{
  "_id": "6a494dacf6c47c4419499d9c",
  "Package": "flowBin",
  "Type": "Package",
  "Title": "Combining multitube flow cytometry data by binning",
  "Version": "1.49.0",
  "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": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:30 UTC",
  "RemoteUrl": "https://github.com/bioc/flowBin",
  "RemoteRef": "HEAD",
  "RemoteSha": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-03 22:03:12 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "flowBin_1.49.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/3d66217abf333f68fdfc4cab062b622345d80760a01ce82757ea1a5dab61b605",
  "_filesize": 609614,
  "_sha256": "3d66217abf333f68fdfc4cab062b622345d80760a01ce82757ea1a5dab61b605",
  "_expires": "2026-10-12T18:15:06.000Z",
  "_created": "2026-07-03T22:03:12.000Z",
  "_published": "2026-07-04T18:15:08.781Z",
  "_bioccheck": {
    "error": 3,
    "warning": 6,
    "note": 14
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28685124240",
  "_status": "success",
  "_upstream": "https://github.com/bioc/flowBin",
  "_commit": {
    "id": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379910
  },
  "_maintainer": {
    "name": "Kieran ONeill",
    "email": "koneill@bccrc.ca"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85155400097,
      "time": 160,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8075385666"
    },
    {
      "job": 85155400243,
      "time": 249,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8075399627"
    },
    {
      "job": 85155400307,
      "time": 231,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8075397038"
    },
    {
      "job": 85155400299,
      "time": 99,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8075375640"
    },
    {
      "job": 85155400196,
      "time": 135,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8075381742"
    },
    {
      "job": 85155400090,
      "time": 223,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8075358150"
    },
    {
      "job": 85155400130,
      "time": 151,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8075384591"
    },
    {
      "job": 85155400191,
      "time": 142,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8075382905"
    },
    {
      "job": 85155400328,
      "time": 118,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8075379168"
    },
    {
      "job": 85155400313,
      "time": 161,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8075385709"
    }
  ],
  "_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": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_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": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/flowBin.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_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": true,
  "_nocasepkg": "flowbin",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.49.0",
      "date": "2026-07-03T22:06:51.000Z",
      "distro": "resolute",
      "commit": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
      "fileid": "https://r2.ropensci.org/18119a6480af58e52109eabf9c3b56369a42fa2d16121e4c2fe4e4beb39ad14e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28685124240"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.49.0",
      "date": "2026-07-03T22:06:36.000Z",
      "distro": "resolute",
      "commit": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
      "fileid": "https://r2.ropensci.org/6f9aff7ce5ff1335cb471ad951ff3c1aecddd74329e2376f891fd34d1fa2d773",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28685124240"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.49.0",
      "date": "2026-07-03T22:04:46.000Z",
      "commit": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
      "fileid": "https://r2.ropensci.org/35af16d77e609abb703a987a6973bdf703a37e481146c4ec398ebe090c00b89d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28685124240"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.49.0",
      "date": "2026-07-03T22:05:10.000Z",
      "commit": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
      "fileid": "https://r2.ropensci.org/5ae0b091e5294ff55edaaf4d785eef0a74657de718822513fb7b3b3a1cb37ca0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28685124240"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.49.0",
      "date": "2026-07-03T22:06:08.000Z",
      "commit": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
      "fileid": "https://r2.ropensci.org/fdcc43735cba16532547f02d74dd2b5187f2481955d41e1f4d10b2ef5f8f9f98",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28685124240"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.49.0",
      "date": "2026-07-03T22:05:00.000Z",
      "commit": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
      "fileid": "https://r2.ropensci.org/dfde2db5a83a82156ccb841b0096e25eb785ddb2c789143d330de459863b1c14",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28685124240"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.49.0",
      "date": "2026-07-03T22:04:38.000Z",
      "commit": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
      "fileid": "https://r2.ropensci.org/956e497dc1fded9c4ee8f6f227a3807a720bf7e7d4106aa97a54b4cb34229521",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28685124240"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.49.0",
      "date": "2026-07-03T22:05:12.000Z",
      "commit": "16517b9134e7a469a7a09a77f8d0f51ee6c4ea68",
      "fileid": "https://r2.ropensci.org/85d4a91caef46181c2100569149c447c20f0b965b237241a7bbcc2a7c8d55380",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28685124240"
    }
  ]
}