2. Installation

System Requirements

• R version: >= 3.5.0 (suggest: R 3.6, not 4.0)
• Hint: For R (version>=4.0) under Windows system, you may need to update the Rtools to version 4.0 from https://cran.r-project.org/bin/windows/Rtools/ and added it into the PATH environment variable. So, if you are not familiar with R environment configuration, we don't suggest to use R (>=4.0).

Installation

Some dependent packages (harmony, liger, and NNLM) on GitHub may not be installed automatically, so you can install them by referring to following scripts. After installing them successfully, then you can install the scCancer.

checkPkg <- function(pkg){
    return(requireNamespace(pkg, quietly = TRUE))
}
if(!checkPkg("BiocManager")) install.packages("BiocManager")
if(!checkPkg("devtools")) install.packages("devtools")

library(devtools)
if(!checkPkg("harmony")) install_github("immunogenomics/harmony")

if(!checkPkg("RcppArmadillo")) install.packages("RcppArmadillo")
if(!checkPkg("RcppProgress")) install.packages("RcppProgress")
if(!checkPkg("NNLM")) install_github("linxihui/NNLM")

if(!checkPkg("liger")) install_github("MacoskoLab/liger")

install_github("wguo-research/scCancer")