epivizr

This is the development version of epivizr; for the stable release version, see epivizr.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

R Interface to epiviz web app

Bioconductor version: Development (3.24)

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")):

Hector Corrada Bravo, Florin Chelaru, Llewellyn Smith, Naomi Goldstein, Jayaram Kancherla, Morgan Walter, Brian Gottfried. epivizr: R Interface to epiviz web app. doi:10.18129/B9.bioc.epivizr, R package version 2.43.0, https://bioconductor.org/packages/epivizr.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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
Video	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GUI, Infrastructure, Software, Visualization
Version	2.43.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 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

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, r-universe

Package Archives

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

Source Package	epivizr_2.43.0.tar.gz
Windows Binary (x86_64)	epivizr_2.43.0.zip
macOS Binary (big-sur-x86_64)	epivizr_2.43.0.tgz
macOS Binary (sonoma-arm64)	epivizr_2.43.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/epivizr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/epivizr
Package Short Url	https://bioconductor.org/packages/epivizr/
Package Downloads Report	Download Stats