Files in prostarproteomics/DAPAR

Tools for the Differential Analysis of Proteins Abundance with R

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md R/DiffAnalysis.R R/agregation.R R/anova_analysis.R R/bioAnalysis.R R/clustering.R R/compute.t.tests.R R/dataset_Validity.R R/get_pep_prot_cc.R R/hypothesisTest.R R/inOutFiles.R R/limmaAnalysis.R R/logText.R R/metacell.R R/metacell_Plots.R R/missingValuesFilter.R R/missingValuesImputation_PeptideLevel.R R/missingValuesImputation_ProteinLevel.R R/normalize.R R/palette.R R/pepa.R R/plots_boxplot.R R/plots_compare_Norm.R R/plots_corr_matrix.R R/plots_density.R R/plots_density_CV.R R/plots_heatmaps.R R/plots_pca.R R/plots_violin.R R/utils.R R/volcanoPlot.R R/zzz.R dev/test_HT.R examples/ex_BuildColumnToProteinDataset.R examples/ex_GetIndices_MetacellFiltering.R examples/ex_MetacellFiltering.R examples/ex_averageIntensities.R examples/ex_checkClusterability.R examples/ex_classic1wayAnova.R examples/ex_formatPHResults.R examples/ex_metacellPerLinesHisto_HC.R examples/ex_metacombine.R examples/ex_postHocTest.R examples/ex_visualizeClusters.R examples/ex_wrapperClassic1wayAnova.R examples/ex_wrapperRunClustering.R man/AggregateMetacell.Rd man/BuildAdjacencyMatrix.Rd man/BuildColumnToProteinDataset.Rd man/BuildMetaCell.Rd man/CVDistD_HC.Rd man/Check_Dataset_Validity.Rd man/Check_NbValues_In_Columns.Rd man/Children.Rd man/CountPep.Rd man/ExtendPalette.Rd man/GOAnalysisSave.Rd man/GetCC.Rd man/GetColorsForConditions.Rd man/GetDetailedNbPeptides.Rd man/GetDetailedNbPeptidesUsed.Rd man/GetIndices_BasedOnConditions.Rd man/GetIndices_MetacellFiltering.Rd man/GetIndices_WholeLine.Rd man/GetIndices_WholeMatrix.Rd man/GetKeyId.Rd man/GetMatAdj.Rd man/GetMetacell.Rd man/GetMetacellTags.Rd man/GetNbPeptidesUsed.Rd man/GetNbTags.Rd man/GetSoftAvailables.Rd man/GetTypeofData.Rd man/GetUniqueTags.Rd man/Get_AllComparisons.Rd man/GlobalQuantileAlignment.Rd man/GraphPepProt.Rd man/LH0.Rd man/LH0.lm.Rd man/LH1.Rd man/LH1.lm.Rd man/LOESS.Rd man/MeanCentering.Rd man/MetaCellFiltering.Rd man/MetacellFilteringScope.Rd man/Metacell_DIA_NN.Rd man/Metacell_generic.Rd man/Metacell_maxquant.Rd man/Metacell_proline.Rd man/NumericalFiltering.Rd man/NumericalgetIndicesOfLinesToRemove.Rd man/OWAnova.Rd man/Parent.Rd man/QuantileCentering.Rd man/SetCC.Rd man/SetMatAdj.Rd man/Set_POV_MEC_tags.Rd man/StringBasedFiltering.Rd man/StringBasedFiltering2.Rd man/SumByColumns.Rd man/SymFilteringOperators.Rd man/UpdateMetacellAfterImputation.Rd man/aggregateIter.Rd man/aggregateIterParallel.Rd man/aggregateMean.Rd man/aggregateSum.Rd man/aggregateTopn.Rd man/applyAnovasOnProteins.Rd man/averageIntensities.Rd man/barplotEnrichGO_HC.Rd man/barplotGroupGO_HC.Rd man/boxPlotD_HC.Rd man/buildGraph.Rd man/check.conditions.Rd man/check.design.Rd man/checkClusterability.Rd man/classic1wayAnova.Rd man/compareNormalizationD_HC.Rd man/compute.selection.table.Rd man/compute_t_tests.Rd man/corrMatrixD_HC.Rd man/createMSnset.Rd man/createMSnset2.Rd man/dapar_hc_ExportMenu.Rd man/dapar_hc_chart.Rd man/deleteLinesFromIndices.Rd man/densityPlotD_HC.Rd man/diffAnaComputeAdjustedPValues.Rd man/diffAnaComputeFDR.Rd man/diffAnaGetSignificant.Rd