Files in Bioconductor-mirror/TPP
Analyze thermal proteome profiling (TPP) experiments

DESCRIPTION
NAMESPACE
NEWS
R/TPP.R R/TPPTR_reference_results_HepG2.R R/addTableToPlot.R R/analyze2DTPP.R R/analyzeTPPCCR.R R/analyzeTPPTR.R R/applyCoeffs.R R/assignCompNumber_to_expName.R R/checkAndReturnDataSetting.R R/checkCPUs.R R/checkFunctionArgs.R R/checkIfLegendPossible.R R/checkResultCols_tppccr.R R/checkResultCols_tpptr.R R/check_if_data_is_eSet_list.R R/computeMPdiffs.R R/computeMinimalSlopes.R R/computeNormFactors.R R/computePvalues.R R/compute_spline_auc.R R/convert_2D_cfgTable_to_CCR_cfgTable.R R/convert_2dData_wide_to_long.R R/convert_trData_wide_to_long.R R/createComparisonTable.R R/createValidPlotPaths.R R/create_spline_plots.R R/curveFitFctCCR_pEC50qualCheckCol.R R/detectLabelColumnsInConfigTable.R R/drCurveParamNames.R R/eSetsToLongTable_fData.R R/eSetsToLongTable_fc.R R/eval_spline_model.R R/exportFct_addPlotColumns.R R/exportFct_addPlotLinks_1DTPP.R R/exportFct_addPlotLinks_2DTPP.R R/exportFct_colorCodeColumns.R R/exportFct_convertBoolean_1DTPP.R R/exportFct_convertBoolean_2DTPP.R R/exportFct_ensureUniqueColumns.R R/exportFct_sortCols.R R/exportFct_trySave.R R/exprSubset.R R/extractConc.R R/extract_fit_factors.R R/fctSigmoidCCR.R R/fctSigmoidTR.R R/filterFCs.R R/filterOther.R R/filterTables.R R/findJointP.R R/fitDRCurve.R R/fitMeltCurves.R R/fitSigmoidCCR.R R/fitSigmoidTR.R R/fit_and_eval_spline_model.R R/fit_spline_model.R R/fit_splines_under_H0_and_H1.R R/generateColors4Temps.R R/guessDRparamBoundaries.R R/guessInitialDRslope.R R/guessInitialpEC50.R R/hdacCCR_smallExample.R R/hdacTR_resultsTable_smallExample.R R/hdacTR_smallExample.R R/helperFctPlotAll.R R/helperFctPlotGood.R R/helperFctPlotSingle.R R/import2DTR_main.R R/importCheckConfigTable.R R/importCheckExperimentNames.R R/importCheckTemperatures.R R/importFct_CheckDataFormat.R R/importFct_checkComparisons.R R/importFct_checkCondtitions.R R/importFct_checkExperimentCol.R R/importFct_createCCRInputFrom2DData.R R/importFct_create_fData.R R/importFct_create_pData.R R/importFct_df_to_eSet.R R/importFct_extractFCs.R R/importFct_fcCols.R R/importFct_makeOutputDirs.R R/importFct_makeUniqueIDs.R R/importFct_readConfigTable.R R/importFct_readFiles.R R/importFct_removeDuplicates.R R/importFct_replaceReplicateColumn.R R/importFct_rmZeroSias.R R/importTR_main.R R/importTR_tidy.R R/inferApparentStabilities.R R/inflectionPoint.R R/invoke_spline_prediction.R R/meltCurveParamNames.R R/meltingCurveSlope.R R/meltingPoint.R R/mergeOutputTables_CCR.R R/mergeOutputTables_TR.R R/merge_cols.R R/modelSelector.R R/mpSinglePval.R R/obtain_fcStr_from_df_annotation.R R/pValFctFilterModels.R R/pValFctPerformComparisons.R R/pValFctPerformSingleComparison.R R/pValFct_addMPdiff_and_MinSlope_Columns.R R/pValsCurrentBin.R R/panobinostat_2DTPP_smallExample.R R/paramsSigmoid.R R/plotColors.R R/plotColors_splineFits.R R/plotDRCurve.R R/plotIndividual.R R/plotLineTypes.R R/plotMeltingCurve.R