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  "Title": "Automated Deconvolution Augmentation of Profiles for Tissue\nSpecific Cells",
  "Version": "1.0.22",
  "Author": "Samuel A Danziger",
  "Maintainer": "Samuel A Danziger <sam.danziger@gmail.com>",
  "Copyright": "Bristol-Myers Squibb",
  "Description": "Tools to construct (or add to) cell-type signature\nmatrices using flow sorted or single cell samples and\ndeconvolve bulk gene expression data. Useful for assessing the\nquality of single cell RNAseq experiments, estimating the\naccuracy of signature matrices, and determining cell-type\nspillover. Please cite: Danziger SA et al. (2019) ADAPTS:\nAutomated Deconvolution Augmentation of Profiles for Tissue\nSpecific cells <doi:10.1371/journal.pone.0224693>.",
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    "buildSeed",
    "buildSpilloverMat",
    "calcAcc",
    "clustWspillOver",
    "collapseCellTypes",
    "estCellCounts.nPass",
    "estCellPercent",
    "estCellPercent.DCQ",
    "estCellPercent.DeconRNASeq",
    "estCellPercent.nnls",
    "estCellPercent.proportionsInAdmixture",
    "estCellPercent.spillOver",
    "estCellPercent.svmdecon",
    "getF1mcc",
    "getLM22cells",
    "gListFromRF",
    "hierarchicalClassify",
    "hierarchicalSplit",
    "loadMGSM27",
    "loadModMap",
    "loopTillConvergence",
    "matrixToGenelist",
    "meanResults",
    "missForest.par",
    "plotKappas",
    "rankByT",
    "remakeLM22p",
    "scSample",
    "shrinkByKappa",
    "shrinkSigMatrix",
    "spillToConvergence",
    "splitSCdata",
    "testAllSigMatrices"
  ],
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      "name": "Licenses",
      "title": "Licenses required by Celgene legal",
      "object": "Licenses",
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      "table": false,
      "tojson": true
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      "title": "Leukocyte 22 data matrix",
      "object": "LM22",
      "class": [
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      ],
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        "B.cells.memory",
        "Plasma.cells",
        "T.cells.CD8",
        "T.cells.CD4.naive",
        "T.cells.CD4.memory.resting",
        "T.cells.CD4.memory.activated",
        "T.cells.follicular.helper",
        "T.cells.regulatory..Tregs.",
        "T.cells.gamma.delta",
        "NK.cells.resting",
        "NK.cells.activated",
        "Monocytes",
        "Macrophages.M0",
        "Macrophages.M1",
        "Macrophages.M2",
        "Dendritic.cells.resting",
        "Dendritic.cells.activated",
        "Mast.cells.resting",
        "Mast.cells.activated",
        "Eosinophils",
        "Neutrophils"
      ],
      "rows": 547,
      "table": true,
      "tojson": true
    },
    {
      "name": "MGSM27",
      "title": "Myeloma Genome Signature Matrix 27",
      "object": "MGSM27",
      "class": [
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      ],
      "fields": [
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        "B.cells.memory",
        "Plasma.cells",
        "T.cells.CD8",
        "T.cells.CD4.naive",
        "T.cells.CD4.memory.resting",
        "T.cells.CD4.memory.activated",
        "T.cells.follicular.helper",
        "T.cells.regulatory..Tregs.",
        "T.cells.gamma.delta",
        "NK.cells.resting",
        "NK.cells.activated",
        "Monocytes",
        "Macrophages.M0",
        "Macrophages.M1",
        "Macrophages.M2",
        "Dendritic.cells.resting",
        "Dendritic.cells.activated",
        "Mast.cells.resting",
        "Mast.cells.activated",
        "Eosinophils",
        "Neutrophils",
        "MM.plasma.cell",
        "osteoblast",
        "osteoclast",
        "PlasmaMemory",
        "adipocyte"
      ],
      "rows": 601,
      "table": true,
      "tojson": true
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      "page": "AugmentSigMatrix",
      "title": "Make an augmented signature matrix",
      "topics": [
        "AugmentSigMatrix"
      ]
    },
    {
      "page": "buildSeed",
      "title": "Build a deconvolution seed matrix, add the proportional option",
      "topics": [
        "buildSeed"
      ]
    },
    {
      "page": "buildSpilloverMat",
      "title": "Build a spillover matrix",
      "topics": [
        "buildSpilloverMat"
      ]
    },
    {
      "page": "calcAcc",
      "title": "Calculate prediction accuracy",
      "topics": [
        "calcAcc"
      ]
    },
    {
      "page": "clustWspillOver",
      "title": "Cluster with spillover",
      "topics": [
        "clustWspillOver"
      ]
    },
    {
      "page": "collapseCellTypes",
      "title": "Collapse cell types",
      "topics": [
        "collapseCellTypes"
      ]
    },
    {
      "page": "estCellCounts.nPass",
      "title": "Deconvolve with an n-pass spillover matrix",
      "topics": [
        "estCellCounts.nPass"
      ]
    },
    {
      "page": "estCellPercent",
      "title": "Wrapper for deconvolution methods",
