Analyze thermal proteome profiling (TPP) experiments


[Up] [Top]

Documentation for package ‘TPP’ version 1.0.3

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.