=========================================================================
coFAST is a spatially-aware cell clustering algorithm with cluster significant assessment. It comprises four key modules: spatially-aware cell-gene co-embedding, cell clustering, signature gene identification, and cluster significant assessment.
Check out our Package Website for a more complete description of the methods and analyses.
Once the coembeddings of dataset are estimated by coFAST, the package provides functionality for further data exploration, analysis, and visualization. Users can:
“coFAST” 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.
if (!require("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("feiyoung/coFAST")
If some dependent packages (such as scater
) on Bioconductor can not be installed nomrally, use following commands, then run abouve command.
install the package on Bioconducter
For usage examples and guided walkthroughs, check the vignettes
directory of the repo.
Tutorials for coFAST method:
For the users that don’t have set up system properly, the following setup on different systems can be referred.
First, download Rtools; second, add the Rtools directory to the environment variable.
First, install Xcode. Installation about Xcode can be referred here.
Second, install “gfortran” for compiling C++ and Fortran at here.
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.
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
install the package on Bioconducter
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
coembedding_umap()
, user may meet the error: “useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE”. Because the matrixStats
R package remove the argument “useNames=NA” and change the warning to error. Thus, user can install the old version of matrixStats
by the following codeall old versions that are less than 1.1.0 are ok. here we take the version 1.1.0 as an example.
For an example of typical coFAST usage, please see our Package Website for a demonstration and overview of the functions included in coFAST.