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  "Description": "Analyze thermal proteome profiling (TPP) experiments with\nvarying temperatures (TR) or compound concentrations (CCR).",
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    "analyzeTPPTR",
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    "tpp2dCalcFractAbundance",
    "tpp2dComputeFoldChanges",
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    "tpp2dExport",
    "tpp2dExportPlots",
    "tpp2dImport",
    "tpp2dMerge2dRef",
    "tpp2dNormalize",
    "tpp2dPlotCCRAllCurves",
    "tpp2dPlotCCRGoodCurves",
    "tpp2dPlotCCRSingleCurves",
    "tpp2dPlotQChist",
    "tpp2dPlotQCpEC50",
    "tpp2dRemoveZeroSias",
    "tpp2dSplineFitAndTest",
    "tpp2dTRReferenceObject",
    "tppccrCurveFit",
    "tppccrImport",
    "tppccrNormalize",
    "tppccrNormalizeToReference",
    "tppccrPlotCurves",
    "tppccrResultTable",
    "tppccrTransform",
    "tppDefaultTheme",
    "tppExport",
    "tppQCPlotsCorrelateExperiments",
    "tpptrAnalyzeMeltingCurves",
    "tpptrCurveFit",
    "tpptrDefaultNormReqs",
    "tpptrFitSplines",
    "tpptrFTest",
    "tpptrImport",
    "tpptrNormalize",
    "tpptrPlotSplines",
    "tpptrSplineFitAndTest",
    "tpptrTidyUpESets"
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      "table": true,
      "tojson": true
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      "name": "hdacCCR_data",
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    {
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      "file": "hdacTR_smallExample.RData",
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        "131L"
      ],
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      "table": true,
      "tojson": true
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    {
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      "title": "TPP-TR example dataset.",
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      "file": "hdacTR_smallExample.RData",
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      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "panobinostat_2DTPP_config",
      "title": "The configuration table to analyze panobinostat_2DTPP_data.",
      "object": "panobinostat_2DTPP_smallExample",
      "file": "panobinostat_2DTPP_smallExample.RData",
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      "table": true,
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    },
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        "passed_filter_Vehicle_1_vs_Panobinostat_1",
        "diff_meltP_Panobinostat_2_vs_Vehicle_2",
        "min_slope_Panobinostat_2_vs_Vehicle_2",
        "pVal_adj_Panobinostat_2_vs_Vehicle_2",
        "passed_filter_Vehicle_2_vs_Panobinostat_2",
        "diff_meltP_Vehicle_1_vs_Vehicle_2",
        "min_pVals_less_0.05_and_max_pVals_less_0.1",
        "meltP_diffs_have_same_sign",
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    {
      "name": "tppRefData",
      "title": "Example of a reference dataset for 2D-TPP experiments.",
      "object": "TPPTR_reference_results_HepG2",
      "file": "TPPTR_reference_results_HepG2.RData",
      "class": [
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      "page": "analyze2DTPP",
      "title": "Analyze a 2D-TPP experiment",
      "topics": [
        "analyze2DTPP"
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    {
      "page": "analyzeTPPCCR",
      "title": "Analyze TPP-CCR experiment",
      "topics": [
        "analyzeTPPCCR"
      ]
    },
    {
      "page": "analyzeTPPTR",
      "title": "Analyze TPP-TR experiment",
      "topics": [
        "analyzeTPPTR"
      ]
    },
    {
      "page": "hdacCCR_config",
      "title": "The configuration table to analyze hdacCCR_data.",
      "topics": [
        "hdacCCR_config"
      ]
    },
    {
      "page": "hdacCCR_data",
      "title": "TPP-CCR example dataset (replicates 1 and 2)",
      "topics": [
        "hdacCCR_data"
      ]
    },
    {
      "page": "hdacCCR_smallExample",
      "title": "Example subsets of a Panobinostat TPP-CCR dataset (replicates 1 and 2) and the corresponding configuration table to start the analysis.",
      "topics": [
        "hdacCCR_smallExample"
      ]
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    {
      "page": "hdacTR_config",
      "title": "The configuration table to analyze hdacTR_data.",
      "topics": [
        "hdacTR_config"
      ]
    },
    {
      "page": "hdacTR_data",
