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, the Rtools needs to be updated to version 4.0 from https://cran.r-project.org/bin/windows/Rtools/. So, if you are not familiar with R environment configuration, we don't suggest to use R (>=4.0).

Installation

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")