Files in DAPAR
Tools for the Differential Analysis of Proteins Abundance with R
DAPAR.Rproj
NAMESPACE
DESCRIPTION
R/inOutFiles.R
R/plots_corr_matrix.R
R/get_pep_prot_cc.R
R/bioAnalysis.R
R/normalize.R
R/plots_boxplot.R
R/DiffAnalysis.R
R/plots_pca.R
R/volcanoPlot.R
R/anova_analysis.R
R/missingValuesFilter.R
R/logText.R
R/plots_compare_Norm.R
R/missingValuesImputation_ProteinLevel.R
R/missingValuesPlots.R
R/clustering.R
R/plots_heatmaps.R
R/plots_density.R
R/pepa.R
R/plots_density_CV.R
R/plots_violin.R
R/agregation.R
R/compute.t.tests.R
R/missingValuesImputation_PeptideLevel.R
R/utils.R
R/limmaAnalysis.R
inst/NEWS.Rd
inst/CITATION
inst/doc/Prostar_UserManual.pdf
inst/doc/Prostar_UserManual.Rnw
inst/doc/Prostar_UserManual.R
build/vignette.rds
tests/testthat.R
tests/testthat/test_Volcanoplot.R
tests/testthat/test_differentialAnalysis.R
tests/testthat/test_normalisation.R
tests/testthat/test_missingValuesPlots.R
tests/testthat/test_descriptiveStatistics.R
tests/testthat/test_agregation.R
tests/testthat/test_limmaAnalysis.R
tests/testthat/test_mvFilter.R
tests/testthat/test_utils.R
tests/testthat/test_missingValuesImputation.R
vignettes/Prostar_UserManual.Rnw
vignettes/images/load-prot.png
vignettes/images/load-pep.png
vignettes/images/desc_CVDist_ZoomIn.png
vignettes/images/desc_missValues.png
vignettes/images/anaDiff4.png
vignettes/images/desc_pdata.png
vignettes/images/exportReport.png
vignettes/images/normalisation.png
vignettes/images/fdr-thresh.png
vignettes/images/cp4p-pb1.png
vignettes/images/anadiffsum.png
vignettes/images/logSession.png
vignettes/images/anaDiff3.png
vignettes/images/home.png
vignettes/images/protein-POV.png
vignettes/images/GO_tab3.png
vignettes/images/desc_quantiData.png
vignettes/images/agregation2.png
vignettes/images/convert_convert.png
vignettes/images/GO_tab2.png
vignettes/images/convert_selectfile.png
vignettes/images/desc_PCA.png
vignettes/images/desc_violinplot.png
vignettes/images/GO_tab4.png
vignettes/images/aggregation.png
vignettes/images/convert_exp_featdata.png
vignettes/images/cp4p-default.png
vignettes/images/peptide-imp4p.png
vignettes/images/desc_CVDist_ZoomOut.png
vignettes/images/desc_density.png
vignettes/images/desc_varDist.png
vignettes/images/cp4p-choice.png
vignettes/images/peptide-basicImputation.png
vignettes/images/anaDiff2.png
vignettes/images/agregation1.png
vignettes/images/equiv-non-fig.txt
vignettes/images/desc_boxplot.png
vignettes/images/filter1.png
vignettes/images/imputation.png
vignettes/images/hp.png
vignettes/images/filter2.png
vignettes/images/Rcode.png
vignettes/images/protein-MEC.png
vignettes/images/GO_tab1.png
vignettes/images/desc_fdata.png
vignettes/images/desc_intdistrib.png
vignettes/images/desc_heatmap.png
vignettes/images/cp4p-pb2.png
vignettes/images/open_msnset.png
vignettes/images/demomode.png
vignettes/images/desc_corrmatrix.png
vignettes/images/convert_sampledata.png
vignettes/images/convert_dataID.png
vignettes/images/pushpval.png
vignettes/images/desc_CVDist.png
vignettes/images/cp4p-ideal.png
vignettes/images/export.png
vignettes/images/descstat-overview.png
vignettes/images/filter3.png
vignettes/images/defaultProstar1.png
vignettes/images/anaDiff1.png
man/wrapper.corrMatrixD_HC.Rd
man/getIndicesOfLinesToRemove.Rd
man/LOESS.Rd
man/plotJitter_rCharts.Rd
man/is.MV.Rd
man/CVDistD_HC.Rd
man/my_hc_ExportMenu.Rd
man/pepa.test.Rd
man/compute_t_tests.Rd
man/getTextForAnaDiff.Rd
man/plotPCA_Eigen.Rd
man/LH0.Rd
man/GetDetailedNbPeptides.Rd
man/compareNormalizationD_HC.Rd
man/classic1wayAnova.Rd
