epivizrStandalone
This is the released version of epivizrStandalone; for the devel version, see epivizrStandalone.
Run Epiviz Interactive Genomic Data Visualization App within R
Bioconductor version: Release (3.23)
This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The 'epivizrServer' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.
Author: Hector Corrada Bravo, Jayaram Kancherla
Maintainer: Hector Corrada Bravo <hcorrada at gmail.com>
citation("epivizrStandalone")):
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("epivizrStandalone")
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("epivizrStandalone")| Introduction to epivizrStandalone | HTML |
| Reference Manual | |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | GUI, Infrastructure, Software, Visualization |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.2.3), epivizr(>= 2.3.6), methods |
| Imports | git2r, epivizrServer, Seqinfo, BiocGenerics, GenomicFeatures, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | testthat, knitr, rmarkdown, OrganismDbi(>= 1.13.9), Mus.musculus, Biobase, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | scTreeViz |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | epivizrStandalone_1.40.0.tar.gz |
| Windows Binary (x86_64) | epivizrStandalone_1.40.0.zip |
| macOS Binary (big-sur-x86_64) | epivizrStandalone_1.40.0.tgz |
| macOS Binary (sonoma-arm64) | epivizrStandalone_1.40.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/epivizrStandalone |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/epivizrStandalone |
| Bioc Package Browser | https://code.bioconductor.org/browse/epivizrStandalone/ |
| Package Short Url | https://bioconductor.org/packages/epivizrStandalone/ |
| Package Downloads Report | Download Stats |