      "title": "TPP-TR example dataset.",
      "topics": [
        "hdacTR_data"
      ]
    },
    {
      "page": "hdacTR_resultsTable_smallExample",
      "title": "Example of a TPP-TR result table.",
      "topics": [
        "hdacTR_resultsTable_smallExample"
      ]
    },
    {
      "page": "hdacTR_smallExample",
      "title": "Example subset of a Panobinostat TPP-TR dataset and the corresponding configuration table to start the analysis.",
      "topics": [
        "hdacTR_smallExample"
      ]
    },
    {
      "page": "panobinostat_2DTPP_config",
      "title": "The configuration table to analyze panobinostat_2DTPP_data.",
      "topics": [
        "panobinostat_2DTPP_config"
      ]
    },
    {
      "page": "panobinostat_2DTPP_data",
      "title": "2D-TPP-CCR example dataset",
      "topics": [
        "panobinostat_2DTPP_data"
      ]
    },
    {
      "page": "panobinostat_2DTPP_smallExample",
      "title": "Example subsets of a Panobinostat 2D-TPP dataset and the corresponding configuration table to start the analysis.",
      "topics": [
        "panobinostat_2DTPP_smallExample"
      ]
    },
    {
      "page": "resultTable",
      "title": "Example of a TPP-TR result table.",
      "topics": [
        "resultTable"
      ]
    },
    {
      "page": "TPP",
      "title": "Thermal proteome profiling (TPP)",
      "topics": [
        "-package",
        ".onLoad",
        "TPP"
      ]
    },
    {
      "page": "TPP-defunct",
      "title": "Defunct functions in package 'TPP'",
      "topics": [
        "TPP-defunct",
        "tpp2dCreateCCRConfigFile",
        "tpp2dEvalConfigTable",
        "tpp2dPlotCCRAllCurves",
        "tpp2dPlotCCRGoodCurves",
        "tpp2dPlotCCRSingleCurves",
        "tpp2dRemoveZeroSias",
        "tpp2dReplaceColNames"
      ]
    },
    {
      "page": "TPP-deprecated",
      "title": "Deprecated functions in package 'TPP'",
      "topics": [
        "TPP-deprecated"
      ]
    },
    {
      "page": "tpp2dAddAdditionalInfo",
      "title": "Add additional info to 2D-TPP CCR output data",
      "topics": [
        "tpp2dAddAdditionalInfo"
      ]
    },
    {
      "page": "tpp2dCalcFractAbundance",
      "title": "Calculate fractional abundance and DMSO ratio of successive sumionareas (usage of function is only reasonable when at least two temperatures are multiplexed!)",
      "topics": [
        "tpp2dCalcFractAbundance"
      ]
    },
    {
      "page": "tpp2dComputeFoldChanges",
      "title": "Compute 2D-TPP fold changes",
      "topics": [
        "tpp2dComputeFoldChanges"
      ]
    },
    {
      "page": "tpp2dCreateDRplots",
      "title": "Create dose response curve plots for 2D-TPP data",
      "topics": [
        "tpp2dCreateDRplots"
      ]
    },
    {
      "page": "tpp2dCreateReport",
      "title": "Create Report of 2D-TPP analysis",
      "topics": [
        "tpp2dCreateReport"
      ]
    },
    {
      "page": "tpp2dCreateTPPTRreference",
      "title": "Create TPP-TR reference for 2D-TPP experiment",
      "topics": [
        "tpp2dCreateTPPTRreference"
      ]
    },
    {
      "page": "tpp2dCurveFit",
      "title": "Run TPP-CCR analysis for 2D-TPP experiment",
      "topics": [
        "tpp2dCurveFit"
      ]
    },
    {
      "page": "tpp2dExport",
      "title": "Produce Excel table of 2D-TPP experiment.",
      "topics": [
        "tpp2dExport"
      ]
    },
    {
      "page": "tpp2dExportPlots",
      "title": "Export plots for 2D-TPP experiment.",
      "topics": [
        "tpp2dExportPlots"
      ]
    },
    {
      "page": "tpp2dImport",
      "title": "Import 2D-TPP data",
      "topics": [
        "tpp2dImport"
      ]
    },
    {
      "page": "tpp2dMerge2dRef",
      "title": "Merge 2D-TPP result data with TPP-TR reference data",
      "topics": [
        "tpp2dMerge2dRef"
      ]
    },
    {
      "page": "tpp2dNormalize",
      "title": "Median normalization of protein fold changes of 2D-TPP data",
      "topics": [
        "tpp2dNormalize"
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    },
    {
      "page": "tpp2dPlotQChist",
      "title": "Plot quality control histograms",
      "topics": [
        "tpp2dPlotQChist"
      ]
    },
    {
      "page": "tpp2dPlotQCpEC50",
      "title": "Plot quality control pEC50 plots",
      "topics": [
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    },
    {
      "page": "tpp2dSplineFitAndTest",
      "title": "Fit splines and perform f-Test",
