{ "_id": "6a1acf601d7bb097a09e06c7", "Package": "flowClust", "Type": "Package", "Title": "Clustering for Flow Cytometry", "Version": "3.51.0", "Author": "Raphael Gottardo, Kenneth Lo , Greg Finak\n", "Maintainer": "Greg Finak , Mike Jiang ", "Description": "Robust model-based clustering using a t-mixture model with\nBox-Cox transformation. Note: users should have GSL installed.\nWindows users: 'consult the README file available in the inst\ndirectory of the source distribution for necessary\nconfiguration instructions'.", "Collate": "'SetClasses.R' 'SetMethods.R' 'flowClust.R' 'coerce.R'\n'flowClust-package.R' 'hist.R' 'miscellaneous.R' 'plot.R'\n'split.R'", "License": "MIT", "Packaged": { "Date": "2026-05-30 08:13:53 UTC", "User": "root" }, "biocViews": "ImmunoOncology, Clustering, Visualization, FlowCytometry", "SystemRequirements": "GNU make", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:32:49 UTC", "RemoteUrl": "https://github.com/bioc/flowClust", "RemoteRef": "HEAD", "RemoteSha": "66e3c7f05d40c4e43983989a51c237027a4650ac", "NeedsCompilation": "yes", "MD5sum": "83daea3a2fcf185f9bc9f41e5f29dfdb", "_user": "bioc", "_type": "src", "_file": "flowClust_3.51.0.tar.gz", "_fileid": "f19314c5bd9bee6a2a1203f7030dce145bfef171c9273d7c3ce971ae742dad24", "_filesize": 2287753, "_sha256": "f19314c5bd9bee6a2a1203f7030dce145bfef171c9273d7c3ce971ae742dad24", "_created": "2026-05-30T08:13:53.000Z", "_published": "2026-05-30T11:51:59.986Z", "_jobs": [ { "job": 78635911614, "time": 249, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306774315" }, { "job": 78635911600, "time": 448, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7306793528" }, { "job": 78635911603, "time": 401, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306788938" }, { "job": 78635911623, "time": 310, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7306779758" }, { "job": 78635911626, "time": 362, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306784937" }, { "job": 78635911594, "time": 333, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307971181" }, { "job": 78635911610, "time": 555, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7306804308" }, { "job": 78635911593, "time": 279, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307966692" }, { "job": 78635911599, "time": 474, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306796962" }, { "job": 78635586496, "time": 379, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306750495" }, { "job": 78635911607, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306764380" }, { "job": 78635911597, "time": 351, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306783835" }, { "job": 78635911601, "time": 340, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306782718" }, { "job": 78635911618, "time": 310, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306779750" } ], "_bioccheck": { "error": 2, "warning": 4, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/flowClust", "_commit": { "id": "66e3c7f05d40c4e43983989a51c237027a4650ac", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379569 }, "_maintainer": { "name": "Greg Finak", "email": "mike@ozette.ai", "login": "gfinak", "twitter": "@GregFinak", "description": "", "uuid": 1385593 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.5.0", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "graph", "role": "Imports" }, { "package": "flowCore", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "flowWorkspace", "role": "Suggests" }, { "package": "flowWorkspaceData", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "openCyto", "role": "Suggests" }, { "package": "flowStats", "version": ">= 4.7.1", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 6, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "3.51.0", "bioc": "3.24" }, { "branch": "release", "version": "3.50.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "clustering", "visualization", "flowcytometry" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1710, "source": "https://www.bioconductor.org/packages/stats/bioc/flowClust" }, "_mentions": 33, "_searchresults": 87, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/flowClust.