{
  "_id": "6aaa496fea78b3e62eaca45b",
  "Package": "flowMerge",
  "Type": "Package",
  "Title": "Cluster Merging for Flow Cytometry Data",
  "Version": "2.60.0",
  "Date": "2011-05-26",
  "Author": "Greg Finak <gfinak@fhcrc.org>, Raphael Gottardo\n<rgottard@fhcrc.org>",
  "Maintainer": "Greg Finak <gfinak@fhcrc.org>",
  "Description": "Merging of mixture components for model-based automated\ngating of flow cytometry data using the flowClust framework.\nNote: users should have a working copy of flowClust 2.0\ninstalled.",
  "License": "Artistic-2.0",
  "LazyLoad": "yes",
  "Collate": "SetClasses.R SetMethods.R flowMerge.R",
  "biocViews": "ImmunoOncology, Clustering, FlowCytometry",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libssl-dev zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:34:00 UTC",
  "RemoteUrl": "https://github.com/bioc/flowMerge",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "06164744cb18ceedd92fdd46912f240a7063fb33",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-16 07:07:46 UTC",
    "User": "root"
  },
  "_user": "bioc-release",
  "_type": "src",
  "_file": "flowMerge_2.60.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/69df7c991d9952994d234a122e72176d735e1e0cb429ebf39d4f462230318c2f",
  "_filesize": 1033296,
  "_sha256": "69df7c991d9952994d234a122e72176d735e1e0cb429ebf39d4f462230318c2f",
  "_expires": "2026-12-25T07:46:53.000Z",
  "_created": "2026-09-16T07:07:46.000Z",
  "_published": "2026-09-16T07:46:55.798Z",
  "_bioccheck": {
    "error": 3,
    "warning": 5,
    "note": 16
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35066631768",
  "_status": "success",
  "_upstream": "https://github.com/bioc/flowMerge",
  "_commit": {
    "id": "06164744cb18ceedd92fdd46912f240a7063fb33",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379640
  },
  "_maintainer": {
    "name": "Greg Finak",
    "email": "gfinak@fhcrc.org"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 104699521480,
      "time": 182,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10434777171"
    },
    {
      "job": 104699521274,
      "time": 327,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10434458738"
    },
    {
      "job": 104699521355,
      "time": 324,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10435295322"
    },
    {
      "job": 104699521321,
      "time": 157,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10436310448"
    },
    {
      "job": 104699521304,
      "time": 144,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10435273395"
    },
    {
      "job": 104698340706,
      "time": 267,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10434706169"
    },
    {
      "job": 104699521270,
      "time": 148,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10434956598"
    },
    {
      "job": 104699521384,
      "time": 176,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10434936798"
    },
    {
      "job": 104699521340,
      "time": 160,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10435145307"
    },
    {
      "job": 104699521368,
      "time": 159,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10434607650"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "graph",
      "role": "Depends"
    },
    {
      "package": "feature",
      "role": "Depends"
    },
    {
      "package": "flowClust",
      "role": "Depends"
    },
    {
      "package": "Rgraphviz",
      "role": "Depends"
    },
    {
      "package": "foreach",
      "role": "Depends"
    },
    {
      "package": "snow",
      "role": "Depends"
    },
    {
      "package": "rrcov",
      "role": "Imports"
    },
    {
      "package": "flowCore",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "doMC",
      "role": "Enhances"
    },
    {
      "package": "multicore",
      "role": "Enhances"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.61.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.60.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "clustering",
    "flowcytometry"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 467,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 592,
    "source": "https://www.bioconductor.org/packages/stats/bioc/flowMerge"
  },
  "_mentions": 6,
  "_searchresults": 8,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/flowMerge.html",
    "extra/manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "BIC",
    "checkForRemoteErrors",
    "ENT",
    "fitPiecewiseLinreg",
    "flowObj",
    "getData",
    "ICL",
    "map",
    "merge",
