Files in prostarproteomics/DAPAR
Tools for the Differential Analysis of Proteins Abundance with R
.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/R-CMD-check.yml
.github/workflows/R-check-Bioc.yml
.gitignore
DAPAR.Rproj
DESCRIPTION
NAMESPACE
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
inst/CITATION
inst/NEWS.Rd
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
results/prepro/metabolites_prepro_res.csv
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
