{
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  "Package": "flowFP",
  "Type": "Package",
  "Title": "Fingerprinting for Flow Cytometry",
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  "Author": "Herb Holyst <holyst@pennmedicine.upenn.edu>, Wade Rogers\n<wade.rogers@spcytomics.com>",
  "Date": "2009",
  "Maintainer": "Herb Holyst <holyst@pennmedicine.upenn.edu>, Wade Rogers\n<wade.rogers@spcytomics.com>",
  "Description": "Fingerprint generation of flow cytometry data, used to\nfacilitate the application of machine learning and datamining\ntools for flow cytometry.",
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  "LazyLoad": "TRUE",
  "License": "Artistic-2.0",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "cellbasedassays",
    "clustering",
    "visualization"
  ],
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    "type": "organization",
    "name": "Bioconductor",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
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  "_exports": [
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    "binBoundary",
    "counts",
    "flowFP",
    "flowFPModel",
    "flowFPPlex",
    "hasClasses",
    "is.flowFP",
    "is.flowFPModel",
    "is.flowFPPlex",
    "name",
    "nFeatures",
    "nInstances",
    "nRecursions",
    "nRecursions<-",
    "parameters",
    "plot",
    "sampleClasses",
    "sampleClasses<-",
    "sampleNames",
    "show",
    "summary",
    "tags"
  ],
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    {
      "name": "fs1",
      "title": "Example FCS flowSet",
      "object": "fs1",
      "file": "fs1.rda",
      "class": [
        "flowSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "fs2",
      "title": "Example FCS flowSet",
      "object": "fs2",
      "file": "fs2.rda",
      "class": [
        "flowSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "plate",
      "title": "96 well plate data.",
      "object": "plate",
      "file": "plate.rda",
      "class": [
        "flowSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "flowFP-package",
      "title": "Package overview",
      "topics": [
        "flowFP-package"
      ]
    },
    {
      "page": "index-methods",
      "title": "Indexing methods for flowFP and flowFPPlex",
      "topics": [
        "[,flowFP,character-method",
        "[,flowFP,numeric-method",
        "[,flowFPPlex,ANY-method",
        "[-methods",
        "[[,flowFPPlex,ANY-method",
        "[[-methods",
        "[[<-,flowFPPlex,numeric,ANY,flowFP-method"
      ]
    },
    {
      "page": "append-methods",
      "title": "Methods to append flowFP fingerprints to a flowFPPlex",
      "topics": [
        "append,flowFPPlex,flowFP-method",
        "append,flowFPPlex,flowFPPlex-method",
        "append,flowFPPlex,list-method",
        "append-methods"
      ]
    },
    {
      "page": "binBoundary-methods",
      "title": "Return bin boundaries for a flowFPModel",
      "topics": [
        "binBoundary",
        "binBoundary,flowFP-method",
        "binBoundary,flowFPModel-method",
        "binBoundary-methods"
      ]
    },
    {
      "page": "counts-methods",
      "title": "Method for getting fingerprint data.",
      "topics": [
        "counts",
        "counts,flowFP-method",
        "counts,flowFPPlex-method"
      ]
    },
    {
      "page": "flowFP",
      "title": "Fingerprint constructor",
      "topics": [
        "flowFP"
      ]
    },
    {
      "page": "flowFP-class",
      "title": "Fingerprint class description.",
      "topics": [
        "flowFP-class"
      ]
    },
    {
      "page": "flowFPModel",
      "title": "Fingerprint model constructor",
      "topics": [
        "flowFPModel"
      ]
    },
    {
      "page": "flowFPModel-class",
      "title": "Fingerprint model class description.",
      "topics": [
        "flowFPModel-class"
      ]
    },
    {
      "page": "flowFPPlex",
      "title": "Fingerprint collection constructor.",
      "topics": [
        "flowFPPlex"
      ]
    },
    {
      "page": "flowFPPlex-class",
      "title": "Fingerprint collection class description.",
      "topics": [
        "flowFPPlex-class"
      ]
    },
    {
      "page": "fs1",
      "title": "Example FCS flowSet",
      "topics": [
        "fs1"
      ]
    },
    {
      "page": "fs2",
      "title": "Example FCS flowSet",
      "topics": [
        "fs2"
      ]
    },
    {
      "page": "hasClasses-methods",
      "title": "Returns TRUE if the flowFP has a class factor for its instances",
      "topics": [
        "hasClasses",
        "hasClasses,flowFP-method",
