{ "_id": "6a571c77ff0138dec5d6ddc8", "Package": "scClassify", "Type": "Package", "Title": "scClassify: single-cell Hierarchical Classification", "Version": "1.25.0", "Author": "Yingxin Lin", "Maintainer": "Yingxin Lin ", "Description": "scClassify is a multiscale classification framework for\nsingle-cell RNA-seq data based on ensemble learning and cell\ntype hierarchies, enabling sample size estimation required for\naccurate cell type classification and joint classification of\ncells using multiple references.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "biocViews": "SingleCell, GeneExpression, Classification", "BugReports": "https://github.com/SydneyBioX/scClassify/issues", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:32 UTC", "RemoteUrl": "https://github.com/bioc/scClassify", "RemoteRef": "HEAD", "RemoteSha": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-15 05:26:51 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "scClassify_1.25.0.tar.gz", "_fileid": "https://r2.ropensci.org/e21419b48c1dcf9f80a8f650fc599c5aff11121f0492067741c0b84b442ea5a9", "_filesize": 2599396, "_sha256": "e21419b48c1dcf9f80a8f650fc599c5aff11121f0492067741c0b84b442ea5a9", "_expires": "2026-10-23T05:36:53.000Z", "_created": "2026-07-15T05:26:51.000Z", "_published": "2026-07-15T05:36:55.279Z", "_bioccheck": { "error": 1, "warning": 2, "note": 11 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29391178346", "_status": "success", "_upstream": "https://github.com/bioc/scClassify", "_commit": { "id": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380752 }, "_maintainer": { "name": "Yingxin Lin", "email": "yingxin.lin@sydney.edu.au", "login": "yingxinlin", "description": "", "uuid": 30995032 }, "_distro": "resolute", "_jobs": [ { "job": 87275846688, "time": 250, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8333487503" }, { "job": 87275846721, "time": 505, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8333555300" }, { "job": 87275846714, "time": 518, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8333561440" }, { "job": 87275846710, "time": 266, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8333491508" }, { "job": 87275846705, "time": 391, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8333525199" }, { "job": 87274895213, "time": 434, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8333419563" }, { "job": 87275846691, "time": 204, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8333474253" }, { "job": 87275846719, "time": 386, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8333524816" }, { "job": 87275846711, "time": 388, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8333524729" }, { "job": 87275846717, "time": 423, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8333534412" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "ggraph", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "minpack.lm", "role": "Imports" }, { "package": "mixtools", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "proxy", "role": "Imports" }, { "package": "proxyC", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "hopach", "role": "Imports" }, { "package": "diptest", "role": "Imports" }, { "package": "mgcv", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "statmod", "role": "Imports" }, { "package": "Cepo", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "pkgdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "singlecell", "geneexpression", "classification" ], "_stars": 29, "_contributors": [ { "user": "yingxinlin", "count": 43, "uuid": 30995032 }, { "user": "nturaga", "count": 6, "uuid": 2746443 }, { "user": "pyanglab", "count": 2, "uuid": 10148940 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 446, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 412, "source": "https://www.bioconductor.org/packages/stats/bioc/scClassify" }, "_mentions": 3, "_devurl": "https://github.com/sydneybiox/scclassify", "_searchresults": 41, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/scClassify.html", "manual.pdf" ], "_homeurl": "https://github.com/sydneybiox/scclassify", "_realowner": "bioc", "_cranurl": false, "_exports": [ "cellTypeTrain", "cellTypeTree", "features", "getN", "learningCurve", "model", "modelweights", "name", "plotCellTypeTree", "predict_scClassify", "predict_scClassifyJoint", "runHOPACH", "runSampleCal", "scClassify", "scClassifyTrainModelList", "train_scClassify" ], "_datasets": [ { "name": "scClassify_example", "title": "Example data used in scClassify package", "object": "scClassify_example", "file": "scClassify_example.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "trainClassExample_wang", "title": "Subset of pretrained model of Wang et al.", "object": "trainClassExample_wang", "file": "trainClassExample_wang.rda", "class": [ "scClassifyTrainModel" ], "fields": [], "table": false, "tojson": false }, { "name": "trainClassExample_xin", "title": "Subset of pretrained model of Xin et al.", "object": "trainClassExample_xin", "file": "trainClassExample_xin.rda", "class": [ "scClassifyTrainModel" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "dot-scClassifyTrainModel", "title": "The scClassifyTrainModel class", "topics": [ ".scClassifyTrainModel" ] }, { "page": "cellTypeTrain", "title": "Accessors of cellTypeTrain for scClassifyTrainModel", "topics": [ "cellTypeTrain", "cellTypeTrain,scClassifyTrainModel-method" ] }, { "page": "cellTypeTree", "title": "Accessors of cellTypeTree for scClassifyTrainModel", "topics": [ "cellTypeTree", "cellTypeTree,scClassifyTrainModel-method" ] }, { "page": "features", "title": "Accessors of features for scClassifyTrainModel", "topics": [ "features", "features,scClassifyTrainModel-method" ] }, { "page": "getN", "title": "Function to get the required N given by the accuracy and the learning curve model", "topics": [ "getN" ] }, { "page": "learningCurve", "title": "Fit learning curve for accuracy matrix", "topics": [ "learningCurve" ] }, { "page": "model", "title": "Accessors of model for scClassifyTrainModel", "topics": [ "model", "model,scClassifyTrainModel-method" ] }, { "page": "modelweights", "title": "Accessors of modelweights for scClassifyTrainModel", "topics": [ "modelweights", "modelweights,scClassifyTrainModel-method" ] }, { "page": "name", "title": "Accessors of name for scClassifyTrainModel", "topics": [ "name", "name,scClassifyTrainModel-method" ] }, { "page": "plotCellTypeTree", "title": "To plot cell type tree", "topics": [ "plotCellTypeTree" ] }, { "page": "predict_scClassify", "title": "Testing scClassify model", "topics": [ "predict_scClassify" ] }, { "page": "predict_scClassifyJoint", "title": "Testing scClassify model (joint training)", "topics": [ "predict_scClassifyJoint" ] }, { "page": "runHOPACH", "title": "Create HOPACH tree", "topics": [ "runHOPACH" ] }, { "page": "runSampleCal", "title": "Run sample size calculation for pilot data for reference dataset", "topics": [ "runSampleCal" ] }, { "page": "scClassify", "title": "Train and test scClassify model", "topics": [ "scClassify" ] }, { "page": "scClassify_example", "title": "Example data used in scClassify package", "topics": [ "scClassify_example" ] }, { "page": "scClassifyTrainModel-class", "title": "An S4 class to stored training model for scClassify", "topics": [ "scClassifyTrainModel-class" ] }, { "page": "scClassifyTrainModelList", "title": "The scClassifyTrainModelList class", "topics": [ "scClassifyTrainModelList" ] }, { "page": "scClassifyTrainModelList-class", "title": "An S4 class to stored a list of training models from scClassify", "topics": [ "scClassifyTrainModelList-class" ] }, { "page": "train_scClassify", "title": "Training scClassify model", "topics": [ "train_scClassify" ] }, { "page": "trainClassExample_wang", "title": "Subset of pretrained model of Wang et al.", "topics": [ "trainClassExample_wang" ] }, { "page": "trainClassExample_xin", "title": "Subset of pretrained model of Xin et al.", "topics": [ "trainClassExample_xin" ] } ], "_readme": "https://github.com/bioc/scClassify/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "base64enc", "BH", "Biobase", "BiocGenerics", "biocmake", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "Cepo", "cli", "cluster", "codetools", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "DelayedArray", "DelayedMatrixStats", "digest", "diptest", "dir.expiry", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggforce", "ggplot2", "ggraph", "ggrepel", "glue", "graph", "graphlayouts", "gridExtra", "GSEABase", "gtable", "h5mread", "HDF5Array", "highr", "hopach", "htmltools", "htmlwidgets", "httr", "igraph", "IRanges", "isoband", "jquerylib", "jsonlite", "KEGGREST", "kernlab", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "minpack.lm", "mixtools", "nlme", "openssl", "otel", "patchwork", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "promises", "proxy", "proxyC", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "rmarkdown", "RSQLite", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "segmented", "Seqinfo", "SingleCellExperiment", "snow", "SparseArray", "sparseMatrixStats", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "systemfonts", "tibble", "tidygraph", "tidyr", "tidyselect", "tinytex", "tweenr", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "pretrainedModel.Rmd", "filename": "pretrainedModel.html", "title": "Performing scClassify using pretrained model", "author": "Yingxin Lin", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Setting up the data", "Running scClassify", "Session Info" ], "created": "2019-09-20 08:32:43", "modified": "2020-04-20 05:41:12", "commits": 5 }, { "source": "scClassify.Rmd", "filename": "scClassify.html", "title": "scClassify Model Building and Prediction", "author": "Yingxin Lin", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Setting up the data", "scClassify", "Non-ensemble scClassify", "Ensemble Classify", "Train your own model", "Session Info" ], "created": "2019-09-20 08:32:43", "modified": "2020-04-20 05:41:12", "commits": 8 } ], "_score": 7.154363100666316, "_indexed": true, "_nocasepkg": "scclassify", "_universes": [ "bioc", "yingxinlin", "sydneybiox" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-07-15T05:31:48.000Z", "distro": "resolute", "commit": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "fileid": "https://r2.ropensci.org/d95ef959c996f3d10a51f91e6d25fd0234d220ed21e2c3c6339b2b164fa0cb8c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29391178346" }, { "r": "4.6.1", "os": "linux", "version": "1.25.0", "date": "2026-07-15T05:32:11.000Z", "distro": "resolute", "commit": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "fileid": "https://r2.ropensci.org/594dba16a4cbd7c3d328307d811b060174593bd83b2297518ea5db0c6b7a3e56", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29391178346" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-07-15T05:28:59.000Z", "commit": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "fileid": "https://r2.ropensci.org/15a2006ed428d6b3311196a5da4be2c58d0c406e2dd2eb8ddce942baaa10318e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29391178346" }, { "r": "4.6.1", "os": "mac", "version": "1.25.0", "date": "2026-07-15T05:29:39.000Z", "commit": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "fileid": "https://r2.ropensci.org/d20971b3990cabc8da9f19a13ba61d815f58c84859c927ccb63555c36f490a37", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29391178346" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-07-15T05:30:59.000Z", "commit": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "fileid": "https://r2.ropensci.org/9057c547b65ee9cd9c46df1648892fd92912de0adeac36a80bb47ba8afbbfa53", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29391178346" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-07-15T05:29:33.000Z", "commit": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "fileid": "https://r2.ropensci.org/a33797d7170cdcaca57fdd90e36750ce0230ec974414df15481dadebb687fef2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29391178346" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-07-15T05:29:03.000Z", "commit": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "fileid": "https://r2.ropensci.org/f10a301b9d6dfa4bbd52a8f76c977ffa8443c1153cf8b52f417d18a85bbf3877", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29391178346" }, { "r": "4.6.1", "os": "win", "version": "1.25.0", "date": "2026-07-15T05:29:15.000Z", "commit": "a6d4665cfa8687a91848163b20a6b020393fa4ce", "fileid": "https://r2.ropensci.org/e15037df397e22881076bbb9a10ae8984564993df6145eacc6c6303c04a835b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29391178346" } ] }