To install SRTpipeline, R version 4.0 or greater is required. We also recommend installing R Studio.
SRTpipeline is available on CRAN for all platforms. To install, run:
# Enter commands in R (or R studio, if installed)
install.packages('SRTpipeline')
library(SRTpipeline)Install the development version of SRTpipeline - directly from GitHub.
# Enter commands in R (or R studio, if installed)
# Install the remotes package
install.packages('remotes')
remotes::install_github(repo = 'feiyoung/SRTpipeline', ref = 'develop')
library(SRTpipeline)When users install SRTpipeline, the dependent R pacakges will be also installed automatically.
If dependent packages in CRAN (such as DR.SC) are not normally installed, then use the following command to install the dependent packages.
install.packages('remotes') remotes::install_github("feiyoung/DR.SC")
or install from CRAN
install.packages("DR.SC")
The package can be loaded with the command:
## Loading required package: parallel## Loading required package: spatstat.geom## Warning: package 'spatstat.geom' was built under R version 4.1.3## Loading required package: spatstat.data## Warning: package 'spatstat.data' was built under R version 4.1.3## spatstat.geom 2.4-0## DR.SC : Joint dimension reduction and spatial clustering is conducted for
## Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to
## Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.You can install the stable version of SRTpipeline from CRAN:
install.packages("SRTpipeline")
, or the development version (containing the latest improvements and bug fixes) from GitHub:
install.packages("remotes")
library(remotes)
install_github("feiyoung/SRTpipeline")To install SRTpipeline on Linux, you need to be able to install the sf package, which requires several dependencies. See here if you have trouble installing sf.
Then, you can install the stable version of SRTpipeline from CRAN:
install.packages("SRTpipeline"), or the development version (containing the latest improvements and bug fixes) from GitHub:
library(devtools)
install_github("feiyoung/SRTpipeline")To install SRTpipeline on Mac, you need to be able to install the sf package, which requires several dependencies. See here if you have trouble installing sf.
Then, you can install the stable version of SRTpipeline from CRAN:
install.packages("SRTpipeline"), or the development version (containing the latest improvements and bug fixes) from GitHub:
library(devtools)
install_github("feiyoung/SRTpipeline")Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.