K562 track from the AnnotationHub" | HTML | R Script |
| "GWAS Tracks" | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GenomeBrowsers, Software, ThirdPartyClient, Visualization |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | igvR_1.32.0.tar.gz |
| Windows Binary (x86_64) | igvR_1.32.0.zip |
| macOS Binary (big-sur-x86_64) | igvR_1.32.0.tgz |
| macOS Binary (sonoma-arm64) | igvR_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/igvR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/igvR |
| Package Short Url | https://bioconductor.org/packages/igvR/ |
| Package Downloads Report | Download Stats |