    "NENT",
    "pFlowMerge",
    "plot",
    "ptree",
    "show",
    "split",
    "summary"
  ],
  "_datasets": [
    {
      "name": "flowClust.res",
      "title": "A flowClust model fitted to the rituximab data for 1:10 clusters.",
      "object": "RituximabFlowClustFit",
      "file": "RituximabFlowClustFit.RData",
      "class": [
        "flowClustList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "flowMerge-package",
      "title": "Merging of mixture components for automated gating of flow cytometry data.",
      "topics": [
        "flowMerge-package",
        "flowMerge"
      ]
    },
    {
      "page": "checkForRemoteErrors",
      "title": "Check output of snow clusters for errors",
      "topics": [
        "checkForRemoteErrors"
      ]
    },
    {
      "page": "fitPiecewiseLinreg",
      "title": "Fit Piecewise Linear Regression for a list of flowMerge Objects",
      "topics": [
        "fitPiecewiseLinreg"
      ]
    },
    {
      "page": "fitPiecewiseLinreg-methods",
      "title": "Methods for fitPiecewiseLinreg in flowMerge package",
      "topics": [
        "fitPiecewiseLinreg,list-method",
        "fitPiecewiseLinreg-methods"
      ]
    },
    {
      "page": "flagOutliers",
      "title": "Update the flagOutliers slot in a flowMerge object",
      "topics": [
        "flagOutliers"
      ]
    },
    {
      "page": "flagOutliers-methods",
      "title": "Methods to update the flagOutliers slot in a flowMerge object.",
      "topics": [
        "flagOutliers,flowMerge-method",
        "flagOutliers-methods"
      ]
    },
    {
      "page": "flowClust.res",
      "title": "A flowClust model fitted to the rituximab data for 1:10 clusters.",
      "topics": [
        "flowClust.res",
        "RituximabFlowClustFit"
      ]
    },
    {
      "page": "flowMerge-class",
      "title": "Class \"flowMerge\"",
      "topics": [
        "flowMerge-class",
        "getData,flowMerge-method",
        "plot,flowMerge,missing-method"
      ]
    },
    {
      "page": "flowObj",
      "title": "Create a flowObj object from a flowClust and flowFrame object",
      "topics": [
        "flowObj"
      ]
    },
    {
      "page": "flowObj-class",
      "title": "Class \"flowObj\"",
      "topics": [
        "flowObj-class",
        "getData,flowObj-method",
        "merge,flowObj,missing-method",
        "plot,flowObj,missing-method"
      ]
    },
    {
      "page": "initPFlowMerge",
      "title": "Initialize a SNOW cluster for use with flowMerge",
      "topics": [
        "initPFlowMerge"
      ]
    },
    {
      "page": "map",
      "title": "Map matrix of probabilities to class assignments.",
      "topics": [
        "map"
      ]
    },
    {
      "page": "merge",
      "title": "Merge clusters in flow cytometry data",
      "topics": [
        "merge",
        "merge,flowObj",
        "merge,flowObj,metric"
      ]
    },
    {
      "page": "merge-methods",
      "title": "Merge mixture components",
      "topics": [
        "merge,flowObj-methods",
        "merge-methods"
      ]
    },
    {
      "page": "mergeClusters",
      "title": "Cluster merging not meant to be called by the user",
      "topics": [
        "mergeClusters"
      ]
    },
    {
      "page": "mergeClusters2",
      "title": "Cluster merging not meant to be called by the user",
      "topics": [
        "mergeClusters2"
      ]
    },
    {
      "page": "NENT",
      "title": "Extract the Normalized Entropy",
      "topics": [
        "NENT"
      ]
    },
    {
      "page": "pFlowClust",
      "title": "Parallelized FlowClust",
      "topics": [
        "pFlowClust"
      ]
    },
    {
      "page": "pFlowMerge",
      "title": "Parellel call to flowMerge",
      "topics": [
        "pFlowMerge"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Methods for plotting flowMerge and flowObj classes",
      "topics": [
        "plot,flowMerge",
        "plot,flowObj",
        "plot-methods"
      ]
    },
    {
      "page": "ptree",
      "title": "Generate a Function to Plot The Merging Tree",
      "topics": [
        "ptree"
      ]
    },
    {
      "page": "show-methods",
      "title": "Describe a flowObj or flowMerge object",
      "topics": [
        "show,flowMerge-method",
        "show,flowObj-method"
      ]
    },
    {
      "page": "split-methods",
      "title": "Split data in a flowMerge object by cluster",
      "topics": [
        "split,flowMerge,missing-method",
        "split-methods"
      ]
    },
    {
      "page": "summary-methods",
