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coFAST

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coFAST is a spatially-aware cell clustering algorithm with clustersignificant assessment. It comprises four key modules: spatially-awarecell-gene co-embedding, cell clustering, signature gene identification,and cluster significant assessment.

Check out our ourCell paper, andPackage Websitefor a more complete description of the methods and analyses.

Once the coembeddings of dataset are estimated by coFAST, the packageprovides functionality for further data exploration, analysis, andvisualization. Users can:

• Conduct Spatially-aware clustering
• Find the signature genes
• Visuzlize the coembeddings on UMAP space
• Visuzlize the signature genes on UMAP space

Please see our new paper for more details:

• Peng Xie^c,Juan Shen^c, Yi Yang^c, Xinrui Wang^c, Wei Liu^c, Hailong Cao^c, YanyingZheng, Chen Wu, Guangyao Mao, Linjin Chen, Jingjing He, Weiheng Zheng,Zepu Yang, Xiao Zhang, Xu Jiang, Xianfa Yang, Ke Fang, Zhao Zhang, XinXue, Xueting Chen, Chaoyi Wang, Xing Liu, Lin Liu, Xuebiao Yao, NaiheJing, Wei Xie, Jin Liu, Hua Cao, Zhuojuan Luo, XiaodongFang, Chengqi Lin* (2025), Digital reconstruction of full embryosduring early mouse organogenesis. Cell.

Installation

“coFAST” depends on the ‘Rcpp’ and ‘RcppArmadillo’ package, whichrequires appropriate setup of computer. For the users that have set upsystem properly for compiling C++ files, the following installationcommand will work.

if (!require("remotes", quietly = TRUE))install.packages("remotes")remotes::install_github("feiyoung/coFAST")

Or install the the packages “coFAST” from ‘CRAN’

install.packages(“coFAST”)

If some dependent packages (such asscater) onBioconductor can not be installed nomrally, use following commands, thenrun abouve command.

if (!require("BiocManager", quietly = TRUE)) ## install BiocManager    install.packages("BiocManager")

install the package on Bioconducter

BiocManager::install(c("scater"))

Usage

For usage examples and guided walkthroughs, check thevignettes directory of the repo.

Tutorials for coFAST method:

• SRTdata analysis for NSCLC

For the users that don’t have set up system properly, the followingsetup on different systems can be referred.

Setup on Windows system

First, downloadRtools;second, add the Rtools directory to the environment variable.

Setup on MacOS system

First, install Xcode. Installation about Xcode can be referredhere.

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

Setup on Linux system

If you use conda environment on Linux system and some dependentpackages (such asscater) can not normally installed, youcan search R package at anaconda.org website. We take thescater package as example, and its search result ishttps://anaconda.org/bioconda/bioconductor-scater. Then you can installit in conda environment by following command.

conda install -c bioconda bioconductor-scater

For the user not using conda environment, if dependent packages (suchasscater) not normally installed are in Bioconductor, thenuse 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 asDR.SC) not normallyinstalled are in CRAN, then use the following command to install thedependent packages.

install the package on CRAN

install.packages("DR.SC")

Common errors

• When using functioncoembedding_umap(), user may meetthe error: “useNames = NA is defunct. Instead, specify either useNames =TRUE or useNames = FALSE”. Because thematrixStats Rpackage remove the argument “useNames=NA” and change the warning toerror. Thus, user can install the old version ofmatrixStats by the following code

all old versions that are less than 1.1.0 are ok. here we take theversion 1.1.0 as an example.

remotes::install_version('matrixStats', version='1.1.0')

Demonstration

For an example of typical coFAST usage, please see ourPackage Websitefor a demonstration and overview of the functions included incoFAST.

NEWs

• coFAST version 0.1.0 (2025-03-14)