TPP: Analyze thermal proteome profiling (TPP) experiments

Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).

Author
Dorothee Childs, Nils Kurzawa, Holger Franken, Carola Doce, Mikhail Savitski and Wolfgang Huber
Date of publication
None
Maintainer
Dorothee Childs <dorothee.childs@embl.de>
License
Artistic-2.0
Version
3.0.2

View on Bioconductor

Man pages

analyze2DTPP
Analyze 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...
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...
panob2D_isobQuant_example
Example subsets of a Panobinostat 2D-TPP dataset and the...
panobinostat_2DTPP_config
The configuration table to analyze panobinostat_2DTPP_data.
panobinostat_2DTPP_data
2D-TPP-CCR example dataset
resultTable
Example of a TPP-TR result table.
TPP
Thermal proteome profiling (TPP)
tpp2dAddAdditionalInfo
Add additional info to 2D-TPP CCR output data
tpp2dCalcFractAbundance
Calculate fractional abundance and DMSO ratio of successive...
tpp2dComputeFoldChanges
Compute 2D-TPP fold changes
tpp2dCreateCCRConfigFile
Create TPP-CCR config files for 2D-TPP experiment
tpp2dCreateDataFrameList
Create data frame list for 2D-TPP experiment
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
Evaluation of 2D-TPP Configuration File
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
Plot all 2D-TPP CCR curves
tpp2dPlotCCRGoodCurves
Plot 2D-TPP CCR curves meeting the requirements
tpp2dPlotCCRSingleCurves
Plot single 2D-TPP CCR curves
tpp2dPlotQChist
Plot quality control histograms
tpp2dPlotQCpEC50
Plot quality control pEC50 plots
tpp2dRemoveNAs
Remove NAs in 2D-TPP data
tpp2dRemoveZeroSias
Remove rows with zero sumionarea values
tpp2dReplaceColNames
Replace column names for 2D-TPP data
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...
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...
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

