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  "Title": "A toolkit for performing KNN-based statistics for flow and mass\ncytometry data",
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  "Author": "Tyler J Burns",
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  "Description": "This package does k-nearest neighbor based statistics and\nvisualizations with flow and mass cytometery data. This gives\ntSNE maps\"fold change\" functionality and provides a data\nquality metric by assessing manifold overlap between fcs files\nexpected to be the same. Other applications using this package\ninclude imputation, marker redundancy, and testing the relative\ninformation loss of lower dimension embeddings compared to the\noriginal manifold.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:32 UTC",
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        "pSTAT3(Gd158)Di.IL7.qvalue",
        "pAKT(Tb159)Di.IL7.qvalue",
        "pBLNK(Gd160)Di.IL7.qvalue",
        "pP38(Tm169)Di.IL7.qvalue",
        "pSTAT5(Nd150)Di.IL7.qvalue",
        "pSyk(Dy162)Di.IL7.qvalue",
        "tIkBa(Er166)Di.IL7.qvalue",
        "pCrkL(Lu175)Di.IL7.change",
        "pCREB(Yb176)Di.IL7.change",
        "pBTK(Yb171)Di.IL7.change",
        "pS6(Yb172)Di.IL7.change",
        "cPARP(La139)Di.IL7.change",
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        "pSrc(Nd144)Di.IL7.change",
        "Ki67(Sm152)Di.IL7.change",
        "pErk12(Gd155)Di.IL7.change",
        "pSTAT3(Gd158)Di.IL7.change",
        "pAKT(Tb159)Di.IL7.change",
        "pBLNK(Gd160)Di.IL7.change",
        "pP38(Tm169)Di.IL7.change",
        "pSTAT5(Nd150)Di.IL7.change",
        "pSyk(Dy162)Di.IL7.change",
        "tIkBa(Er166)Di.IL7.change",
        "IL7.fraction.cond.2",
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      "table": true,
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    }
  ],
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    {
      "page": "AddTsne",
      "title": "Add tSNE to your results.",
      "topics": [
        "AddTsne"
      ]
    },
    {
      "page": "bz.gmcsf.final",
      "title": "Bodenmiller-Zunder GM-CSF post-SCONE final data",
      "topics": [
        "bz.gmcsf.final"
      ]
    },
    {
      "page": "bz.gmcsf.final.norm.scale",
      "title": "Bodenmiller-Zunder GM-CSF post-SCONE final data, that's been quantile normalized and z scored.",
      "topics": [
        "bz.gmcsf.final.norm.scale"
      ]
    },
    {
      "page": "exist",
      "title": "Random musing",
      "topics": [
        "exist"
      ]
    },
    {
      "page": "FcsToTibble",
      "title": "Takes a file as input and returns a data frame of cells by features",
      "topics": [
        "FcsToTibble"
      ]
    },
    {
      "page": "Fnn",
      "title": "Compute knn using the fnn algorithm",
      "topics": [
        "Fnn"
      ]
    },
    {
      "page": "funct.markers",
      "title": "Functional markers from the Wanderlust dataset.",
      "topics": [
        "funct.markers"
      ]
    },
    {
      "page": "GetKnnDe",
      "title": "Get the KNN density estimaion",
      "topics": [
        "GetKnnDe"
      ]
    },
    {
      "page": "GetMarkerNames",
      "title": "Takes in an example file as input and returns all marker names",
      "topics": [
        "GetMarkerNames"
      ]
    },
    {
      "page": "Impute",
      "title": "Imputes values for all markers (used as input) for each cell",
      "topics": [
        "Impute"
      ]
    },
    {
      "page": "ImputeTesting",
      "title": "Impute testing",
      "topics": [
        "ImputeTesting"
      ]
    },
    {
      "page": "input.markers",
      "title": "Input markers for the Wanderlust dataset",
      "topics": [
        "input.markers"
      ]
    },
    {
      "page": "LogTransformQ",
      "title": "Log transform the q values",
      "topics": [
        "LogTransformQ"
      ]
    },
    {
      "page": "MakeHist",
      "title": "make.hist",
      "topics": [
        "MakeHist"
      ]
    },
    {
      "page": "MakeKnnList",
      "title": "Make list of cells by features for each KNN member",
      "topics": [
        "MakeKnnList"
      ]
    },
    {
      "page": "markers",
      "title": "Markers for the Wanderlust dataset",
      "topics": [
        "markers"
      ]
    },
    {
      "page": "MeaningOfLife",
      "title": "Meaning of life",
      "topics": [
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      ]
    },
    {
      "page": "MultipleDonorStatistics",
      "title": "Runs a t test on the medians or means of multiple donors for the same condition",
      "topics": [
        "MultipleDonorStatistics"
      ]
    },
    {
      "page": "ParseMarkers",
      "title": "Parse markers contained in a Sconify-directed marker file",
      "topics": [
        "ParseMarkers"
      ]
    },
    {
      "page": "PostProcessing",
      "title": "Post-processing for scone analysks.",
      "topics": [
        "PostProcessing"
      ]
    },
    {
      "page": "ProcessMultipleFiles",
      "title": "Converts multiple files into a concatenated data frame",
      "topics": [
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      ]
    },
    {
      "page": "QCorrectionThresholding",
      "title": "Corrects all p values for multiple hypotheses, sets threshold for which change values should be reported",
      "topics": [
        "QCorrectionThresholding"
      ]
    },
    {
      "page": "QuantNormalize",
      "title": "Performs quantile normalization on the data frame (patient) of interest",
      "topics": [
        "QuantNormalize"
      ]
    },
    {
      "page": "QuantNormalizeElements",
      "title": "Takes a list of tibbles as input, and performs per-column quantile normalization, then outputs the quantile normalized list",
      "topics": [
        "QuantNormalizeElements"
      ]
    },
    {
      "page": "RunStatistics",
      "title": "Performs a series of statistical tests on the batch of cells of interest.",
      "topics": [
        "RunStatistics"
      ]
    },
    {
      "page": "SconeValues",
      "title": "Master function for per-knn statistics functionality, integrating the other non-exported functions within this script.",
      "topics": [
        "SconeValues"
      ]
    },
    {
      "page": "SplitFile",
      "title": "Runs \"process.multiple.files\" on a single file, splits it randomly, and presends half of it is \"unstim\" and half of it is \"stim\"",
      "topics": [
        "SplitFile"
      ]
    },
    {
      "page": "StringToNumbers",
      "title": "Transform strings to numbers.",
      "topics": [
        "StringToNumbers"
      ]
    },
    {
      "page": "SubsampleAndTsne",
      "title": "Subsample data and run tSNE",
      "topics": [
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      ]
    },
    {
      "page": "TsneVis",
      "title": "Plot a tSNE map colored by a marker of interest",
      "topics": [
        "TsneVis"
      ]
    },
    {
      "page": "wand.combined",
      "title": "Wanderlust data combined basal and IL7 cells",
      "topics": [
        "wand.combined"
      ]
    },
    {
      "page": "wand.final",
      "title": "Post-scone output of the \"combiend\" Wanderlust data.",
      "topics": [
        "wand.final"
      ]
    },
    {
      "page": "wand.ideal.k",
      "title": "A named vector to help the user determine the ideal k for the Wanderlust dataset.",
      "topics": [
        "wand.ideal.k"
      ]
    },
    {
      "page": "wand.il7",
      "title": "Wanderlust IL7 data",
      "topics": [
        "wand.il7"
      ]
    },
    {
      "page": "wand.scone",
      "title": "Wanderlust scone output",
      "topics": [
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      "engine": "knitr::rmarkdown",
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      "headings": [
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