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "%in%", "box", "criterion", "criterion<-", "density", "dmvt", "dmvtmix", "flowClust", "getEstimates", "importance", "Map", "plot", "posterior", "rbox", "ruleOutliers", "ruleOutliers<-", "show", "split", "Subset", "summarizeFilter", "summary", "tmixFilter", "uncertainty" ], "_datasets": [ { "name": "rituximab", "title": "The Rituximab Dataset", "object": "rituximab", "file": "rituximab.RData", "class": [ "flowFrame" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "flowClust-package", "title": "Clustering for Flow Cytometry", "topics": [ "flowClust-package" ] }, { "page": "BIC", "title": "Extract the BIC for a flowClust fit.", "topics": [ "BIC", "BIC.flowClust", "BIC.flowClustList" ] }, { "page": "box", "title": "Box-Cox Transformation", "topics": [ "box" ] }, { "page": "miscellaneous", "title": "Various Functions for Retrieving Information from Clustering Results", "topics": [ "criterion", "criterion,flowClust-method", "criterion,flowClustList-method", "criterion<-", "criterion<-,flowClustList,character-method", "getEstimates", "importance", "posterior", "uncertainty" ] }, { "page": "dmvt", "title": "Density of the Multivariate t Distribution with Box-Cox Tranformation", "topics": [ "dmvt" ] }, { "page": "dmvtmix", "title": "Density of the Multivariate t Mixture Distribution with Box-Cox Tranformation", "topics": [ "dmvtmix" ] }, { "page": "flowClust", "title": "Robust Model-based Clustering for Flow Cytometry", "topics": [ "flowClust", "flowClust-class", "flowClustList-class", "fowClust" ] }, { "page": "flowClust.den", "title": "generate the curve that reflects the tmixture fitting outcome", "topics": [ "flowClust.den" ] }, { "page": "density", "title": "Grid of Density Values for the Fitted t Mixture Model with Box-Cox Transformation", "topics": [ "density,flowClust-method", "density,flowClustList-method", "density-method", "density.flowClust", "flowDens-class" ] }, { "page": "hist", "title": "1-D Density Plot (Histogram) of Clustering Results", "topics": [ "hist.flowClust", "hist.flowClustList" ] }, { "page": "Map", "title": "Cluster Assignment Based on Clustering Results", "topics": [ "Map", "Map,flowClust-method", "Map,flowClustList-method", "Map.flowClust" ] }, { "page": "plot.flowClust", "title": "Scatterplot of Clustering Results", "topics": [ "plot", "plot,flowClust,missing-method", "plot,flowClust-method", "plot,flowClustList,missing-method" ] }, { "page": "plot.flowDens", "title": "Contour or Image Plot of Clustering Results", "topics": [ "plot,flowDens,missing-method", "plot,flowDens-method", "plot.flowDens" ] }, { "page": "plot.flowCore", "title": "Scatterplot / 1-D Density Plot of Filtering (Clustering) Results", "topics": [ "plot,flowFrame,tmixFilterResult-method", "plot,flowFrame,tmixFilterResultList-method", "plot,tmixFilterResult-method", "plot.flowFrame", "plot.flowFrame.tmixFilterResult", "plot.tmixFilterResult" ] }, { "page": "rbox", "title": "Reverse Box-Cox Transformation", "topics": [ "rbox" ] }, { "page": "rituximab", "title": "The Rituximab Dataset", "topics": [ "rituximab" ] }, { "page": "ruleOutliers", "title": "Showing or Modifying the Rule used to Identify Outliers", "topics": [ "ruleOutliers", "ruleOutliers,flowClust-method", "ruleOutliers,flowClustList-method", "ruleOutliers.flowClust", "ruleOutliers<-", "ruleOutliers<-,flowClust,list-method", "ruleOutliers<-,flowClustList,list-method" ] }, { "page": "show.flowClust", "title": "Show Method for flowClust / tmixFilterResult Object", "topics": [ "show,flowClust-method", "show,flowClustList-method", "show,tmixFilter-method", "show,tmixFilterResult-method", "show,tmixFilterResultList-method", "show.flowClust", "show.tmixFilterResult" ] }, { "page": "split", "title": "Splitting Data Based on Clustering Results", "topics": [ "split", "split,data.frame,flowClust-method", "split,data.frame,flowClustList-method", "split,flowClust-method", "split,flowFrame,flowClust-method", "split,flowFrame,flowClustList-method", "split,flowFrame,tmixFilterResult-method", "split,flowFrame,tmixFilterResultList-method", "split,matrix,flowClust-method", "split,matrix,flowClustList-method", "split,vector,flowClust-method", "split,vector,flowClustList-method", "split.flowClust", "split.flowFrame", "split.tmixFilterResult" ] }, { "page": "Subset", "title": "Subsetting Data Based on Clustering Results", "topics": [ "Subset", "Subset,ANY,flowClustList-method", "Subset,data.frame,flowClust-method", "Subset,flowClust-method", "Subset,flowFrame,flowClust-method", "Subset,flowFrame,tmixFilterResult-method", "Subset,flowFrame,tmixFilterResultList-method", "Subset,matrix,flowClust-method", "Subset,vector,flowClust-method", "Subset.flowClust", "Subset.flowFrame", "Subset.flowFrame.tmixFilterResult", "Subset.tmixFilterResult" ] }, { "page": "summary", "title": "Summary Method for flowClust Object", "topics": [ "summary", "summary,flowClust-method", "summary,flowClustList-method", "summary,tmixFilterResult-method", "summary,tmixFilterResultList-method", "summary.flowClust", "summary.tmixFilterResult" ] }, { "page": "tmixFilter", "title": "Creating Filters and Filtering Flow Cytometry Data", "topics": [ "%in%,ANY,flowClust-method", "%in%,ANY,flowClustList-method", "%in%,ANY,tmixFilterResult-method", "%in%,ANY,tmixFilterResultList-method", "%in%,flowFrame,tmixFilter-method", "%in%,flowFrame,tmixFilterResult-method", "length,tmixFilterResultList-method", "summarizeFilter,tmixFilterResult,tmixFilter-method", "tmixFilter", "tmixFilter-class", "tmixFilterResult-class", "tmixFilterResultList", "tmixFilterResultList-class", "[,flowFrame,flowClust-method", "[,flowFrame,flowClustList-method", "[,flowFrame,tmixFilterResult-method", "[,flowFrame,tmixFilterResultList-method", "[[,tmixFilterResultList,ANY-method" ] } ], "_readme": "https://github.com/bioc/flowClust/raw/HEAD/README.md", "_rundeps": [ "BH", "Biobase", "BiocGenerics", "biocmake", "cpp11", "cytolib", "dir.expiry", "filelock", "flowCore", "generics", "graph", "matrixStats", "Rcpp", "Rhdf5lib", "RProtoBufLib", "S4Vectors" ], "_vignettes": [ { "source": "flowClust.Rmd", "filename": "flowClust.html", "title": "Robust Model-based Clustering of Flow Cytometry Data The flowClust package", "author": "Raphael Gottardo, Kenneth Lo and Greg Finak", "engine": "knitr::rmarkdown", "headings": [ "Licensing", "Overview", "Installation", "Unix/Linux/Mac Users", "Windows Users", "Example: Clustering of the Rituximab Dataset", "The Core Function \\label", "Visualization of Clustering Results", "Integration with flowCore", "Using Priors" ], "created": "2019-04-04 17:17:50", "modified": "2022-03-15 04:28:16", "commits": 2 } ], "_score": 7.427787868114079, "_indexed": true, "_nocasepkg": "flowclust", "_universes": [ "bioc", "gfinak" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.51.0", "date": "2026-05-30T08:20:30.000Z", "distro": "noble", "arch": "aarch64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "f1d973a9c7169f3650510abc2592e757cdc243e63e703c03220bea6c0b946455", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.7.0", "os": "linux", "version": "3.51.0", "date": "2026-05-30T08:19:28.000Z", "distro": "noble", "arch": "x86_64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "2585a316b07d2fc0ca8fe4222f9f4d07fcaa24e8687353256026675314999f17", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.6.0", "os": "linux", "version": "3.51.0", "date": "2026-05-30T08:18:39.000Z", "distro": "noble", "arch": "aarch64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "ffb992a3032d7a4070bfdce1c8e418939f38c856e3d1b020fe81ddf6f5f6ea8f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.6.0", "os": "linux", "version": "3.51.0", "date": "2026-05-30T08:18:55.000Z", "distro": "noble", "arch": "x86_64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "dfcc3aa1e1e94112b045634008b3996e7fb1bb00dc27fd25dcb54f8fec5067dc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.5.3", "os": "mac", "version": "3.51.0", "date": "2026-05-30T11:49:18.000Z", "arch": "aarch64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "1be14b6da07fd505d9259213bb6ad1c2baffd0b5f2a5bdb23af94552c5a528f4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.5.3", "os": "mac", "version": "3.51.0", "date": "2026-05-30T08:20:55.000Z", "arch": "x86_64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "a272bab751a5988022fd22e588f2b7ec4d1d455353d3788e3aef372c375bdecb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.6.0", "os": "mac", "version": "3.51.0", "date": "2026-05-30T11:49:06.000Z", "arch": "aarch64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "bd013d59dfb82c1f5ae0c018228579c07dd6e62ea13eb093d5c8d802bdc626f4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.6.0", "os": "mac", "version": "3.51.0", "date": "2026-05-30T08:19:42.000Z", "arch": "x86_64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "a202440c6cd86b8310ce74e5d8c89d70e7475a3699885b251b29b0cb71a9c148", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.6.0", "os": "wasm", "version": "3.51.0", "date": "2026-05-30T08:17:32.000Z", "arch": "emscripten", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "a670a9135522d260a35d53bc64abc6afb29970a43b30bb531f8cafead7c294de", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.7.0", "os": "win", "version": "3.51.0", "date": "2026-05-30T08:16:53.000Z", "arch": "x86_64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "d5869948a6179e289fc6c6848a470cfa81799bb43e424ba768f6da590cfc88a2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.5.3", "os": "win", "version": "3.51.0", "date": "2026-05-30T08:16:41.000Z", "arch": "x86_64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "332c4433ee7bf7a6885026313b16706f88baa66bf33e8fe38751c5a7cc99c005", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" }, { "r": "4.6.0", "os": "win", "version": "3.51.0", "date": "2026-05-30T08:16:46.000Z", "arch": "x86_64", "commit": "66e3c7f05d40c4e43983989a51c237027a4650ac", "fileid": "7382f8dcf8316857a377d95b06f1351996bdb27f34c7f2916b6e47995f0147b7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678858967" } ] }