Epivizr

Table of Contents


The epivizr Bioconductor package implements two-way communication between the R/Bioconductor environment and {% link Epiviz http://epiviz.cbbc.umd.edu/4 %}. Objects in the R environment can be displayed as tracks or plots on {% link Epiviz http://epiviz.cbbc.umd.edu/4 %}. Epivizr uses the Websocket data provider API for communication between the browser Javascript client and the R environment.

To use epivizr with the epiviz APIs described here, you must use its development branch (version 1.3.3 or higher)

Installation and requirements

Epivizr is available as part of the Bioconductor project as of version 2.13. To install the release version of epivizr:

source("http://bioconductor.org/biocLite.R")
biocLite("epivizr")

Try it out

The easiest way to try epivizr out is to follow the package vignette:

require(epivizr)
browseVignettes("epivizr")

Development version

The epivizr github repository contains the latest and greatest version of epivizr and is tracked by the devel version in Bioconductor (see http://bioconductor.org/developers/how-to/useDevel/ for more info. In summary, if you install R-devel, you’ll be set.

Non-blocking

Epivizr (as of version 1.2) supports a non-blocking workflow on both UNIX-like and Windows systems where data is served to the webapp without blocking the R/bioc interactive session. Make sure you are using the latest version of the httpuv package (version 1.3 or greater to use this. (Thanks to the Rstudio folks for folding our daemonizing code into the main httpuv release).