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  "Title": "A Versatile Toolkit for Copy Number Variation Relationship Data\nAnalysis and Visualization",
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  "Author": "James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer",
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    "calcCNVKernelProbDist",
    "calcVecLMs",
    "CNVScopeserver",
    "createChromosomalMatrixSet",
    "divisors",
    "downsample_genomic_matrix",
    "extractNegLogPval",
    "formSampleMatrixFromRawGDCData",
    "freadGDCfile",
    "getAnnotationMatrix",
    "getAsymmetricBlockIndices",
    "getBlockAverageMatrixFromBreakpoints",
    "getGlobalRescalingStats",
    "getInterchromosomalInteractivePlot",
    "GRanges_to_underscored_pos",
    "importBreakpointBed",
    "mathead",
    "postProcessLinRegMatrix",
    "rebinGenomicInteractions",
    "runCNVScopeLocal",
    "runCNVScopeShiny",
    "signedRescale",
    "underscored_pos_to_GRanges",
    "writeAsymmetricMeltedChromosomalMatrixToDisk",
    "writeMeltedChromosomalMatrixToDisk"
  ],
  "_datasets": [
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      "name": "nbl_result_matrix_sign_small",
      "title": "Neuroblastoma sample CNV relationship matrix",
      "object": "nbl_result_matrix_sign_small",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "chr1_1_1000000",
        "chr1_1000001_2000000",
        "chr1_2000001_3000000",
        "chr1_3000001_4000000",
        "chr1_4000001_5000000",
        "chr1_5000001_6000000",
        "chr1_6000001_7000000",
        "chr1_7000001_8000000",
        "chr1_8000001_9000000",
        "chr1_9000001_10000000",
        "chr1_10000001_11000000",
        "chr1_11000001_12000000",
        "chr1_12000001_13000000",
        "chr1_13000001_14000000",
        "chr1_14000001_15000000",
        "chr1_15000001_16000000",
        "chr1_16000001_17000000",
        "chr1_17000001_18000000",
        "chr1_18000001_19000000",
        "chr1_19000001_20000000",
        "chr1_20000001_21000000",
        "chr1_21000001_22000000",
        "chr1_22000001_23000000",
        "chr1_23000001_24000000",
        "chr1_24000001_25000000"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "averageMatrixEdges",
      "title": "Average edges of a matrix to facilitate downsampling.",
      "topics": [
        "averageMatrixEdges"
      ]
    },
    {
      "page": "calcCNVKernelProbDist",
      "title": "Calculate the probability distribution of CNV concordance events with a fast kernel",
      "topics": [
        "calcCNVKernelProbDist"
      ]
    },
    {
      "page": "calcVecLMs",
      "title": "Create a linear regression matrix.",
      "topics": [
        "calcVecLMs"
      ]
    },
    {
      "page": "CNVScopeserver",
      "title": "Server component of the CNVScope plotly shiny application.",
      "topics": [
        "CNVScopeserver"
      ]
    },
    {
      "page": "createChromosomalMatrixSet",
      "title": "Create chromosomal interaction matrices for CNVScope shiny application.",
      "topics": [
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      ]
    },
    {
      "page": "divisors",
      "title": "List of Divisors",
      "topics": [
        "divisors"
      ]
    },
    {
      "page": "downsample_genomic_matrix",
      "title": "Rescale positive and negative data, preserving sign information.",
      "topics": [
        "downsample_genomic_matrix"
      ]
    },
    {
      "page": "extractNegLogPval",
      "title": "Find the negative log p-value of a pair of vectors.",
      "topics": [
        "extractNegLogPval"
      ]
    },
    {
      "page": "formSampleMatrixFromRawGDCData",
      "title": "Form sample matrix from GDC copy number data files.",
      "topics": [
        "formSampleMatrixFromRawGDCData"
      ]
    },
    {
      "page": "freadGDCfile",
      "title": "Read GDC segmentation datafile for low-pass sequencing data.",
      "topics": [
        "freadGDCfile"
      ]
    },
    {
      "page": "getAnnotationMatrix",
      "title": "Get the genes in the genomic ranges indicated by the row and column labels.",
      "topics": [
        "getAnnotationMatrix"
      ]
    },
    {
      "page": "getAsymmetricBlockIndices",
      "title": "Get Block Indices from an asymmetric (or symmetric) matrix.",
      "topics": [
        "getAsymmetricBlockIndices"
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    },
    {
      "page": "getBlockAverageMatrixFromBreakpoints",
      "title": "Calculate block averages and areas in a matrix given breakpoints.",
      "topics": [
        "getBlockAverageMatrixFromBreakpoints"
      ]
    },
    {
      "page": "getGlobalRescalingStats",
      "title": "Calculate several base statistics for color rescaling.",
      "topics": [
        "getGlobalRescalingStats"
      ]
    },
    {
      "page": "getInterchromosomalInteractivePlot",
      "title": "Create an HTML widget for use in shiny or webshot for a given pair of chromosomes.",
      "topics": [
        "getInterchromosomalInteractivePlot"
      ]
    },
    {
      "page": "GRanges_to_underscored_pos",
      "title": "Convert GRanges object to underscord positions.",
      "topics": [
        "GRanges_to_underscored_pos"
      ]
    },
    {
      "page": "importBreakpointBed",
      "title": "Import a breakpoint BED file.",
      "topics": [
        "importBreakpointBed"
      ]
    },
    {
      "page": "mathead",
      "title": "Gets a small piece of a matrix (top left corner) for viewing, rather than pulling the first n rows.",
      "topics": [
        "mathead"
      ]
    },
    {
      "page": "nbl_result_matrix_sign_small",
      "title": "Neuroblastoma sample CNV relationship matrix",
      "topics": [
        "nbl_result_matrix_sign_small"
      ]
    },
    {
      "page": "postProcessLinRegMatrix",
      "title": "Postprocess linear regression matrix.",
      "topics": [
        "postProcessLinRegMatrix"
      ]
    },
    {
      "page": "rebinGenomicInteractions",
      "title": "Assign GenomicInteractions to a predefined series of bins for row and column, corresponding to a genomic matrix.",
      "topics": [
        "rebinGenomicInteractions"
      ]
    },
    {
      "page": "runCNVScopeLocal",
      "title": "Runs the CNVScope plotly shiny application.",
      "topics": [
        "runCNVScopeLocal"
      ]
    },
    {
      "page": "runCNVScopeShiny",
      "title": "Runs the CNVScope plotly shiny application.",
      "topics": [
        "runCNVScopeShiny"
      ]
    },
    {
      "page": "signedRescale",
      "title": "Rescale positive and negative data, preserving sign information.",
      "topics": [
        "signedRescale"
      ]
    },
    {
      "page": "underscored_pos_to_GRanges",
      "title": "Convert coordinates in underscored format to a GRanges object.",
      "topics": [
        "underscored_pos_to_GRanges"
      ]
    },
    {
      "page": "writeAsymmetricMeltedChromosomalMatrixToDisk",
      "title": "Write a matrix, with genes, of a submatrix of a whole genome interaction matrix to disk.",
      "topics": [
        "writeAsymmetricMeltedChromosomalMatrixToDisk"
      ]
    },
    {
      "page": "writeMeltedChromosomalMatrixToDisk",
      "title": "Write a matrix, with genes, of a submatrix of a whole genome interaction matrix to disk.",
      "topics": [
        "writeMeltedChromosomalMatrixToDisk"
      ]
    }
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