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epivizr

R Interface to epiviz web app


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("epivizr")):

Installation

To install this package, start R (version "4.3") 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")
Introduction to epivizr HTML R Script
Reference Manual PDF
NEWS Text
Epiviz quick tour Video

Details

biocViews GUI, Infrastructure, Software, Visualization
Version 2.32.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 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
System Requirements
URL
See More
Suggests testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown
Linking To
Enhances
Depends On Me epivizrStandalone, scTreeViz
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 epivizr_2.32.0.tar.gz
Windows Binary epivizr_2.32.0.zip
macOS Binary (x86_64) epivizr_2.32.0.tgz
macOS Binary (arm64) epivizr_2.32.0.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