Installation

Source: vignettes/Installation.Rmd

System Requirements

  • R >= 3.5
  • Java >= 11
  • git, tar, scp, ssh
    • Mac/Linux: typically installed by default
    • Windows: Cygwin or Windows Subsystem for Linux (Windows 10)
  • C compiler
    • Mac: Xcode
    • Linux: gcc
    • Windows: Rtools or Rtools40 (Windows 10)
  • NGCHMSupportFiles R package
    • This package requires Java >= 11
    • This package contains a compiled .jar file and minified JavaScript file

R Packages Installation

The NG-CHM R package can be installed from CRAN:

The NGCHMSupportFiles can be installed from our R-Universe repository:

install.packages('NGCHMSupportFiles', repos = c('https://md-anderson-bioinformatics.r-universe.dev', 'https://cloud.r-project.org'))

Using the Docker Image

There is also a Docker image, ngchm/rstudio-ngchm, containing RStudio, the NGCHM-R package, and all needed dependencies available on Docker Hub.

The YouTube Video, How to Create Next-Generation Clustered Heat Map in R Studio details usage of the Docker image. Further installation and usage information is available in this the RStudio NGCHM GitHub project.