Files in TPP

Analyze thermal proteome profiling (TPP) experiments

R/tpptrSplineAUCs.R R/guessDRparamBoundaries.R R/computeNormFactors.R R/pValFctPerformComparisons.R R/tppDefaultTheme.R R/importTR_main.R R/compute_spline_auc.R R/tppQCPlotsCorrelateExperiments.R R/helperFctPlotGood.R R/tpp2dCreateTPPTRreference.R R/hdacTR_smallExample.R R/fit_and_eval_spline_model.R R/computeMPdiffs.R R/generateColors4Temps.R R/create_spline_plots.R R/fitMeltCurves.R R/tpp2dImport.R R/exportFct_sortCols.R R/tpp2dPlotQChist.R R/qcPlotFctVennTable.R R/importFct_readConfigTable.R R/qcPlotFct_MeltPointHist.R R/exprSubset.R R/analyze2DTPP.R R/eval_spline_model.R R/tppccrNormalizeToReference.R R/exportFct_trySave.R R/importFct_df_to_eSet.R R/checkResultCols_tpptr.R R/plotIndividual.R R/exportFct_convertBoolean_1DTPP.R R/importFct_checkComparisons.R R/exportFct_colorCodeColumns.R R/plot_2D_data_on_temperature_range.R R/qcPlotFct_Bottleplot.R R/tppccrTransform.R R/convert_trData_wide_to_long.R R/tpptrFitSplines.R R/computeMinimalSlopes.R R/importTR_tidy.R R/tpptrDefaultNormReqs.R R/removeInvalidPaths.R R/convert_2dData_wide_to_long.R R/tpptrAnalyzeMeltingCurves.R R/importFct_checkCondtitions.R R/checkCPUs.R R/exportFct_addPlotColumns.R R/findJointP.R R/plotMeltingCurve.R R/eSetsToLongTable_fData.R R/meltCurveParamNames.R R/rSquared.R R/extractConc.R R/exportFct_convertBoolean_2DTPP.R R/guessInitialDRslope.R R/createComparisonTable.R R/detectLabelColumnsInConfigTable.R R/retrieveDataFromESets_CCR.R R/mergeOutputTables_TR.R R/fitSigmoidTR.R R/pValsCurrentBin.R R/tppDefunct.R R/pValFct_addMPdiff_and_MinSlope_Columns.R R/tpptrCurveFit.R R/importFct_makeOutputDirs.R R/TPP.R R/tppccrNormalize.R R/pValFctFilterModels.R R/tpp2dPlotQCpEC50.R R/checkFunctionArgs.R R/obtain_fcStr_from_df_annotation.R R/AICc.R R/summarizeResultTable.R R/curveFitFctCCR_pEC50qualCheckCol.R R/check_if_data_is_eSet_list.R R/tppccrImport.R R/filterFCs.R R/splitIDsIntoSeparateRows.R R/tpp2dExport.R R/import2DTR_main.R R/tpptrImport.R R/plot_pVal_distribution.R R/tpp2dCalcFractAbundance.R R/importFct_readFiles.R R/hdacTR_resultsTable_smallExample.R R/filterOther.R R/importFct_extractFCs.R R/meltingCurveSlope.R R/computePvalues.R R/importFct_rmZeroSias.R R/hdacCCR_smallExample.R R/importFct_replaceReplicateColumn.R R/robustNlsPredict.R R/qcPlotFct_createVenn.R R/helperFctPlotSingle.R R/TPPTR_reference_results_HepG2.R R/importFct_checkExperimentCol.R R/tpp2dSplineFitAndTest.R R/retrieveDataFromESets_TR.R R/tpptrPlotSplines.R R/importFct_createCCRInputFrom2DData.R R/tpptrTidyUpESets.R R/pValFctPerformSingleComparison.R R/fitSigmoidCCR.R R/fitDRCurve.R R/tppccrCurveFit.R R/helperFctPlotAll.R R/tppccrPlotCurves.R R/fctSigmoidCCR.R