man/plotPCA_Var.Rd
man/impute.pa2.Rd
man/group_GO.Rd
man/mvHisto_HC.Rd
man/corrMatrixD_HC.Rd
man/is.OfType.Rd
man/CountPep.Rd
man/wrapper.hc_mvTypePlot2.Rd
man/BuildPalette.Rd
man/getListNbValuesInLines.Rd
man/dapar_hc_ExportMenu.Rd
man/make.design.1.Rd
man/wrapperCalibrationPlot.Rd
man/GetNbPeptidesUsed.Rd
man/wrapper.mvHisto_HC.Rd
man/wrapper.impute.KNN.Rd
man/aggregateIterParallel.Rd
man/wrapper.mvPerLinesHistoPerCondition_HC.Rd
man/findMECBlock.Rd
man/getTextForpeptideImputation.Rd
man/removeLines.Rd
man/LH0.lm.Rd
man/barplotGroupGO_HC.Rd
man/getTextForNormalization.Rd
man/impute.detQuant.Rd
man/wrapper.compareNormalizationD_HC.Rd
man/setMEC.Rd
man/wrapper.heatmapD.Rd
man/MeanCentering.Rd
man/dapar_hc_chart.Rd
man/averageIntensities.Rd
man/getTextForGOAnalysis.Rd
man/violinPlotD.Rd
man/aggregateSum.Rd
man/vsn.Rd
man/addOriginOfValue.Rd
man/heatmapD.Rd
man/hc_logFC_DensityPlot.Rd
man/getNumberOfEmptyLines.Rd
man/samLRT.Rd
man/inner.aggregate.topn.Rd
man/LH1.lm.Rd
man/scatterplotEnrichGO_HC.Rd
man/check.conditions.Rd
man/display.CC.visNet.Rd
man/limmaCompleteTest.Rd
man/mvPerLinesHisto_HC.Rd
man/Get_AllComparisons.Rd
man/plotPCA_Eigen_hc.Rd
man/univ_AnnotDbPkg.Rd
man/make.contrast.Rd
man/make.design.3.Rd
man/plotJitter.Rd
man/normalizeMethods.dapar.Rd
man/aggregateTopn.Rd
man/getIndicesConditions.Rd
man/mvPerLinesHistoPerCondition_HC.Rd
man/heatmap.DAPAR.Rd
man/get.pep.prot.cc.Rd
man/StringBasedFiltering.Rd
man/aggregateMean.Rd
man/inner.mean.Rd
man/StringBasedFiltering2.Rd
man/wrapper.CVDistD.Rd
man/mvFilterGetIndices.Rd
man/rbindMSnset.Rd
man/diffAnaVolcanoplot.Rd
man/getTextForNewDataset.Rd
man/diffAnaSave.Rd
man/wrapper.impute.pa.Rd
man/barplotEnrichGO_HC.Rd
man/NumericalFiltering.Rd
man/getTextForFiltering.Rd
man/BuildColumnToProteinDataset.Rd
man/make.design.2.Rd
man/GOAnalysisSave.Rd
man/my_hc_chart.Rd
man/writeMSnsetToCSV.Rd
man/fudge2LRT.Rd
man/postHocTest.Rd
man/checkClusterability.Rd
man/mvFilter.Rd
man/GraphPepProt.Rd
man/createMSnset.Rd
man/GlobalQuantileAlignment.Rd
man/wrapper.pca.Rd
man/inner.aggregate.iter.Rd
man/densityPlotD.Rd
man/BuildAdjacencyMatrix.Rd
man/nonzero.Rd
man/wrapper.impute.slsa.Rd
man/diffAnaVolcanoplot_rCharts.Rd
man/plotPCA_Ind.Rd
man/inner.sum.Rd
man/BuildColumnToProteinDataset_par.Rd
man/formatLimmaResult.Rd
man/aggregateIter.Rd
man/wrapper.impute.detQuant.Rd
man/wrapper.dapar.impute.mi.Rd
man/GetDetailedNbPeptidesUsed.Rd
man/diffAnaComputeFDR.Rd
man/wrapper.impute.mle.Rd
man/boxPlotD_HC.Rd
man/hc_mvTypePlot2.Rd
man/wrapper.impute.pa2.Rd
man/diffAnaGetSignificant.Rd
man/finalizeAggregation.Rd
man/wrapper.CVDistD_HC.Rd
man/test.design.Rd
man/splitAdjacencyMat.Rd
man/histPValue_HC.Rd
man/CVDistD.Rd
man/enrich_GO.Rd
man/translatedRandomBeta.Rd
man/check.design.Rd
man/listSheets.Rd
man/wrapper.mvImage.Rd
man/getTextForHypothesisTest.Rd
man/mvImage.Rd
man/getTextForAggregation.Rd
man/getNumberOf.Rd
man/wrapperRunClustering.Rd
man/deleteLinesFromIndices.Rd
man/visualizeClusters.Rd
man/mvFilterFromIndices.Rd
man/NumericalgetIndicesOfLinesToRemove.Rd
man/getTextForproteinImputation.Rd
man/getProteinsStats.Rd
man/LH1.Rd
man/getProcessingInfo.Rd
man/QuantileCentering.Rd
man/SumByColumns.Rd
man/getQuantile4Imp.Rd
man/wrapperClassic1wayAnova.Rd
man/densityPlotD_HC.Rd
man/getPourcentageOfMV.Rd
man/reIntroduceMEC.Rd
man/make.design.Rd
man/wrapper.impute.fixedValue.Rd
man/writeMSnsetToExcel.Rd
man/formatPHResults.Rd
man/saveParameters.Rd
man/readExcel.Rd
man/buildGraph.Rd
man/wrapper.mvPerLinesHisto_HC.Rd
man/proportionConRev_HC.Rd
man/wrapper.normalizeD.Rd
