Package: coFAST 0.3.0

Wei Liu

coFAST: Spatially-Aware Cell Clustering Algorithm with Cluster Significant Assessment

A spatially-aware cell clustering algorithm is provided with cluster significance assessment. It comprises four key modules: spatially-aware cell-gene co-embedding, cell clustering, signature gene identification, and cluster significant assessment. More details can be referred to Peng Xie, et al. (2025) <doi:10.1016/j.cell.2025.05.035>.

Authors:Wei Liu [aut, cre], Xiao Zhang [aut], Yi Yang [aut], Peng Xie [aut], Chengqi Lin [aut], Jin Liu [aut]

coFAST_0.3.0.tar.gz
coFAST_0.3.0.zip(r-4.7)coFAST_0.3.0.zip(r-4.6)coFAST_0.3.0.zip(r-4.5)
coFAST_0.3.0.tgz(r-4.6-x86_64)coFAST_0.3.0.tgz(r-4.6-arm64)coFAST_0.3.0.tgz(r-4.5-x86_64)coFAST_0.3.0.tgz(r-4.5-arm64)
coFAST_0.3.0.tar.gz(r-4.7-arm64)coFAST_0.3.0.tar.gz(r-4.7-x86_64)coFAST_0.3.0.tar.gz(r-4.6-arm64)coFAST_0.3.0.tar.gz(r-4.6-x86_64)
coFAST_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
coFAST/json (API)

# Install 'coFAST' in R:

install.packages('coFAST', repos = c('https://feiyoung.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/feiyoung/cofast/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

CosMx_subset - A CosMix spatial transcriptomics data
pbmc3k_subset - A toy single-cell RNA-seq data
top5_signatures - A dataframe including top five signature genes

On CRAN:

openblas cpp

4.18 score 159 downloads 12 exports 155 dependencies

Last updated from:2875287302. Checks:12 OK, 1 ERROR. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	309
linux-devel-x86_64	OK	332
source / vignettes	OK	442
linux-release-arm64	OK	365
linux-release-x86_64	OK	419
macos-release-arm64	OK	215
macos-release-x86_64	OK	412
macos-oldrel-arm64	ERROR	284
macos-oldrel-x86_64	OK	732
windows-devel	OK	450
windows-release	OK	439
windows-oldrel	OK	395
wasm-release	OK	281

Exports:AddAdj AddCluster Addcoord2embed AggregationScore coembed_plot coembedding_umap coFAST diagnostic.cor.eigs find.signature.genes get.top.signature.dat NCFM pdistance

Dependencies:abind ade4 askpass base64enc BH BiocGenerics bitops bslib cachem caTools cli cluster codetools commonmark CompQuadForm cowplot cpp11 crayon crosstalk curl data.table deldir digest dotCall64 dplyr dqrng DR.SC evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs furrr future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr hms htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix matrixStats mclust memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pixmap pkgconfig plotly plyr png polyclip prettyunits ProFAST progress progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S4Vectors S7 sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

coFAST: NSCLC CosMx data coembedding

Load and view data | Preprocessing | Coembedding using coFAST | Downstream analysis | Clustering and assess the cluster significance

Rendered fromCosMx.Rmdusingknitr::rmarkdown

Last update: 2025-11-17
Started: 2025-03-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate the adjacency matrix given a spatial coordinate matrix	AddAdj
Find clusters for SRT data	AddCluster
Add the spatial coordinates to the reduction slot	Addcoord2embed
Calculate the aggregation score for specific clusters	AggregationScore
Coembedding dimensional reduction plot	coembed_plot
Calculate UMAP projections for coembedding of cells and features	coembedding_umap
Cell-feature coembedding for SRT data	coFAST
A CosMix spatial transcriptomics data	CosMx_subset
Determine the dimension of low dimensional embedding	diagnostic.cor.eigs diagnostic.cor.eigs.default diagnostic.cor.eigs.Seurat
Find the signature genes for each group of cell/spots	find.signature.genes
Obtain the top signature genes and related information	get.top.signature.dat
Cell-feature coembedding for scRNA-seq data	NCFM
A toy single-cell RNA-seq data	pbmc3k_subset
Calculate the cell-feature distance matrix	pdistance
A dataframe including top five signature genes	top5_signatures