      "topics": [
        "estCellPercent"
      ]
    },
    {
      "page": "estCellPercent.DCQ",
      "title": "DCQ Deconvolution",
      "topics": [
        "estCellPercent.DCQ"
      ]
    },
    {
      "page": "estCellPercent.DeconRNASeq",
      "title": "DeconRNASeq deconvolution",
      "topics": [
        "estCellPercent.DeconRNASeq"
      ]
    },
    {
      "page": "estCellPercent.nnls",
      "title": "Non-negative least squares deconvolution",
      "topics": [
        "estCellPercent.nnls"
      ]
    },
    {
      "page": "estCellPercent.proportionsInAdmixture",
      "title": "WGCNA::proportionsInAdmixture deconvolution",
      "topics": [
        "estCellPercent.proportionsInAdmixture"
      ]
    },
    {
      "page": "estCellPercent.spillOver",
      "title": "Estimate cell percentage from spillover",
      "topics": [
        "estCellPercent.spillOver"
      ]
    },
    {
      "page": "estCellPercent.svmdecon",
      "title": "SVMDECON deconvolution",
      "topics": [
        "estCellPercent.svmdecon"
      ]
    },
    {
      "page": "findConvergenceIter",
      "title": "Find out at which iteration the results converge, i.e. the mean results are stable.",
      "topics": [
        "findConvergenceIter"
      ]
    },
    {
      "page": "getF1mcc",
      "title": "Get f1 / mcc",
      "topics": [
        "getF1mcc"
      ]
    },
    {
      "page": "getLM22cells",
      "title": "LM22 look up table",
      "topics": [
        "getLM22cells"
      ]
    },
    {
      "page": "gListFromRF",
      "title": "Build a gList using random forest",
      "topics": [
        "gListFromRF"
      ]
    },
    {
      "page": "hierarchicalClassify",
      "title": "Hierarchical Deconvolution",
      "topics": [
        "hierarchicalClassify"
      ]
    },
    {
      "page": "hierarchicalSplit",
      "title": "Build hierarchical cell clusters.",
      "topics": [
        "hierarchicalSplit"
      ]
    },
    {
      "page": "licenses",
      "title": "Licenses required by Celgene legal",
      "topics": [
        "Licenses"
      ]
    },
    {
      "page": "LM22",
      "title": "Leukocyte 22 data matrix",
      "topics": [
        "LM22"
      ]
    },
    {
      "page": "loadMGSM27",
      "title": "Load MGSM27",
      "topics": [
        "loadMGSM27"
      ]
    },
    {
      "page": "loadModMap",
      "title": "LM22 to xCell LUT",
      "topics": [
        "loadModMap"
      ]
    },
    {
      "page": "loopTillConvergence",
      "title": "Loop testAllSigMatrices until convergence",
      "topics": [
        "loopTillConvergence"
      ]
    },
    {
      "page": "matrixToGenelist",
      "title": "Make a GSVA genelist",
      "topics": [
        "matrixToGenelist"
      ]
    },
    {
      "page": "meanResults",
      "title": "A meta analysis for the results from multiple iterations",
      "topics": [
        "meanResults"
      ]
    },
    {
      "page": "MGSM27",
      "title": "Myeloma Genome Signature Matrix 27",
      "topics": [
        "MGSM27"
      ]
    },
    {
      "page": "missForest.par",
      "title": "Use parallel missForest to impute missing values.",
      "topics": [
        "missForest.par"
      ]
    },
    {
      "page": "plotKappas",
      "title": "Plot condition numbers",
      "topics": [
        "plotKappas"
      ]
    },
    {
      "page": "rankByT",
      "title": "Rank genes for each cell type",
      "topics": [
        "rankByT"
      ]
    },
    {
      "page": "remakeLM22p",
      "title": "Make an Augmented Signature Matrix",
      "topics": [
        "remakeLM22p"
      ]
    },
    {
      "page": "scSample",
      "title": "Build groupSize pools according to cellIDs",
      "topics": [
        "scSample"
      ]
    },
    {
      "page": "shrinkByKappa",
      "title": "Calculate conditions numbers for signature subsets",
      "topics": [
        "shrinkByKappa"
      ]
    },
    {
      "page": "shrinkSigMatrix",
      "title": "Shrink a signature matrix",
      "topics": [
        "shrinkSigMatrix"
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    },
    {
      "page": "spillToConvergence",
      "title": "Spillover to convergence",
      "topics": [
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    },
    {
      "page": "splitSCdata",
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      "topics": [
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    {
      "page": "SVMDECON",
      "title": "Support vector machine deconvolution",
      "topics": [
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    },
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      "page": "testAllSigMatrices",
      "title": "Generate all the signature matrices one time with the option to leave out half of the data as a test set",
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    },
    {
      "page": "weightNorm",
      "title": "SVMDECONV helper function",
      "topics": [
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