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  "Title": "ncdfFlow: A package that provides HDF5 based storage for flow\ncytometry data.",
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  "Author": "Mike Jiang,Greg Finak,N. Gopalakrishnan",
  "Description": "Provides HDF5 storage based methods and functions for\nmanipulation of flow cytometry data.",
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    "curl",
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    "colnames",
    "colnames<-",
    "compensate",
    "filter",
    "getFileName",
    "getIndices",
    "initIndices",
    "keyword",
    "keyword<-",
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    "load_ncfs",
    "markernames",
    "markernames<-",
    "ncdfFlowList",
    "ncdfFlowSet",
    "ncfsApply",
    "pData",
    "pData<-",
    "phenoData",
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    "rbind2",
    "read.ncdfFlowSet",
    "sampleNames<-",
    "save_ncfs",
    "split",
    "Subset",
    "transform",
    "unlink",
    "updateIndices"
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    {
      "page": "subset-methods",
      "title": "subsetting by sampleNames,channels(not for events) methods",
      "topics": [
        "[,ncdfFlowList,ANY-method",
        "[,ncdfFlowSet,ANY-method"
      ]
    },
    {
      "page": "extractFlowFrame",
      "title": "extract a 'flowFrame' object from 'ncdfFlowSet'",
      "topics": [
        "[[,ncdfFlowList,character,missing-method",
        "[[,ncdfFlowList,character-method",
        "[[,ncdfFlowList,logical-method",
        "[[,ncdfFlowList,numeric-method",
        "[[,ncdfFlowSet,ANY-method"
      ]
    },
    {
      "page": "as.flowSet",
      "title": "convert from a 'ncdfFlowSet' to a 'flowSet'",
      "topics": [
        "as.flowSet"
      ]
    },
    {
      "page": "clone.ncdfFlowSet",
      "title": "Clone a ncdfFlowSet",
      "topics": [
        "clone.ncdfFlowSet"
      ]
    },
    {
      "page": "flowSet-accessor",
      "title": "Accessors compatible with those for 'flowSet'",
      "topics": [
        "colnames,ncdfFlowList-method",
        "colnames<-",
        "colnames<-,ncdfFlowList-method",
        "colnames<-,ncdfFlowSet,ANY-method",
        "colnames<-,ncdfFlowSet-method",
        "compensate,flowSet,data.frame-method",
        "compensate,ncdfFlowSet,ANY-method",
        "compensate,ncdfFlowSet,list-method",
        "filter,ncdfFlowList,filter-method",
        "filter,ncdfFlowList,filterList-method",
        "filter,ncdfFlowList,list-method",
        "keyword,ncdfFlowSet,list-method",
        "keyword<-,ncdfFlowSet,list-method",
        "length,ncdfFlowList-method",
        "markernames,ncdfFlowList-method",
        "markernames<-,ncdfFlowList-method",
        "pData,ncdfFlowList-method",
        "pData<-,ncdfFlowList,data.frame-method",
        "phenoData,ncdfFlowList-method",
        "phenoData<-,ncdfFlowList,AnnotatedDataFrame-method",
        "sampleNames,ncdfFlowList-method",
        "sampleNames<-",
        "sampleNames<-,ncdfFlowSet,ANY-method",
        "transform,ncdfFlowSet-method"
      ]
    },
    {
      "page": "getFileName",
      "title": "get the cdf file name associated with ncdfFlowSet object",
      "topics": [
        "getFileName"
      ]
    },
    {
      "page": "Indices",
      "title": "'getIndices' extracts the event indices of one or multiple samples from ncdfFlowSet",
      "topics": [
        "getIndices",
        "getIndices,ncdfFlowSet,character-method",
        "initIndices",
        "initIndices,ncdfFlowSet-method",
        "updateIndices",
        "updateIndices,ncdfFlowSet,character,logical-method"
      ]
    },
    {
      "page": "lapply-methods",
      "title": "lapply method for ncdfFlowList",
      "topics": [
        "lapply,ncdfFlowList-method"
      ]
    },
    {
      "page": "ncdfFlow",
      "title": "ncdfFlow: A package that provides CDF storage based flow cytometry data analysis.",
      "topics": [
        "ncdfFlow"
      ]
    },
    {
      "page": "ncdfFlowList-class",
      "title": "a class that stores multiple ncdfFlowSet objects",
      "topics": [
        "ncdfFlowList",
        "ncdfFlowList-class",
        "show,ncdfFlowList-method"
      ]
    },
    {
      "page": "ncdfFlowSet-class",
      "title": "a class for storing flow cytometry raw data in HDF5 format",
      "topics": [
        "ncdfFlowSet-class",
        "show",
        "show,ncdfFlowSet-method"
      ]
    },
    {
      "page": "ncdfFlowSet-constructor",
      "title": "create ncdfFlowSet from flowSet",
      "topics": [
        "ncdfFlowSet",
        "ncdfFlowSet,flowSet-method"
      ]
    },
    {
      "page": "ncfsApply-ncdfFlowSet-method",
      "title": "apply method for ncdfFlowSet (for internal use)",
      "topics": [
        "ncfsApply",
        "ncfsApply,ncdfFlowSet-method"
      ]
    },
    {
      "page": "rbind2-method",
      "title": "combine multiple ncdfFlowSet objects into one",
      "topics": [
        "rbind2,ncdfFlowList,ANY-method"
      ]
    },
    {
      "page": "read.ncdfFlowSet",
      "title": "create ncdfFlowSet from FCS files",
      "topics": [
        "read.ncdfFlowSet",
        "read.ncdfFlowset"
      ]
    },
    {
      "page": "replacement-method-for-ncdfFlowSet",
      "title": "write the flow data from a 'flowFrame' to 'ncdfFlowSet' flowFrame can have less channels than ncdfFlowSet,which is used for partial updating(useful for 'normalization')",
      "topics": [
        "replacement method for ncdfFlowSet",
        "[[<-,ncdfFlowSet,ANY,ANY,flowFrame-method",
        "[[<-,ncdfFlowSet,flowFrame-method"
      ]
    },
    {
      "page": "save_ncfs",
      "title": "save/load a ncdfFlowSet object to/from disk.",
      "topics": [
        "load_ncfs",
        "save_ncfs"
      ]
    },
    {
      "page": "ncdfFlowSet-split",
      "title": "split a 'ncdfFlowSet' object.",
      "topics": [
        "split,ncdfFlowList,character-method",
        "split,ncdfFlowList,factor-method",
        "split,ncdfFlowSet,character-method",
        "split,ncdfFlowSet,factor-method",
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        "split,ncdfFlowSet,filterResultList-method",
        "split,ncdfFlowSet,list-method"
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    },
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      "topics": [
        "Subset,ncdfFlowList,filter-method",
        "Subset,ncdfFlowList,filterResultList-method",
        "Subset,ncdfFlowSet,filter-method",
        "Subset,ncdfFlowSet,filterResultList-method",
        "Subset,ncdfFlowSet,list-method"
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      "topics": [
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        "subset.ncdfFlowSet"
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      "page": "unlink-ncdfFlowSet-method",
      "title": "delete the cdf file associated with the ncdfFlowSet object ncdfFlowSet object is unrecoverable after cdf is deleted. So this method is usually called when ncdfFlowSet object is no longer in need.",
      "topics": [
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