R/inflectionPoint.R R/mpSinglePval.R R/eSetsToLongTable_fc.R R/tpp2dCreateDRplots.R R/tpptrSplineFitAndTest.R R/storeDRCurveParams.R R/exportFct_addPlotLinks_1DTPP.R R/guessInitialpEC50.R R/merge_cols.R R/plotColors_splineFits.R R/panobinostat_2DTPP_smallExample.R R/assignCompNumber_to_expName.R R/tpp2dAddAdditionalInfo.R R/tpp2dComputeFoldChanges.R R/writeTRRefOutputTable.R R/applyCoeffs.R R/tppccrResultTable.R R/createValidPlotPaths.R R/predict_and_plot_spline_models.R R/tpp2dNormalize.R R/exportFct_ensureUniqueColumns.R R/plotLineTypes.R R/convert_2D_cfgTable_to_CCR_cfgTable.R R/plotDRCurve.R R/analyzeTPPTR.R R/tpptrNormalize.R R/importFct_CheckDataFormat.R R/qcPlotFct_invokeBottleplots.R R/tpp2dMerge2dRef.R R/importFct_removeDuplicates.R R/tpp2dExportPlots.R R/checkAndReturnDataSetting.R R/extract_fit_factors.R R/invoke_spline_prediction.R R/tppDeprecated.R R/filterTables.R R/qcPlotFct_VennWrapper.R R/plot_fSta_distribution.R R/meltingPoint.R R/tpp2dCreateReport.R R/addTableToPlot.R R/mergeOutputTables_CCR.R R/exportFct_addPlotLinks_2DTPP.R R/fit_splines_under_H0_and_H1.R R/splitTidyMeasurementsForExport.R R/importCheckTemperatures.R R/paramsSigmoid.R R/tppExport.R R/tpptrFTest.R R/modelSelector.R R/storeMeltCurveParams.R R/stopImplicitCluster.R R/analyzeTPPCCR.R R/importFct_makeUniqueIDs.R R/importCheckConfigTable.R R/checkResultCols_tppccr.R R/tidyUpReferenceObject.R R/importFct_create_fData.R R/importFct_fcCols.R R/fctSigmoidTR.R R/inferApparentStabilities.R R/importFct_create_pData.R R/predict_spline.R R/plotColors.R R/tpp2dSplinePlot.R R/tpptrQCplots.R R/fit_spline_model.R R/tpp2dTRReferenceObject.R R/importCheckExperimentNames.R R/drCurveParamNames.R R/tpp2dCurveFit.R R/checkIfLegendPossible.R R/plotNormCurves.R man/hdacCCR_config.Rd man/hdacCCR_data.Rd man/tpptrFitSplines.Rd man/tpptrImport.Rd man/TPP-defunct.Rd man/resultTable.Rd man/tpptrTidyUpESets.Rd man/tpp2dTRReferenceObject.Rd man/tppccrImport.Rd man/tpptrFTest.Rd man/tpp2dSplinePlot.Rd man/hdacTR_data.Rd man/hdacCCR_smallExample.Rd man/tpp2dComputeFoldChanges.Rd man/TPP-deprecated.Rd man/panobinostat_2DTPP_data.Rd man/hdacTR_smallExample.Rd man/tpp2dCalcFractAbundance.Rd man/tppRefData.Rd man/tpp2dMerge2dRef.Rd man/tpp2dExportPlots.Rd man/tpptrNormalize.Rd man/tppccrNormalize.Rd man/TPPTR_reference_results_HepG2.Rd man/analyzeTPPTR.Rd man/analyzeTPPCCR.Rd man/tpp2dImport.Rd man/tppccrCurveFit.Rd man/tpptrDefaultNormReqs.Rd man/tpp2dPlotQChist.Rd man/tpptrAnalyzeMeltingCurves.Rd man/tppccrResultTable.Rd man/tpp2dAddAdditionalInfo.Rd man/analyze2DTPP.Rd man/panobinostat_2DTPP_config.Rd man/tpptrCurveFit.Rd man/TPP.Rd man/hdacTR_resultsTable_smallExample.Rd man/panobinostat_2DTPP_smallExample.Rd