        "hasClasses,flowFPPlex-method",
        "hasClasses-methods"
      ]
    },
    {
      "page": "is.flowFP",
      "title": "Test to see if object is a flowFP",
      "topics": [
        "is.flowFP"
      ]
    },
    {
      "page": "is.flowFPModel",
      "title": "Test to see if object is a flowFPModel",
      "topics": [
        "is.flowFPModel"
      ]
    },
    {
      "page": "is.flowFPPlex",
      "title": "Test to see if object is a flowFPPlex",
      "topics": [
        "is.flowFPPlex"
      ]
    },
    {
      "page": "length-methods",
      "title": "The number of fingerprints in a flowFPPlex",
      "topics": [
        "length,flowFPPlex-method",
        "length-methods",
        "length<-,flowFPPlex,numeric-method"
      ]
    },
    {
      "page": "name-methods",
      "title": "Get Model Name",
      "topics": [
        "name",
        "name,flowFP-method",
        "name,flowFPModel-method",
        "name,flowFPPlex-method",
        "name-methods"
      ]
    },
    {
      "page": "nFeatures-methods",
      "title": "Returns the number of features in an object.",
      "topics": [
        "nFeatures",
        "nFeatures,flowFP-method",
        "nFeatures,flowFPModel-method",
        "nFeatures,flowFPPlex-method",
        "nFeatures-methods"
      ]
    },
    {
      "page": "nInstances-methods",
      "title": "Returns the number of instances in an object.",
      "topics": [
        "nInstances",
        "nInstances,flowFP-method",
        "nInstances,flowFPPlex-method",
        "nInstances-methods"
      ]
    },
    {
      "page": "nRecursions-methods",
      "title": "Methods to set or get nRecursions",
      "topics": [
        "nRecursions",
        "nRecursions,flowFP-method",
        "nRecursions,flowFPModel-method",
        "nRecursions,flowFPPlex-method",
        "nRecursions-methods",
        "nRecursions<-",
        "nRecursions<-,flowFP,numeric-method",
        "nRecursions<-,flowFPModel,numeric-method"
      ]
    },
    {
      "page": "parameters-methods",
      "title": "Return the parameters considered for fingerprinting",
      "topics": [
        "parameters,flowFP-method",
        "parameters,flowFPModel-method",
        "parameters-methods"
      ]
    },
    {
      "page": "plate",
      "title": "96 well plate data.",
      "topics": [
        "plate"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Methods for visualizing flowFP objects",
      "topics": [
        "plot,flowFP,flowFrame-method",
        "plot,flowFP,flowSet-method",
        "plot,flowFP,missing-method",
        "plot,flowFPModel,flowFrame-method",
        "plot,flowFPModel,flowSet-method",
        "plot,flowFPModel,missing-method",
        "plot,flowFPPlex,missing-method",
        "plot-methods"
      ]
    },
    {
      "page": "sampleClasses-methods",
      "title": "Gets/Sets the sample classes for a fingerprint.",
      "topics": [
        "sampleClasses",
        "sampleClasses,flowFP-method",
        "sampleClasses,flowFPPlex-method",
        "sampleClasses-methods",
        "sampleClasses<-",
        "sampleClasses<-,flowFP-method",
        "sampleClasses<-,flowFPPlex-method"
      ]
    },
    {
      "page": "sampleNames-methods",
      "title": "Methods to return sample names from a flowFP object.",
      "topics": [
        "sampleNames",
        "sampleNames,flowFP-method",
        "sampleNames,flowFPPlex-method",
        "sampleNames-methods"
      ]
    },
    {
      "page": "show-methods",
      "title": "Methods to view flowFP objects",
      "topics": [
        "show,flowFP-method",
        "show,flowFPModel-method",
        "show,flowFPPlex-method",
        "show-methods"
      ]
    },
    {
      "page": "summary-methods",
      "title": "Summerizes a flowFP object.",
      "topics": [
        "summary,flowFP-method",
        "summary-methods"
      ]
    },
    {
      "page": "tags-methods",
      "title": "Returns tags from a flowFP object.",
      "topics": [
        "tags",
        "tags,flowFP-method",
        "tags-methods"
      ]
    }
  ],
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      "source": "flowFP_HowTo.Rnw",
      "filename": "flowFP_HowTo.pdf",
      "title": "Fingerprinting for Flow Cytometry",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Algorithm Description",
        "Fingerprint Representation",
        "Fingerprinting for Gating Quality Control",
        "Limitations, Caveats and Comments",
        "Acknowledgements"
      ],
      "created": "2013-11-01 20:09:09",
      "modified": "2013-11-01 20:09:09",
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