Analyze thermal proteome profiling (TPP) experiments

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Documentation for package ‘TPP’ version 3.28.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.onLoad	Thermal proteome profiling (TPP)
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.
TPP	Thermal proteome profiling (TPP)
TPP-defunct	Defunct functions in package 'TPP'
TPP-deprecated	Deprecated functions in package 'TPP'
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
tpp2dCreateCCRConfigFile	Defunct functions in package 'TPP'
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
tpp2dEvalConfigTable	Defunct functions in package 'TPP'
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
tpp2dPlotCCRAllCurves	Defunct functions in package 'TPP'
tpp2dPlotCCRGoodCurves	Defunct functions in package 'TPP'
tpp2dPlotCCRSingleCurves	Defunct functions in package 'TPP'
tpp2dPlotQChist	Plot quality control histograms
tpp2dPlotQCpEC50	Plot quality control pEC50 plots
tpp2dRemoveZeroSias	Defunct functions in package 'TPP'
tpp2dReplaceColNames	Defunct functions in package 'TPP'
tpp2dSplineFitAndTest	Fit splines and perform f-Test
tpp2dSplinePlot	Fit splines and generate ggplot visualizations
tpp2dTRReferenceObject	TPP-TR reference object
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
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.
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
tpptrFitSplines	Perform spline fitting
tpptrFTest	Analyze spline fits to detect differential behavior over time
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
TPPTR_reference_results_HepG2	Example of a reference dataset for 2D-TPP experiments.