TPP: Analyze thermal proteome profiling (TPP) experiments

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

AuthorDorothee Childs, Nils Kurzawa, Holger Franken, Carola Doce, Mikhail Savitski and Wolfgang Huber
Date of publicationNone
MaintainerDorothee Childs <dorothee.childs@embl.de>
LicenseArtistic-2.0
Version3.0.3

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

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