{ "_id": "6a1b0b251d7bb097a0a06c15", "Package": "coFAST", "Type": "Package", "Title": "Spatially-Aware Cell Clustering Algorithm with Cluster\nSignificant Assessment", "Version": "0.2.0", "Date": "2025-12-14", "Authors@R": "c(person(given = \"Wei\",\nfamily = \"Liu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"liuweideng@gmail.com\"),\nperson(given = \"Xiao\",\nfamily = \"Zhang\",\nrole = c(\"aut\")),\nperson(given = \"Yi\",\nfamily = \"Yang\",\nrole = \"aut\"),\nperson(given = \"Peng\",\nfamily = \"Xie\",\nrole = c(\"aut\")),\nperson(given = \"Chengqi\",\nfamily = \"Lin\",\nrole = \"aut\"),\nperson(given = \"Jin\",\nfamily = \"Liu\",\nrole = \"aut\"))", "Author": "Wei Liu [aut, cre], Xiao Zhang [aut], Yi Yang [aut], Peng Xie\n[aut], Chengqi Lin [aut], Jin Liu [aut]", "Maintainer": "Wei Liu ", "Description": "A spatially-aware cell clustering algorithm is provided\nwith cluster significance assessment. It comprises four key\nmodules: spatially-aware cell-gene co-embedding, cell\nclustering, signature gene identification, and cluster\nsignificant assessment. More details can be referred to Peng\nXie, et al. (2025) .", "License": "GPL-3", "LazyData": "true", "URL": "https://github.com/feiyoung/coFAST", "BugReports": "https://github.com/feiyoung/coFAST/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev libssl-dev python3\nzlib1g-dev", "Repository": "https://feiyoung.r-universe.dev", "Date/Publication": "2025-12-14 02:36:58 UTC", "RemoteUrl": "https://github.com/feiyoung/cofast", "RemoteRef": "HEAD", "RemoteSha": "4232715b0935988dc9c8b2b26865c530fe34ac32", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 11:02:43 UTC", "User": "root" }, "MD5sum": "f217f06757c6fce78a91060b105887e1", "_user": "feiyoung", "_type": "src", "_file": "coFAST_0.2.0.tar.gz", "_fileid": "ddb7e54f32be615bde523bf450bfd48d209bc1f37337c0a5a9fa099d827fbc51", "_filesize": 4455376, "_sha256": "ddb7e54f32be615bde523bf450bfd48d209bc1f37337c0a5a9fa099d827fbc51", "_created": "2026-05-30T11:02:43.000Z", "_published": "2026-05-30T16:07:01.388Z", "_distro": "noble", "_jobs": [ { "job": 78644415848, "time": 402, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7307753446" }, { "job": 78644415863, "time": 428, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307814407" }, { "job": 78644415899, "time": 464, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7307758893" }, { "job": 78644415855, "time": 527, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307822654" }, { "job": 78644415846, "time": 265, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7309487946" }, { "job": 78644415878, "time": 705, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7307787633" }, { "job": 78644415838, "time": 303, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7309491644" }, { "job": 78644415845, "time": 539, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307772007" }, { "job": 78643905063, "time": 403, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307716719" }, { "job": 78644415826, "time": 320, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307804768" }, { "job": 78644415893, "time": 447, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307814786" }, { "job": 78644415837, "time": 346, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307806151" }, { "job": 78644415833, "time": 351, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307806582" } ], "_buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/feiyoung/cofast", "_commit": { "id": "4232715b0935988dc9c8b2b26865c530fe34ac32", "author": "feiyoung <1029725413@qq.com>", "committer": "feiyoung <1029725413@qq.com>", "message": "'update'\n", "time": 1765679818 }, "_maintainer": { "name": "Wei Liu", "email": "liuweideng@gmail.com" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.10", "role": "Imports" }, { "package": "furrr", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "irlba", "role": "Imports" }, { "package": "DR.SC", "role": "Imports" }, { "package": "PRECAST", "role": "Imports" }, { "package": "ProFAST", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "ade4", "role": "Imports" }, { "package": "progress", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "Seurat", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "scater", "role": "Suggests" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "RANN", "role": "Suggests" }, { "package": "grDevices", "role": "Suggests" } ], "_owner": "feiyoung", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-47", "n": 3 }, { "week": "2025-50", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "feiyoung", "count": 