README.md

NGCHMR

An R package for creating Next-Generation Clustered Heat Maps (NG-CHM)

A docker image containing RStudio with this package preinstalled is available. Follow the instructions for using rstudio, but substitute "bmbroom/rstudio-ngchm" for the name of the repository.

Installing on Linux or Mac

To install this package into your own R system:

> install.packages("devtools")
> devtools::install_github("bmbroom/tsvio")
> devtools::install_github("bmbroom/NGCHMR", ref="stable")

You might also choose to install the beta version of the package, or for the really daring the master branch.

Installing on Windows

Precompiled packages suitable for the Microsoft Windows version of R are available from our downloads site. Install the tsvio package before the NGCHM package.

Using the Package

The installed package will be called NGCHM:

> library (NGCHM)

A basic guide to creating NG-CHMs using the R package is available at http://bioinformatics.mdanderson.org/main/NG-CHM:NGCHMR-Using .

Installing the Java Component (all platforms)

To use this package you need access to a Java application for generating standalone NG-CHMs and/or an NG-CHM server to which you can upload NG-CHMs.

To create standalone NG-CHMs you also need the Java application ShaidyMapGen.jar. The easiest way to get a copy is to download it from http://tcga.ngchm.net/NGCHM/ShaidyMapGen.jar. You can also download it from our downloads site. Finally, you can build it from the source code.

Once downloaded, set the environment variable SHAIDYMAPGEN to its location.

Running an NG-CHM server

A system administrator can create a local instance of a docker based NG-CHM server by following these instructions.

You will also need to create a configuration file describing, among other things, any NG-CHM server(s) to which you have access.



bmbroom/NGCHMR documentation built on July 28, 2018, 11:17 a.m.