{
  "_id": "6aab91393d719c1f8406bc3b",
  "Package": "flowBin",
  "Type": "Package",
  "Title": "Combining multitube flow cytometry data by binning",
  "Version": "1.48.0",
  "Date": "2013-5-11",
  "Author": "Kieran O'Neill",
  "Maintainer": "Kieran O'Neill <koneill@bccrc.ca>",
  "Description": "Software to combine flow cytometry data that has been\nmultiplexed into multiple tubes with common markers between\nthem, by establishing common bins across tubes in terms of the\ncommon markers, then determining expression within each tube\nfor each bin in terms of the tube-specific markers.",
  "License": "Artistic-2.0",
  "LazyLoad": "yes",
  "biocViews": "ImmunoOncology, CellBasedAssays, FlowCytometry",
  "Collate": "'AllClasses.R' 'AllGenerics.R' 'BinnedFlowSample-accessors.R'\n'checkQNorm.R' 'flowBin.R' 'flowFPBin.R'\n'FlowSample-accessors.R' 'getBinExpr.R' 'kMeansBin.R'\n'mapClustersKNN.R' 'quantileNormalise.R' 'removeSparseBins.R'",
  "Config/pak/sysreqs": "libjpeg-dev libpng-dev libssl-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:38:30 UTC",
  "RemoteUrl": "https://github.com/bioc/flowBin",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-17 07:00:56 UTC",
    "User": "root"
  },
  "_user": "bioc-release",
  "_type": "src",
  "_file": "flowBin_1.48.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d6ca0971c9688d6db8a3f14673b50950f7b841f10bb74e0811a83536f6a8c5c5",
  "_filesize": 610020,
  "_sha256": "d6ca0971c9688d6db8a3f14673b50950f7b841f10bb74e0811a83536f6a8c5c5",
  "_expires": "2026-12-26T07:05:27.000Z",
  "_created": "2026-09-17T07:00:56.000Z",
  "_published": "2026-09-17T07:05:29.708Z",
  "_bioccheck": {
    "error": 3,
    "warning": 6,
    "note": 15
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35192170600",
  "_status": "success",
  "_upstream": "https://github.com/bioc/flowBin",
  "_commit": {
    "id": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
    "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": 1777379910
  },
  "_maintainer": {
    "name": "Kieran ONeill",
    "email": "koneill@bccrc.ca"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 105107977938,
      "time": 188,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10485056189"
    },
    {
      "job": 105107977909,
      "time": 222,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10484811603"
    },
    {
      "job": 105107977939,
      "time": 204,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10485180265"
    },
    {
      "job": 105107978090,
      "time": 106,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10485090407"
    },
    {
      "job": 105107978071,
      "time": 167,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10484676924"
    },
    {
      "job": 105107036020,
      "time": 223,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10484671433"
    },
    {
      "job": 105107977968,
      "time": 127,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10484467540"
    },
    {
      "job": 105107978015,
      "time": 136,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10485010497"
    },
    {
      "job": 105107978006,
      "time": 138,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10484507343"
    },
    {
      "job": 105107978135,
      "time": 132,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10484472550"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "flowCore",
      "role": "Depends"
    },
    {
      "package": "flowFP",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "class",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "snow",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.49.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.48.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "cellbasedassays",
    "flowcytometry"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 467,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 530,
    "source": "https://www.bioconductor.org/packages/stats/bioc/flowBin"
  },
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/flowBin.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bin.labels",
    "bin.labels<-",
    "bin.pars",
    "bin.pars<-",
    "checkQNorm",
    "control.tubes",
    "control.tubes<-",
    "eventsInBins",
    "flowBin",
    "flowFPBin",
    "getBinExpr",
    "kMeansBin",
    "mapBinsKNN",
    "measure.pars",
    "measure.pars<-",
    "name",
    "name<-",
    "quantileNormalise",
    "removeSparseBins",
    "show",
    "tube.set",
    "tube.set<-"
  ],
  "_datasets": [
    {
      "name": "aml.sample",
      "title": "Multitube AML sample as example data for flowBin",
      "object": "amlsample",
      "file": "amlsample.rda",
      "class": [
        "FlowSample"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "amlsample",
      "title": "Multitube AML sample as example data for flowBin",
      "topics": [
        "aml.sample",
        "amlsample"
      ]
    },
    {
      "page": "BinnedFlowSample",
      "title": "A 'FlowSample', but with binning information for each tube",
      "topics": [
        "bin.labels",
        "bin.labels,BinnedFlowSample-method",
        "bin.labels<-",
        "bin.labels<-,BinnedFlowSample,list-method",
        "BinnedFlowSample",
        "BinnedFlowSample-class"
      ]
    },
    {
      "page": "checkQNorm",
      "title": "Function to check the quantile normalisation of a FlowSample using flowFP",
      "topics": [
        "checkQNorm",
        "checkQNorm,",
        "checkQNorm,FlowSample,FlowSample-method"
      ]
    },
    {
      "page": "eventsInBins",
      "title": "Count number of events for each tube in each bin",
      "topics": [
        "eventsInBins",
        "eventsInBins,BinnedFlowSample-method"
      ]
    },
    {
      "page": "flowBin",
      "title": "function to run the entire flowBin pipeline",
      "topics": [
        "flowbin-package",
        "flowBin"
      ]
    },
    {
      "page": "flowFPBin",
      "title": "Bin sample using flowFP binning",
      "topics": [
        "flowFPBin",
        "flowFPBin,FlowSample-method"
      ]
    },
    {
      "page": "FlowSample",
