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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| 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 | 1.32.0 |
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/igvR/ |
| Package Short Url | https://bioconductor.org/packages/igvR/ |
| Package Downloads Report | Download Stats |