R Packages Installation
The NG-CHM R package can be installed from CRAN:
install.packages("NGCHM")The required NGCHMSupportFiles can be installed from our R-Universe repository:
install.packages("NGCHMSupportFiles", repos = c("https://md-anderson-bioinformatics.r-universe.dev"))The optional NGCHMDemoData (used in the vignette examples) can similarly be installed:
install.packages("NGCHMDemoData", repos = c("https://md-anderson-bioinformatics.r-universe.dev"))System Requirements
- R >= 3.5
- Java >= 11
- git
- 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
-
Optional: The following are only required if using a remote
NG-CHM server:
- tar, ssh, scp (most users will not need these)
Docker Image
A Docker image containing RStudio, the NGCHM-R package, and all needed dependencies is available on Docker Hub: ngchm/rstudio-ngchm.
Detailed usage information for the docker image is available in this the RStudio NGCHM GitHub project, and the YouTube Video, How to Create Next-Generation Clustered Heat Maps in R Studio.