      "title": "A class similar to flowSet, but with extra information needed by flowBin",
      "topics": [
        "bin.pars",
        "bin.pars,FlowSample-method",
        "bin.pars<-",
        "bin.pars<-,FlowSample,vector-method",
        "control.tubes",
        "control.tubes,FlowSample-method",
        "control.tubes<-",
        "control.tubes<-,FlowSample,vector-method",
        "FlowSample",
        "FlowSample-class",
        "measure.pars",
        "measure.pars,FlowSample-method",
        "measure.pars<-",
        "measure.pars<-,FlowSample,list-method",
        "name",
        "name,FlowSample-method",
        "name<-",
        "name<-,FlowSample,character-method",
        "show,FlowSample-method",
        "tube.set",
        "tube.set,FlowSample-method",
        "tube.set<-",
        "tube.set<-,FlowSample,list-method"
      ]
    },
    {
      "page": "getBinExpr",
      "title": "Calculate the expression of each bin in a BinnedFlowSample in terms of the measurement markers",
      "topics": [
        "getBinExpr",
        "getBinExpr,BinnedFlowSample-method"
      ]
    },
    {
      "page": "kMeansBin",
      "title": "Bin sample using K-means binning",
      "topics": [
        "kMeansBin",
        "kMeansBin,FlowSample-method"
      ]
    },
    {
      "page": "mapBinsKNN",
      "title": "Internal function to map bins by KNN",
      "topics": [
        "mapBinsKNN",
        "mapBinsKNN,FlowSample-method"
      ]
    },
    {
      "page": "quantileNormalise",
      "title": "quantileNormalise normalise binning paramaters across all tubes of a flowSample",
      "topics": [
        "quantileNormalise",
        "quantileNormalise,FlowSample-method"
      ]
    },
    {
      "page": "removeSparseBins",
      "title": "Remove bins from a BinnedFlowSample with few events in them",
      "topics": [
        "removeSparseBins",
        "removeSparseBins,BinnedFlowSample-method"
      ]
    },
    {
      "page": "show-methods",
      "title": "Methods to view flowBin objects",
      "topics": [
        "show,BinnedFlowExprSet-method",
        "show,CVResult-method",
        "show-methods"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "Biobase",
    "BiocGenerics",
    "biocmake",
    "class",
    "cpp11",
    "cytolib",
    "deldir",
    "dir.expiry",
    "filelock",
    "flowCore",
    "flowFP",
    "flowViz",
    "generics",
    "hexbin",
    "IDPmisc",
    "interp",
    "jpeg",
    "KernSmooth",
    "lattice",
    "latticeExtra",
    "limma",
    "MASS",
    "matrixStats",
    "png",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "Rhdf5lib",
    "RProtoBufLib",
    "S4Vectors",
    "snow",
    "statmod"
  ],
  "_vignettes": [
    {
      "source": "flowBin.Rnw",
      "filename": "flowBin.pdf",
      "title": "flowBin",
      "engine": "utils::Sweave",
      "headings": [
        "Licensing",
        "Introduction",
        "An example of constructing a flowExprSet de novo",
        "Looking a little more closly at the example data",
        "Quantile normalisation",
        "Running flowBin"
      ],
      "created": "2013-12-19 23:25:31",
      "modified": "2014-06-26 21:18:49",
      "commits": 2
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": false,
  "_nocasepkg": "flowbin",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/flowBin",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.48.0",
      "date": "2026-09-17T07:04:01.000Z",
      "distro": "resolute",
      "commit": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
      "fileid": "https://r2.ropensci.org/917cd7f04c65b13c75a8e397c00fe47826c7059cf1b49d78969fb33f6a6017bf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35192170600"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.48.0",
      "date": "2026-09-17T07:03:47.000Z",
      "distro": "resolute",
      "commit": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
      "fileid": "https://r2.ropensci.org/74b33d58d6e7dc6b05a158beb06de15ddda78f4f3e9a67680cc7aafe0288ff34",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35192170600"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.48.0",
      "date": "2026-09-17T07:03:20.000Z",
      "commit": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
      "fileid": "https://r2.ropensci.org/e4fda87750fbd43a96df026086ea13740505f3ceb2572ba7180effc447b619b1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35192170600"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.48.0",
      "date": "2026-09-17T07:03:56.000Z",
      "commit": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
      "fileid": "https://r2.ropensci.org/5f0e7cee15cd0206259c447cf97a52a9cd929aa2bd9048b00162676e8941d39a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35192170600"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.48.0",
      "date": "2026-09-17T07:03:22.000Z",
      "commit": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
      "fileid": "https://r2.ropensci.org/4de14356daeebf93bad98351026b9020a4903b02af5bf825fb004d0feb62f27c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35192170600"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.48.0",
      "date": "2026-09-17T07:02:28.000Z",
      "commit": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
      "fileid": "https://r2.ropensci.org/ece3cefbf932f1c3048271e4f759bc8e7f5e26d9649b602c854f93d3dcb3e4e3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35192170600"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.48.0",
      "date": "2026-09-17T07:02:29.000Z",
      "commit": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
      "fileid": "https://r2.ropensci.org/7d16b2f7ea0ec8a99eca10ac5309373995c91a848be2fd9b8425253a544be720",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35192170600"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.48.0",
      "date": "2026-09-17T07:02:29.000Z",
      "commit": "e7f17861f4fd1b69866728bc149311b5fe3b3a60",
      "fileid": "https://r2.ropensci.org/d3fc765780a8e4f1c77021d07b5496ab0b06cf16c0f336f8173d36d365e5af87",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35192170600"
    }
  ]
}