PRECAST

PRECAST: a probabilistic embedding and clustering with alignment for spatial transcriptomics data integration.

Installation

“PRECAST” depends on the ‘Rcpp’ and ‘RcppArmadillo’ package, which requires appropriate setup of computer. For the users that have set up system properly for compiling C++ files, the following installation command will work.

# Method 1: install PRECAST from CRAN
install.packages('PRECAST')



# Method 2: Install PRECAST from Github
if (!require("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("feiyoung/PRECAST")

# If some dependent packages (such as `scater`) on Bioconductor can not be installed nomrally, use following commands, then run abouve command.
if (!require("BiocManager", quietly = TRUE)) ## install BiocManager
    install.packages("BiocManager")
# install the package on Bioconducter
BiocManager::install(c("scater"))

For the users that don’t have set up system properly, the following setup on different systems can be referred. ## Setup on Windows system First, download Rtools; second, add the Rtools directory to the environment variable. Users can follow here to add Windows PATH Environment Variable.

Setup on MacOS system

First, install Xcode. Installation about Xcode can be referred here.

Second, install “gfortran” for compiling C++ and Fortran at here.

Setup on Linux system

If you use conda environment on Linux system and some dependent packages (such as scater) can not normally installed, you can search R package at anaconda.org website. We take the scater package as example, and its search result is https://anaconda.org/bioconda/bioconductor-scater. Then you can install it in conda environment by following command.

conda install -c bioconda bioconductor-scater

For the user not using conda environment, if dependent packages (such as scater) not normally installed are in Bioconductor, then use the following command to install the dependent packages.

# install BiocManager
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
# install the package on Bioconducter
BiocManager::install(c("scater"))

If dependent packages (such as DR.SC) not normally installed are in CRAN, then use the following command to install the dependent packages.

# install the package on CRAN
install.packages("DR.SC")

Other notes

For running big data, users can use the following system command to set the C_stack unlimited in case of R Error: C stack usage is too close to the limit.

ulimit -s unlimited

Demonstration

For an example of typical PRECAST usage, please see our Package Website for a demonstration and overview of the functions included in PRECAST.