R/plotNormCurves.R R/plot_2D_data_on_temperature_range.R R/plot_fSta_distribution.R R/plot_pVal_distribution.R R/predict_and_plot_spline_models.R R/predict_spline.R R/qcPlotFctVennTable.R R/qcPlotFct_Bottleplot.R R/qcPlotFct_MeltPointHist.R R/qcPlotFct_VennWrapper.R R/qcPlotFct_createVenn.R R/qcPlotFct_invokeBottleplots.R R/rSquared.R R/removeInvalidPaths.R R/retrieveDataFromESets_CCR.R R/retrieveDataFromESets_TR.R R/robustNlsPredict.R R/splitIDsIntoSeparateRows.R R/splitTidyMeasurementsForExport.R R/stopImplicitCluster.R R/storeDRCurveParams.R R/storeMeltCurveParams.R R/summarizeResultTable.R R/tidyUpReferenceObject.R R/tpp2dAddAdditionalInfo.R R/tpp2dCalcFractAbundance.R R/tpp2dComputeFoldChanges.R R/tpp2dCreateDRplots.R R/tpp2dCreateReport.R R/tpp2dCreateTPPTRreference.R R/tpp2dCurveFit.R R/tpp2dExport.R R/tpp2dExportPlots.R R/tpp2dImport.R R/tpp2dMerge2dRef.R R/tpp2dNormalize.R R/tpp2dPlotQChist.R R/tpp2dPlotQCpEC50.R R/tpp2dSplineFitAndTest.R R/tpp2dSplinePlot.R R/tpp2dTRReferenceObject.R R/tppDefaultTheme.R R/tppDeprecated.R R/tppExport.R R/tppQCPlotsCorrelateExperiments.R R/tppccrCurveFit.R R/tppccrImport.R R/tppccrNormalize.R R/tppccrNormalizeToReference.R R/tppccrPlotCurves.R R/tppccrResultTable.R R/tppccrTransform.R R/tpptrAnalyzeMeltingCurves.R R/tpptrCurveFit.R R/tpptrDefaultNormReqs.R R/tpptrFTest.R R/tpptrFitSplines.R R/tpptrImport.R R/tpptrNormalize.R R/tpptrPlotSplines.R R/tpptrQCplots.R R/tpptrSplineAUCs.R R/tpptrSplineFitAndTest.R R/tpptrTidyUpESets.R R/writeTRRefOutputTable.R
data/TPPTR_reference_results_HepG2.RData
data/hdacCCR_smallExample.RData
data/hdacTR_resultsTable_smallExample.RData
data/hdacTR_smallExample.RData
data/panobinostat_2DTPP_smallExample.RData
inst/example_data/2D_example_data/PFC_39093_PF1_QV1_P0101918C.txt
inst/example_data/2D_example_data/PFC_39099_PF1_QV1_P0101908C.txt
inst/example_data/2D_example_data/PFC_39101_PF1_QV1_P0101898C.txt
inst/example_data/2D_example_data/PFC_39106_PF1_QV1_P0101868C.txt
inst/example_data/2D_example_data/PFC_39108_PF1_QV1_P0101878C.txt
inst/example_data/2D_example_data/PFC_39110_PF1_QV1_P0101888C.txt
inst/example_data/2D_example_data/Panobinostat_TPP-2D_config.xlsx
inst/example_data/2D_example_data/fractAbundInData.RData
inst/example_data/2D_example_data/referenceNormData.RData
inst/example_data/2D_example_data/shortCCRresults.RData
inst/example_data/2D_example_data/shortData2d.RData
inst/example_data/CCR_example_data/Panobinostat_TPP-CCR_config.xlsx
inst/example_data/CCR_example_data/panobinostat_1_merged_results_20150227_1017_proteins.txt
inst/example_data/CCR_example_data/panobinostat_2_merged_results_20150227_1110_proteins.txt
inst/example_data/TR_example_data/Panobinostat_TPP-TR_config.xlsx
inst/example_data/TR_example_data/panobinostat_1_merged_results_20150226_1013_proteins.txt
inst/example_data/TR_example_data/panobinostat_2_merged_results_20150226_1139_proteins.txt
inst/example_data/TR_example_data/vehicle_1_merged_results_20150227_0908_proteins.txt