man/diffAnaSave.Rd man/diffAnaVolcanoplot.Rd man/diffAnaVolcanoplot_rCharts.Rd man/display.CC.visNet.Rd man/enrich_GO.Rd man/finalizeAggregation.Rd man/findMECBlock.Rd man/formatHSDResults.Rd man/formatLimmaResult.Rd man/formatPHResults.Rd man/formatPHTResults.Rd man/fudge2LRT.Rd man/get.pep.prot.cc.Rd man/getDesignLevel.Rd man/getIndicesConditions.Rd man/getIndicesOfLinesToRemove.Rd man/getListNbValuesInLines.Rd man/getNumberOf.Rd man/getNumberOfEmptyLines.Rd man/getPourcentageOfMV.Rd man/getProcessingInfo.Rd man/getProteinsStats.Rd man/getQuantile4Imp.Rd man/getTextForAggregation.Rd man/getTextForAnaDiff.Rd man/getTextForFiltering.Rd man/getTextForGOAnalysis.Rd man/getTextForHypothesisTest.Rd man/getTextForNewDataset.Rd man/getTextForNormalization.Rd man/getTextForpeptideImputation.Rd man/getTextForproteinImputation.Rd man/globalAdjPval.Rd man/group_GO.Rd man/hc_logFC_DensityPlot.Rd man/hc_mvTypePlot2.Rd man/heatmapD.Rd man/heatmapForMissingValues.Rd man/histPValue_HC.Rd man/impute.pa2.Rd man/inner.aggregate.iter.Rd man/inner.aggregate.topn.Rd man/inner.mean.Rd man/inner.sum.Rd man/is.subset.Rd man/limmaCompleteTest.Rd man/listSheets.Rd man/make.contrast.Rd man/make.design.1.Rd man/make.design.2.Rd man/make.design.3.Rd man/make.design.Rd man/match.metacell.Rd man/metacell.def.Rd man/metacellHisto_HC.Rd man/metacellPerLinesHistoPerCondition_HC.Rd man/metacellPerLinesHisto_HC.Rd man/metacombine.Rd man/mvImage.Rd man/my_hc_ExportMenu.Rd man/my_hc_chart.Rd man/nonzero.Rd man/normalizeMethods.dapar.Rd man/pepa.test.Rd man/pkgs.require.Rd man/plotJitter.Rd man/plotJitter_rCharts.Rd man/plotPCA_Eigen.Rd man/plotPCA_Eigen_hc.Rd man/plotPCA_Ind.Rd man/plotPCA_Var.Rd man/postHocTest.Rd man/proportionConRev_HC.Rd man/rbindMSnset.Rd man/reIntroduceMEC.Rd man/readExcel.Rd man/removeLines.Rd man/samLRT.Rd man/saveParameters.Rd man/scatterplotEnrichGO_HC.Rd man/search.metacell.tags.Rd man/separateAdjPval.Rd man/splitAdjacencyMat.Rd man/test.design.Rd man/testAnovaModels.Rd man/thresholdpval4fdr.Rd man/translatedRandomBeta.Rd man/univ_AnnotDbPkg.Rd man/violinPlotD.Rd man/visualizeClusters.Rd man/vsn.Rd man/wrapper.CVDistD_HC.Rd man/wrapper.compareNormalizationD_HC.Rd man/wrapper.corrMatrixD_HC.Rd man/wrapper.dapar.impute.mi.Rd man/wrapper.heatmapD.Rd man/wrapper.impute.KNN.Rd man/wrapper.impute.detQuant.Rd man/wrapper.impute.fixedValue.Rd man/wrapper.impute.mle.Rd man/wrapper.impute.pa.Rd man/wrapper.impute.pa2.Rd man/wrapper.impute.slsa.Rd man/wrapper.mvImage.Rd man/wrapper.normalizeD.Rd man/wrapper.pca.Rd man/wrapperCalibrationPlot.Rd man/wrapperClassic1wayAnova.Rd man/wrapperRunClustering.Rd man/write.excel.Rd man/writeMSnsetToCSV.Rd man/writeMSnsetToExcel.Rd tests/testthat.R tests/testthat/test_Volcanoplot.R tests/testthat/test_agregation.R tests/testthat/test_descriptiveStatistics.R tests/testthat/test_differentialAnalysis.R tests/testthat/test_limmaAnalysis.R tests/testthat/test_metacell.R tests/testthat/test_missingValuesImputation.R tests/testthat/test_missingValuesPlots.R tests/testthat/test_mvFilter.R tests/testthat/test_normalisation.R tests/testthat/test_peptide_imputation.R tests/testthat/test_protein_imputation.R tests/testthat/test_utils.R