2. Installation

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wguo-research edited this page May 11, 2020 · 17 revisions

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: ❗ ❗ ❗

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')

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: devtools::install_github("constantAmateur/SoupX")
harmony: devtools::install_github("immunogenomics/harmony")
liger: devtools::install_github("MacoskoLab/liger")

Any questions about installation, please contact the author.

© G-Lab, Tsinghua University