Files in this package

TPP/DESCRIPTION
TPP/NAMESPACE
TPP/NEWS
TPP/R
TPP/R/TPP.R
TPP/R/addTableToPlot.R
TPP/R/analyze2DTPP.R
TPP/R/analyzeTPPCCR.R
TPP/R/analyzeTPPTR.R
TPP/R/applyCoeffs.R
TPP/R/computeNormFactors.R
TPP/R/computePvalues.R
TPP/R/convertESetsToLongTables.R
TPP/R/createTPP_TPdataset.R
TPP/R/curveFitFctCCR_pEC50qualCheckCol.R
TPP/R/curveFitFunctions_fit.R
TPP/R/curveFitFunctions_wrappers.R
TPP/R/dataFormatFunctions.R
TPP/R/drCurveParamNames.R
TPP/R/exprSubset.R
TPP/R/extractConc.R
TPP/R/filterFCs.R
TPP/R/filterOther.R
TPP/R/filterTables.R
TPP/R/findJointP.R
TPP/R/generalFct_handleComparisons.R
TPP/R/generateColors4Temps.R
TPP/R/guessDRparamBoundaries.R
TPP/R/guessInitialDRslope.R
TPP/R/guessInitialpEC50.R
TPP/R/hdacCCR_smallExample.R
TPP/R/hdacTR_resultsTable_smallExample.R
TPP/R/hdacTR_smallExample.R
TPP/R/importCheckConfigTable.R
TPP/R/importCheckExperimentNames.R
TPP/R/importCheckTemperatures.R
TPP/R/importFct_checkComparisons.R
TPP/R/importFct_checkCondtitions.R
TPP/R/importFct_checkExperimentCol.R
TPP/R/importFct_makeOutputDirs.R
TPP/R/importFct_readConfigTable.R
TPP/R/importFunctions_processSingleExp.R
TPP/R/importTR_main.R
TPP/R/importTR_tidy.R
TPP/R/inferApparentStabilities.R
TPP/R/inflectionPoint.R
TPP/R/meltCurveParamNames.R
TPP/R/meltingCurveSlope.R
TPP/R/meltingPoint.R
TPP/R/mpSinglePval.R
TPP/R/pValFctFilterModels.R
TPP/R/pValFctPerformComparisons.R
TPP/R/pValFctPerformSingleComparison.R
TPP/R/pValFct_addMPdiff_and_MinSlope_Columns.R
TPP/R/pValsCurrentBin.R
TPP/R/panob2D_isobQuant_example.R
TPP/R/parallelizationFunctions.R
TPP/R/paramsSigmoid.R
TPP/R/plotColors.R
TPP/R/plotFct_plotDRorMeltcurve.R
TPP/R/plotLineTypes.R
TPP/R/plotNormCurves.R
TPP/R/plotSplines.R
TPP/R/qcColFunctions.R
TPP/R/qcPlotFunctions.R
TPP/R/rSquared.R
TPP/R/resultTableFunctions.R
TPP/R/robustNlsPredict.R
TPP/R/storeDRCurveParams.R
TPP/R/storeMeltCurveParams.R
TPP/R/summarizeResultTable.R
TPP/R/tpp2dAddAdditionalInfo.R
TPP/R/tpp2dCalcFractAbundance.R
TPP/R/tpp2dComputeFoldChanges.R
TPP/R/tpp2dCreateCCRConfigFile.R
TPP/R/tpp2dCreateDataFrameList.R
TPP/R/tpp2dCreateReport.R
TPP/R/tpp2dCreateTPPTRreference.R
TPP/R/tpp2dCurveFit.R
TPP/R/tpp2dEvalConfigTable.R
TPP/R/tpp2dExport.R
TPP/R/tpp2dExportPlots.R
TPP/R/tpp2dGeneratePlotLinkCols.R
TPP/R/tpp2dImport.R
TPP/R/tpp2dMerge2dRef.R
TPP/R/tpp2dNormalize.R
TPP/R/tpp2dPlotCCRAllCurves.R
TPP/R/tpp2dPlotCCRGoodCurves.R
TPP/R/tpp2dPlotCCRSingleCurves.R
TPP/R/tpp2dPlotQChist.R
TPP/R/tpp2dPlotQCpEC50.R
TPP/R/tpp2dRemoveNAs.R
TPP/R/tpp2dRemoveZeroSias.R
TPP/R/tpp2dReplaceColNames.R
TPP/R/tpp2dSplineFitAndTest.R
TPP/R/tpp2dSplinePlot.R
TPP/R/tpp2dTRReferenceObject.R
TPP/R/tppDefaultTheme.R
TPP/R/tppExport.R
TPP/R/tppQCPlotsCorrelateExperiments.R
TPP/R/tppccrCurveFit.R
TPP/R/tppccrImport.R
TPP/R/tppccrNormalize.R
TPP/R/tppccrNormalizeToReference.R
TPP/R/tppccrPlotCurves.R
TPP/R/tppccrResultTable.R
TPP/R/tppccrTransform.R
TPP/R/tpptrAnalyzeMeltingCurves.R
TPP/R/tpptrCurveFit.R
TPP/R/tpptrDefaultNormReqs.R
TPP/R/tpptrFTest.R
TPP/R/tpptrFitSplines.R
TPP/R/tpptrImport.R
TPP/R/tpptrNormalize.R
TPP/R/tpptrPlotSplines.R
TPP/R/tpptrQCplots.R
TPP/R/tpptrSplineFitAndTest.R
TPP/R/writeTRRefOutputTable.R
TPP/build
TPP/build/vignette.rds
TPP/data
TPP/data/hdacCCR_smallExample.RData
TPP/data/hdacTR_resultsTable_smallExample.RData
TPP/data/hdacTR_smallExample.RData
TPP/data/panob2D_isobQuant_example.RData
TPP/inst
TPP/inst/doc
TPP/inst/doc/NPARC_analysis_of_TPP_TR_data.R
TPP/inst/doc/NPARC_analysis_of_TPP_TR_data.Rnw
TPP/inst/doc/NPARC_analysis_of_TPP_TR_data.pdf
TPP/inst/doc/TPP_introduction_1D.R
TPP/inst/doc/TPP_introduction_1D.Rnw
TPP/inst/doc/TPP_introduction_1D.pdf
TPP/inst/doc/TPP_introduction_2D.R
TPP/inst/doc/TPP_introduction_2D.Rnw
TPP/inst/doc/TPP_introduction_2D.pdf
TPP/inst/example_data
TPP/inst/example_data/2D_example_data
TPP/inst/example_data/2D_example_data/exampleRunCCRInput.RData
TPP/inst/example_data/2D_example_data/fractAbundInData.RData
TPP/inst/example_data/2D_example_data/hdac2D_config.txt
TPP/inst/example_data/2D_example_data/panobinostat_2DTPP_smallExample.RData
TPP/inst/example_data/2D_example_data/panobinostat_ex_confg.csv
TPP/inst/example_data/2D_example_data/panobinostat_ex_confg.txt
TPP/inst/example_data/2D_example_data/referenceCCRConfig.RData
TPP/inst/example_data/2D_example_data/referenceFcData.RData
TPP/inst/example_data/2D_example_data/referenceNormData.RData
TPP/inst/example_data/2D_example_data/referenceReadInData.RData
TPP/inst/example_data/2D_example_data/shortCCRresults.RData
TPP/inst/example_data/2D_example_data/shortData2d.RData
TPP/inst/example_data/CCR_example_data
TPP/inst/example_data/CCR_example_data/Panobinostat_TPP-CCR_config.xlsx
TPP/inst/example_data/CCR_example_data/panobinostat_1_merged_results_20150227_1017_proteins.txt
TPP/inst/example_data/CCR_example_data/panobinostat_2_merged_results_20150227_1110_proteins.txt
TPP/inst/example_data/TR_example_data
TPP/inst/example_data/TR_example_data/Panobinostat_TPP-TR_config.xlsx
TPP/inst/example_data/TR_example_data/panobinostat_1_merged_results_20150226_1013_proteins.txt
TPP/inst/example_data/TR_example_data/panobinostat_2_merged_results_20150226_1139_proteins.txt
TPP/inst/example_data/TR_example_data/vehicle_1_merged_results_20150227_0908_proteins.txt
TPP/inst/example_data/TR_example_data/vehicle_2_merged_results_20150227_0847_proteins.txt
TPP/inst/extdata
TPP/inst/extdata/randomESet.Rdata
TPP/inst/extdata/validationData_meltCurveFilter.Rdata
TPP/inst/extdata/validationData_pvalBinning.Rdata
TPP/inst/extdata/validationData_pvalComputation.Rdata
TPP/inst/tpp2d_report.Rmd
TPP/man
TPP/man/TPP.Rd
TPP/man/analyze2DTPP.Rd
TPP/man/analyzeTPPCCR.Rd
TPP/man/analyzeTPPTR.Rd
TPP/man/hdacCCR_config.Rd
TPP/man/hdacCCR_data.Rd
TPP/man/hdacCCR_smallExample.Rd
TPP/man/hdacTR_config.Rd
TPP/man/hdacTR_data.Rd
TPP/man/hdacTR_resultsTable_smallExample.Rd
TPP/man/hdacTR_smallExample.Rd
TPP/man/panob2D_isobQuant_example.Rd
TPP/man/panobinostat_2DTPP_config.Rd
TPP/man/panobinostat_2DTPP_data.Rd
TPP/man/resultTable.Rd
TPP/man/tpp2dAddAdditionalInfo.Rd
TPP/man/tpp2dCalcFractAbundance.Rd
TPP/man/tpp2dComputeFoldChanges.Rd
TPP/man/tpp2dCreateCCRConfigFile.Rd
TPP/man/tpp2dCreateDataFrameList.Rd
TPP/man/tpp2dCreateReport.Rd
TPP/man/tpp2dCreateTPPTRreference.Rd
TPP/man/tpp2dCurveFit.Rd
TPP/man/tpp2dEvalConfigTable.Rd
TPP/man/tpp2dExport.Rd
TPP/man/tpp2dExportPlots.Rd
TPP/man/tpp2dImport.Rd
TPP/man/tpp2dMerge2dRef.Rd
TPP/man/tpp2dNormalize.Rd
TPP/man/tpp2dPlotCCRAllCurves.Rd
TPP/man/tpp2dPlotCCRGoodCurves.Rd
TPP/man/tpp2dPlotCCRSingleCurves.Rd
TPP/man/tpp2dPlotQChist.Rd
TPP/man/tpp2dPlotQCpEC50.Rd
TPP/man/tpp2dRemoveNAs.Rd
TPP/man/tpp2dRemoveZeroSias.Rd
TPP/man/tpp2dReplaceColNames.Rd
TPP/man/tpp2dSplineFitAndTest.Rd
TPP/man/tpp2dSplinePlot.Rd
TPP/man/tpp2dTRReferenceObject.Rd
TPP/man/tppDefaultTheme.Rd
TPP/man/tppExport.Rd
TPP/man/tppQCPlotsCorrelateExperiments.Rd
TPP/man/tppccrCurveFit.Rd
TPP/man/tppccrImport.Rd
TPP/man/tppccrNormalize.Rd
TPP/man/tppccrNormalizeToReference.Rd
TPP/man/tppccrPlotCurves.Rd
TPP/man/tppccrResultTable.Rd
TPP/man/tppccrTransform.Rd
TPP/man/tpptrAnalyzeMeltingCurves.Rd
TPP/man/tpptrCurveFit.Rd
TPP/man/tpptrDefaultNormReqs.Rd
TPP/man/tpptrFTest.Rd
TPP/man/tpptrFitSplines.Rd
TPP/man/tpptrImport.Rd
TPP/man/tpptrNormalize.Rd
TPP/man/tpptrPlotSplines.Rd
TPP/man/tpptrSplineFitAndTest.Rd
TPP/man/tpptrTidyUpESets.Rd
TPP/tests
TPP/tests/testthat
TPP/tests/testthat.R
TPP/tests/testthat/test_ITDR_functions.R
TPP/tests/testthat/test_import_functions.R
TPP/tests/testthat/test_normalization_functions.R
TPP/tests/testthat/test_output_filters.R
TPP/tests/testthat/test_pValFctPerformSingleComparison.R
TPP/tests/testthat/test_pvalues.R
TPP/tests/testthat/test_tpp2dComputeFoldChanges.R
TPP/tests/testthat/test_tpp2dCreateCCRConfigFile.R
TPP/tests/testthat/test_tpp2dDoMedianNorm.R
TPP/tests/testthat/test_tpp2dEvalConfigTable.R
TPP/tests/testthat/test_tpp2dRunTPPCCR.R
TPP/vignettes
TPP/vignettes/NPARC_analysis_of_TPP_TR_data.Rnw
TPP/vignettes/TPP_introduction_1D.Rnw
TPP/vignettes/TPP_introduction_2D.Rnw
TPP/vignettes/TPP_references.bib