# Analyze thermal proteome profiling (TPP) experiments

## Documentation for package ‘TPP’ version 3.20.0

- 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.