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