# Analyze thermal proteome profiling (TPP) experiments

## Documentation for package ‘TPP’ version 1.0.3

- 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_repl1 | The configuration table to analyze hdacCCR_data_repl1.
hdacCCR_config_repl2 | The configuration table to analyze hdacCCR_data_repl2.
hdacCCR_data_repl1 | TPP-CCR example dataset (replicate 1)
hdacCCR_data_repl2 | TPP-CCR example dataset (replicate 2)
hdacCCR_smallExample | Example subsets of a Panobinostat TPP-CCR dataset (replicates 1 and 2) and the corresponding configuration tables 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 and analyse dose response curves
tppccrImport | Import TPP-CCR dataset for analysis by the 'TPP' package.
tppccrNormalize | Normalize data from TPP-CCR experiments
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.
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
tpptrQCPlotsMinSlopes_vs_MPdiffs | Plot minSlope vs. melting point differences
tpptrResultTable | Statistical analysis of melting curve parameters.
tppVenn | Venn diagrams of detected proteins per experiment.
trDataFitted | Example of a TPP-TR dataset with fitted melting curve parameters.