      "title": "Summary methods for flowMerge",
      "topics": [
        "summary,flowMerge-method",
        "summary,flowObj-method"
      ]
    },
    {
      "page": "updateU",
      "title": "Update uncertainties",
      "topics": [
        "updateU"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "Biobase",
    "BiocGenerics",
    "biocmake",
    "codetools",
    "cpp11",
    "cytolib",
    "DEoptimR",
    "dir.expiry",
    "feature",
    "filelock",
    "flowClust",
    "flowCore",
    "FNN",
    "foreach",
    "generics",
    "graph",
    "iterators",
    "kernlab",
    "KernSmooth",
    "ks",
    "lattice",
    "Matrix",
    "matrixStats",
    "mclust",
    "mgcv",
    "misc3d",
    "multicool",
    "mvtnorm",
    "nlme",
    "pcaPP",
    "plot3D",
    "pracma",
    "Rcpp",
    "Rgraphviz",
    "Rhdf5lib",
    "robustbase",
    "RProtoBufLib",
    "rrcov",
    "S4Vectors",
    "snow"
  ],
  "_vignettes": [
    {
      "source": "flowmerge.Rmd",
      "filename": "flowmerge.html",
      "title": "Merging Mixture Components for Cell Population Identification in Flow Cytometry Data The flowMerge package",
      "author": "Greg Finak, Raphael Gottardo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Licensing",
        "Overview",
        "Installation",
        "Example: Cluster merging applied to the Rituximab data set",
        "The core function  \\label",
        "Parallel computations with the snow package",
        "Recent updates",
        "Upcoming improvements",
        "Frequently Asked Questions"
      ],
      "created": "2019-04-04 17:56:01",
      "modified": "2019-04-04 17:56:01",
      "commits": 1
    }
  ],
  "_score": 4.556302500767288,
  "_indexed": false,
  "_nocasepkg": "flowmerge",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/flowMerge",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.60.0",
      "date": "2026-09-16T07:12:11.000Z",
      "distro": "resolute",
      "commit": "06164744cb18ceedd92fdd46912f240a7063fb33",
      "fileid": "https://r2.ropensci.org/982e7428f250a51080349165f46d6a8db857d92696a75f597e28c7f51f495324",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35066631768"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.60.0",
      "date": "2026-09-16T07:12:16.000Z",
      "distro": "resolute",
      "commit": "06164744cb18ceedd92fdd46912f240a7063fb33",
      "fileid": "https://r2.ropensci.org/7cbbd380eb4d58dd23aa6edfa75f2edd56b7ae8eb001a8ba090ee9a4a01b98e2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35066631768"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.60.0",
      "date": "2026-09-16T07:45:17.000Z",
      "commit": "06164744cb18ceedd92fdd46912f240a7063fb33",
      "fileid": "https://r2.ropensci.org/e768c527b7178bd81aca6860dfb871e4360667fd36af9783967b8cc095a609b5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35066631768"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.60.0",
      "date": "2026-09-16T07:43:54.000Z",
      "commit": "06164744cb18ceedd92fdd46912f240a7063fb33",
      "fileid": "https://r2.ropensci.org/e09ad782c5d7b3a98b7cf1c549665a8b2376d004bc49c1b53b93a43f66e1f341",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35066631768"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.60.0",
      "date": "2026-09-16T07:10:47.000Z",
      "commit": "06164744cb18ceedd92fdd46912f240a7063fb33",
      "fileid": "https://r2.ropensci.org/8f94f80c52c1d53317f4b520135347ae12d926e98752724870080cbbb008fe25",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35066631768"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.60.0",
      "date": "2026-09-16T07:10:00.000Z",
      "commit": "06164744cb18ceedd92fdd46912f240a7063fb33",
      "fileid": "https://r2.ropensci.org/86a46ba586b4d0ebcd8871ad682ed917c917689d1a146a5e9674fde49355cbec",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35066631768"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.60.0",
      "date": "2026-09-16T07:09:47.000Z",
      "commit": "06164744cb18ceedd92fdd46912f240a7063fb33",
      "fileid": "https://r2.ropensci.org/3bdc3c4bc57e4e623ad8a53acbbfdd6033c13a2d5784b2ae3fdf91ea30f387df",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35066631768"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.60.0",
      "date": "2026-09-16T07:09:47.000Z",
      "commit": "06164744cb18ceedd92fdd46912f240a7063fb33",
      "fileid": "https://r2.ropensci.org/2b4138b153155014d4bed3a8cff05946557dc9c23ca9dd460260590f8c2a2ded",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35066631768"
    }
  ]
}