6, "uuid": 11505493 } ], "_userbio": { "uuid": 11505493, "type": "user", "name": "Wei Liu", "description": "Stastistics" }, "_downloads": { "count": 150, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/coFAST" }, "_devurl": "https://github.com/feiyoung/cofast", "_searchresults": 0, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/coFAST.html", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/feiyoung/cofast", "_realowner": "feiyoung", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2025-11-17" }, { "version": "0.2.0", "date": "2025-12-14" } ], "_exports": [ "AddAdj", "AddCluster", "Addcoord2embed", "AggregationScore", "coembed_plot", "coembedding_umap", "coFAST", "diagnostic.cor.eigs", "find.signature.genes", "get.top.signature.dat", "NCFM", "pdistance" ], "_datasets": [ { "name": "CosMx_subset", "title": "A CosMix spatial transcriptomics data", "object": "CosMx_subset", "class": [ "Seurat" ], "fields": [], "table": false, "tojson": false }, { "name": "pbmc3k_subset", "title": "A toy single-cell RNA-seq data", "object": "pbmc3k_subset", "class": [ "Seurat" ], "fields": [], "table": false, "tojson": false }, { "name": "top5_signatures", "title": "A dataframe including top five signature genes", "object": "top5_signatures", "class": [ "data.frame" ], "fields": [ "distance", "expr.prop", "label", "gene" ], "rows": 45, "table": true, "tojson": true } ], "_help": [ { "page": "AddAdj", "title": "Calculate the adjacency matrix given a spatial coordinate matrix", "topics": [ "AddAdj" ] }, { "page": "AddCluster", "title": "Find clusters for SRT data", "topics": [ "AddCluster" ] }, { "page": "Addcoord2embed", "title": "Add the spatial coordinates to the reduction slot", "topics": [ "Addcoord2embed" ] }, { "page": "AggregationScore", "title": "Calculate the aggregation score for specific clusters", "topics": [ "AggregationScore" ] }, { "page": "coembed_plot", "title": "Coembedding dimensional reduction plot", "topics": [ "coembed_plot" ] }, { "page": "coembedding_umap", "title": "Calculate UMAP projections for coembedding of cells and features", "topics": [ "coembedding_umap" ] }, { "page": "coFAST", "title": "Cell-feature coembedding for SRT data", "topics": [ "coFAST" ] }, { "page": "CosMx_subset", "title": "A CosMix spatial transcriptomics data", "topics": [ "CosMx_subset" ] }, { "page": "diagnostic.cor.eigs", "title": "Determine the dimension of low dimensional embedding", "topics": [ "diagnostic.cor.eigs", "diagnostic.cor.eigs.default", "diagnostic.cor.eigs.Seurat" ] }, { "page": "find.signature.genes", "title": "Find the signature genes for each group of cell/spots", "topics": [ "find.signature.genes" ] }, { "page": "get.top.signature.dat", "title": "Obtain the top signature genes and related information", "topics": [ "get.top.signature.dat" ] }, { "page": "NCFM", "title": "Cell-feature coembedding for scRNA-seq data", "topics": [ "NCFM" ] }, { "page": "pbmc3k_subset", "title": "A toy single-cell RNA-seq data", "topics": [ "pbmc3k_subset" ] }, { "page": "pdistance", "title": "Calculate the cell-feature distance matrix", "topics": [ "pdistance" ] }, { "page": "top5_signatures", "title": "A dataframe including top five signature genes", "topics": [ "top5_signatures" ] } ], "_readme": "https://github.com/feiyoung/cofast/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "askpass", "assorthead", "backports", "base64enc", "beachmat", "beeswarm", "BH", "Biobase", "BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "bitops", "boot", "broom", "bslib", "cachem", "Cairo", "car", "carData", "caTools", "cli", "cluster", "codetools", "colorspace", "commonmark", "CompQuadForm", "corrplot", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DelayedArray", "deldir", "Deriv", "digest", "doBy", "dotCall64", "dplyr", "dqrng", "DR.SC", "evaluate", "farver", "fastDummies", "fastmap", "fitdistrplus", "FNN", "fontawesome", "forecast", "formatR", "Formula", "fracdiff", "fs", "furrr", "futile.logger", "futile.options", "future", "future.apply", "generics", "GenomicRanges", "ggbeeswarm", "ggplot2", "ggpubr", "ggrastr", "ggrepel", "ggridges", "ggsci", "ggsignif", "ggthemes", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "harmony", "here", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "IRanges", "irlba", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "mclust", "memoise", "mgcv", "microbenchmark", "mime", "miniUI", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pbkrtest", "pheatmap", "pillar", "pixmap", "pkgconfig", "plotly", "plyr", "png", "polyclip", "polynom", "PRECAST", "prettyunits", "ProFAST", "progress", "progressr", "promises", "purrr", "quantreg", "R6", "ragg", "RANN", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppML", "RcppProgress", "RcppTOML", "Rdpack", "reformulas", "reshape2", "reticulate", "RhpcBLASctl", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSpectra", "rstatix", "rsvd", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sass", "ScaledMatrix", "scales", "scater", "scattermore", "sctransform", "scuttle", "Seqinfo", "Seurat", "SeuratObject", "shiny", "SingleCellExperiment", "sitmo", "snow", "sourcetools", "sp", "spam", "SparseArray", "SparseM", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "systemfonts", "tensor", "textshaping", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "uwot", "vctrs", "vipor", "viridis", "viridisLite", "withr", "xfun", "xtable", "XVector", "yaml", "zoo" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "CosMx.Rmd", "filename": "CosMx.html", "title": "coFAST: NSCLC CosMx data coembedding", "author": "Wei Liu", "engine": "knitr::rmarkdown", "headings": [ "Load and view data", "Preprocessing", "Coembedding using coFAST", "Downstream analysis", "Clustering and assess the cluster significance" ], "created": "2025-03-14 13:17:43", "modified": "2025-11-17 13:55:44", "commits": 3 } ], "_score": 4, "_indexed": true, "_nocasepkg": "cofast", "_universes": [ "feiyoung" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-05-30T11:06:50.000Z", "distro": "noble", "arch": "aarch64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "f7d3c0495f596bbad5cd2007f9bbfea35fdc3a3dbf32f8ffb4c78098146a34be", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-05-30T11:18:05.000Z", "distro": "noble", "arch": "x86_64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "fa02d8dc2bf4c6af6d33b887535b177661418f1c79370101a8362392caa6eee5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.6.0", "os": "linux", "version": "0.2.0", "date": "2026-05-30T11:08:03.000Z", "distro": "noble", "arch": "aarch64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "407d6bfd5a2d04ff21d3530949fcdd235cf67d1f46ed4c94c81d6d12121b479b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.6.0", "os": "linux", "version": "0.2.0", "date": "2026-05-30T11:19:25.000Z", "distro": "noble", "arch": "x86_64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "61e87b5cbd14e3b12b9be1fc58d54bfc53706e3f81f5e85e43453620e1efb11b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.5.3", "os": "mac", "version": "0.2.0", "date": "2026-05-30T16:03:07.000Z", "arch": "aarch64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "b4eb814363656971067c9d37c161ec43af97706c838478411545ca7f9cf42907", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.5.3", "os": "mac", "version": "0.2.0", "date": "2026-05-30T11:08:26.000Z", "arch": "x86_64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "69c9aac58f955445f40c6217b28e6b57c7d8422be047f5823e8956a45f8e79cd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.6.0", "os": "mac", "version": "0.2.0", "date": "2026-05-30T16:03:24.000Z", "arch": "aarch64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "768003b71b83bbff2146dfa7ccadba9ab6587bafacdc7ca2996e1ecf52cbaa0d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.6.0", "os": "mac", "version": "0.2.0", "date": "2026-05-30T11:08:53.000Z", "arch": "x86_64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "924f3a5b25fbda3f46183592bbf72c2d2157a566486946da5a37a895f6308a36", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.0", "date": "2026-05-30T11:19:57.000Z", "arch": "emscripten", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "a60dac36ceb87195a30faa00ad0be9eae0bfa80c579c6e647bb3c80c2b367912", "status": "success", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.7.0", "os": "win", "version": "0.2.0", "date": "2026-05-30T11:17:42.000Z", "arch": "x86_64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "73e0a242e340583f8cbd842970733aee831c7d90c71b26f64b0d50819e155121", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.5.3", "os": "win", "version": "0.2.0", "date": "2026-05-30T11:16:17.000Z", "arch": "x86_64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "582e209f22920bc65e09fae902af77a56f1928539d308ca0cbba8ac422c33f73", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" }, { "r": "4.6.0", "os": "win", "version": "0.2.0", "date": "2026-05-30T11:16:25.000Z", "arch": "x86_64", "commit": "4232715b0935988dc9c8b2b26865c530fe34ac32", "fileid": "4a9c0ba341cdb9d4211500ee589c5fef21b95634d6b9796a9be3e7117dfef828", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/feiyoung/actions/runs/26681320425" } ] }