      "topics": [
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    },
    {
      "page": "tpp2dSplinePlot",
      "title": "Fit splines and generate ggplot visualizations",
      "topics": [
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    },
    {
      "page": "tpp2dTRReferenceObject",
      "title": "TPP-TR reference object",
      "topics": [
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    },
    {
      "page": "tppccrCurveFit",
      "title": "Fit dose response curves",
      "topics": [
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      ]
    },
    {
      "page": "tppccrImport",
      "title": "Import TPP-CCR dataset for analysis by the 'TPP' package.",
      "topics": [
        "tppccrImport"
      ]
    },
    {
      "page": "tppccrNormalize",
      "title": "Normalize data from TPP-CCR experiments",
      "topics": [
        "tppccrNormalize"
      ]
    },
    {
      "page": "tppccrNormalizeToReference",
      "title": "Normalize fold changes of TPP-CCR experiment to a reference column",
      "topics": [
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    },
    {
      "page": "tppccrPlotCurves",
      "title": "Plot dose response curves",
      "topics": [
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      ]
    },
    {
      "page": "tppccrResultTable",
      "title": "Summarize results of a TPP-CCR study",
      "topics": [
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    },
    {
      "page": "tppccrTransform",
      "title": "Transform fold changes of TPP-CCR experiment",
      "topics": [
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    },
    {
      "page": "tppDefaultTheme",
      "title": "Default ggplot theme for melting curve plots.",
      "topics": [
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    },
    {
      "page": "tppExport",
      "title": "Produce Excel table of TPP-TR or TPP-CCR experiment.",
      "topics": [
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    },
    {
      "page": "tppQCPlotsCorrelateExperiments",
      "title": "Visually compare fold changes of different TPP experiments.",
      "topics": [
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      ]
    },
    {
      "page": "tppRefData",
      "title": "Example of a reference dataset for 2D-TPP experiments.",
      "topics": [
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      ]
    },
    {
      "page": "TPPTR_reference_results_HepG2",
      "title": "Example of a reference dataset for 2D-TPP experiments.",
      "topics": [
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      ]
    },
    {
      "page": "tpptrAnalyzeMeltingCurves",
      "title": "Analyze fitted curve parameters to detect significant shifts in melting points.",
      "topics": [
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      ]
    },
    {
      "page": "tpptrCurveFit",
      "title": "Fit melting curves to all proteins in a dataset.",
      "topics": [
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    },
    {
      "page": "tpptrDefaultNormReqs",
      "title": "Default filter criteria for fold change normalization",
      "topics": [
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    },
    {
      "page": "tpptrFitSplines",
      "title": "Perform spline fitting",
      "topics": [
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    },
    {
      "page": "tpptrFTest",
      "title": "Analyze spline fits to detect differential behavior over time",
      "topics": [
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    },
    {
      "page": "tpptrImport",
      "title": "Import TPP-TR datasets for analysis by the 'TPP' package.",
      "topics": [
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    },
    {
      "page": "tpptrNormalize",
      "title": "Normalize protein fold changes",
      "topics": [
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    },
    {
      "page": "tpptrPlotSplines",
      "title": "Plot spline fits per protein",
      "topics": [
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      ]
    },
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      "page": "tpptrSplineFitAndTest",
      "title": "Perform spline fitting and analyze by moderated F-test",
      "topics": [
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    },
    {
      "page": "tpptrTidyUpESets",
      "title": "Tidy up expressionSets",
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