2. Installation

System Requirements

• R version: >= 3.5.0

Installation

Firstly, please install or update the package devtools by running

install.packages("devtools")

Then the scCancer can be installed via

library(devtools)
devtools::install_github("wguo-research/scCancer")

Hint: ❗ ❗ ❗

1. A dependent package NNLM was removed from the CRAN repository recently, so an error about it may be reported during the installation. If so, you can install its a formerly available version by following codes or install manually from its archive.

install.packages("RcppArmadillo")
install.packages("RcppProgress")
install.packages('http://lifeome.net/software/sccancer/packages/NNLM_0.4.3.tar.gz', type='source')

2. Some dependent packages on GitHub (as follows) may not be able to install automatically, if you encounter such errors, please refer to their GitHub and install them via corresponding commands.

• SoupX:

  • Link: GitHub
  • Installation: devtools::install_github("constantAmateur/SoupX")

• harmony:

  • Link: GitHub
  • Installation: devtools::install_github("immunogenomics/harmony")

• liger:

  • Link: GitHub
  • Installation: devtools::install_github("MacoskoLab/liger")

Any questions about installation, please contact the author.