epivizr

DOI: 10.18129/B9.bioc.epivizr  

R Interface to epiviz web app

Bioconductor version: Release (3.16)

This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.

Author: Hector Corrada Bravo, Florin Chelaru, Llewellyn Smith, Naomi Goldstein, Jayaram Kancherla, Morgan Walter, Brian Gottfried

Maintainer: Hector Corrada Bravo <hcorrada at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("epivizr")

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("epivizr")

 

HTML	R Script	Introduction to epivizr
PDF		Reference Manual
Text		NEWS
Video		Epiviz quick tour

Details

biocViews	GUI, Infrastructure, Software, Visualization
Version	2.28.0
In Bioconductor since	BioC 2.13 (R-3.0) (9.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), methods
Imports	epivizrServer(>= 1.1.1), epivizrData(>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb
LinkingTo
Suggests	testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me	epivizrStandalone, scTreeViz
Imports Me	metavizr
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	epivizr_2.28.0.tar.gz
Windows Binary	epivizr_2.28.0.zip
macOS Binary (x86_64)	epivizr_2.28.0.tgz
macOS Binary (arm64)	epivizr_2.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/epivizr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/epivizr
Bioc Package Browser	https://code.bioconductor.org/browse/epivizr/
Package Short Url	https://bioconductor.org/packages/epivizr/
Package Downloads Report	Download Stats