inst/example_data/TR_example_data/vehicle_2_merged_results_20150227_0847_proteins.txt
inst/extdata/randomESet.Rdata
inst/extdata/validationData_meltCurveFilter.Rdata
inst/extdata/validationData_pvalBinning.Rdata
inst/extdata/validationData_pvalComputation.Rdata
inst/test_data/Panobinostat_2DTPP_smallExample.R
inst/test_data/panobinostat_2DTPP_smallExample.RData
inst/test_data/panobinostat_2D_fcResults.rds
inst/test_data/panobinostat_2D_fcResults2.rds
inst/test_data/panobinostat_2D_fitResults.rds
inst/test_data/panobinostat_2D_fitResults2.rds
inst/test_data/panobinostat_2D_fitResults3.rds
inst/test_data/panobinostat_2D_importResults.rds
inst/test_data/panobinostat_2D_importResults2.rds
inst/test_data/panobinostat_2D_normResults.rds
inst/test_data/panobinostat_2D_normResults2.rds
inst/test_data/panobinostat_2D_normResults3.rds
inst/test_data/panobinostat_CCR_fitResults.rds
inst/test_data/panobinostat_ex_confg.txt
inst/test_data/panobinostat_ex_confg2.txt
inst/tpp2d_report.Rmd man/TPP-deprecated.Rd man/TPP.Rd man/TPPTR_reference_results_HepG2.Rd man/analyze2DTPP.Rd man/analyzeTPPCCR.Rd man/analyzeTPPTR.Rd man/hdacCCR_config.Rd man/hdacCCR_data.Rd man/hdacCCR_smallExample.Rd man/hdacTR_config.Rd man/hdacTR_data.Rd man/hdacTR_resultsTable_smallExample.Rd man/hdacTR_smallExample.Rd man/panobinostat_2DTPP_config.Rd man/panobinostat_2DTPP_data.Rd man/panobinostat_2DTPP_smallExample.Rd man/resultTable.Rd man/tpp2dAddAdditionalInfo.Rd man/tpp2dCalcFractAbundance.Rd man/tpp2dComputeFoldChanges.Rd man/tpp2dCreateDRplots.Rd man/tpp2dCreateReport.Rd man/tpp2dCreateTPPTRreference.Rd man/tpp2dCurveFit.Rd man/tpp2dExport.Rd man/tpp2dExportPlots.Rd man/tpp2dImport.Rd man/tpp2dMerge2dRef.Rd man/tpp2dNormalize.Rd man/tpp2dPlotQChist.Rd man/tpp2dPlotQCpEC50.Rd man/tpp2dSplineFitAndTest.Rd man/tpp2dSplinePlot.Rd man/tpp2dTRReferenceObject.Rd man/tppDefaultTheme.Rd man/tppExport.Rd man/tppQCPlotsCorrelateExperiments.Rd man/tppRefData.Rd man/tppccrCurveFit.Rd man/tppccrImport.Rd man/tppccrNormalize.Rd man/tppccrNormalizeToReference.Rd man/tppccrPlotCurves.Rd man/tppccrResultTable.Rd man/tppccrTransform.Rd man/tpptrAnalyzeMeltingCurves.Rd man/tpptrCurveFit.Rd man/tpptrDefaultNormReqs.Rd man/tpptrFTest.Rd man/tpptrFitSplines.Rd man/tpptrImport.Rd man/tpptrNormalize.Rd man/tpptrPlotSplines.Rd man/tpptrSplineFitAndTest.Rd man/tpptrTidyUpESets.Rd tests/testthat.R tests/testthat/test_filterOther.R tests/testthat/test_fitDRCurve.R tests/testthat/test_importCheckConfigTable.R tests/testthat/test_importCheckTemperatures.R tests/testthat/test_importFct_checkComparisons.R tests/testthat/test_importFct_checkConditions.R tests/testthat/test_importFct_checkExperimentCol.R tests/testthat/test_importFct_replaceReplicateCol.R
vignettes/NPARC_analysis_of_TPP_TR_data.Rnw
vignettes/TPP_introduction_1D.Rnw
vignettes/TPP_introduction_2D.Rnw
vignettes/TPP_references.bib
Bioconductor-mirror/TPP documentation built on July 7, 2017, 11:01 p.m.