# Analyze thermal proteome profiling (TPP) experiments

## Documentation for package ‘TPP’ version 2.0.4

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

## Help Pages

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_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 | Visually compare fold changes of 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