igvR
igvR: integrative genomics viewer
Bioconductor version: 3.24 · Package version: 1.33.2
Access to igv.js, the Integrative Genomics Viewer running in a web browser.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("igvR")Details
| Maintainer | Arkadiusz Gladki <gladki.arkadiusz@gmail.com> |
| Author | Paul Shannon [aut], Arkadiusz Gladki [aut, cre] |
| License | MIT + file LICENSE |
| URL | https://gladkia.github.io/igvR/ |
| Downloads rank | 609 |
| Source branch | devel |
| biocViews | GenomeBrowsers, Software, ThirdPartyClient, Visualization |
Documentation
- Explore CTCF ChIP-seq alignments, MACS2 narrowPeaks, Motif Matching and H3K4me3 methylation
- GWAS Tracks
- Introduction: a simple demo
- Obtain and Display H3K27ac K562 track from the AnnotationHub
- Obtain and Display H3K4Me3 K562 track from UCSC table browser
- Paired-end Interaction Tracks
- Use a Custom Genome
- Use a Stock Genome
- Visualizing CRAM Alignments
Download
Follow the installation instructions to use this package in your R session.
| Source package | igvR_1.33.2.tar.gz |
| Windows binary (x86_64) | igvR_1.33.2.zip |
| macOS binary (arm64) | igvR_1.33.2.tgz |
| macOS binary (x86_64) | igvR_1.33.2.tgz |
Dependencies
Depends: R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>= 2.17.1)
Imports: methods, BiocGenerics, httpuv, utils, rtracklayer, VariantAnnotation, RColorBrewer, httr
Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo