Analyze thermal proteome profiling (TPP) experiments


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Documentation for package ‘TPP’ version 2.0.1

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TPP-package Thermal proteome profiling (TPP)
.onLoad Thermal proteome profiling (TPP)
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_fittedData_smallExample Example of a TPP-TR dataset with fitted melting curve parameters.
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.
resultTable Example of a TPP-TR result table.
TPP Thermal proteome profiling (TPP)
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 Plot pairwise relationships between the proteins in different 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
tpptrImport Import TPP-TR datasets for analysis by the 'TPP' package.
tpptrNormalize Normalize protein fold changes
trDataFitted Example of a TPP-TR dataset with fitted melting curve parameters.