man/tppccrPlotCurves.Rd man/tpp2dCreateTPPTRreference.Rd man/tpp2dCreateReport.Rd man/tpp2dCreateDRplots.Rd man/tpp2dCurveFit.Rd man/tppExport.Rd man/tpp2dExport.Rd man/tpptrPlotSplines.Rd man/hdacTR_config.Rd man/tppccrNormalizeToReference.Rd man/tppQCPlotsCorrelateExperiments.Rd man/tppccrTransform.Rd man/tpp2dSplineFitAndTest.Rd man/tpp2dPlotQCpEC50.Rd man/tpp2dNormalize.Rd man/tppDefaultTheme.Rd man/tpptrSplineFitAndTest.Rd tests/testthat.R tests/testthat/test_tppccrNormalize.R tests/testthat/test_importFct_checkExperimentCol.R tests/testthat/test_splitTidyMeasurementsForExport.R tests/testthat/test_tpp2dNormalize.R tests/testthat/test_tpptrSplineAUCs.R tests/testthat/test_predict_and_plot_spline_models.R tests/testthat/test_tpp2dImport.R tests/testthat/test_tpptrPlotSplines.R tests/testthat/test_checkResultCols_tppccr.R tests/testthat/test_importFct_makeOutputDirs.R tests/testthat/test_extract_fit_factors.R tests/testthat/test_tpptrFitSplines.R tests/testthat/test_plotIndividual.R tests/testthat/test_tpp2dMerge2dRef.R tests/testthat/test_importCheckTemperatures.R tests/testthat/test_importCheckConfigTable.R tests/testthat/test_detectLabelColumnsInConfigTable.R tests/testthat/test_applyCoeffs.R tests/testthat/test_evalSplineModel.R tests/testthat/test_filterOther.R tests/testthat/test_obtain_fcStr_from_df_annotation.R tests/testthat/test_pvalues.R tests/testthat/test_importFct_checkComparisons.R tests/testthat/test_tpptrSplineFitAndTest.R tests/testthat/test_mergeOutputTables_TR.R tests/testthat/test_predict_spline.R tests/testthat/test_fitDRCurve.R tests/testthat/test_tpp2dComputeFoldChanges.R tests/testthat/test_importFct_replaceReplicateCol.R tests/testthat/test_checkAndReturnDataSetting.R tests/testthat/test_analyzeTPPTR.R tests/testthat/test_invoke_spline_prediction.R tests/testthat/test_importFct_readConfigTable.R tests/testthat/test_create_spline_plots.R tests/testthat/test_tpp2dExport.R tests/testthat/test_tpp2dCurveFit.R tests/testthat/test_modelSelector.R tests/testthat/test_compute_spline_auc.R tests/testthat/test_convert_2D_cfgTable_to_CCR_cfgTable.R tests/testthat/test_analyze2DTPP.R tests/testthat/test_curveFitFctCCR_pEC50qualCheckCol.R tests/testthat/test_output_filters.R tests/testthat/test_tpp2dCalcFractAbundance.R tests/testthat/test_importFct_checkConditions.R tests/testthat/test_pValFctPerformSingleComparison.R tests/testthat/test_tpptrNormalize.R inst/tpp2d_report.Rmd inst/doc/TPP_introduction_1D.pdf inst/doc/TPP_introduction_2D.pdf inst/doc/TPP_introduction_2D.R inst/doc/NPARC_analysis_of_TPP_TR_data.pdf inst/doc/TPP_introduction_1D.R inst/doc/NPARC_analysis_of_TPP_TR_data.R inst/test_data/Panobinostat_2DTPP_smallExample.R