NAMESPACE

# Generated by roxygen2: do not edit by hand

export(AggregateMetacell)
export(BuildAdjacencyMatrix)
export(BuildColumnToProteinDataset)
export(BuildColumnToProteinDataset_par)
export(BuildMetaCell)
export(CVDistD_HC)
export(CountPep)
export(ExtendPalette)
export(GOAnalysisSave)
export(GetCC)
export(GetColorsForConditions)
export(GetDetailedNbPeptides)
export(GetDetailedNbPeptidesUsed)
export(GetIndices_BasedOnConditions)
export(GetIndices_MetacellFiltering)
export(GetIndices_WholeLine)
export(GetIndices_WholeMatrix)
export(GetKeyId)
export(GetMatAdj)
export(GetMetacell)
export(GetNbPeptidesUsed)
export(GetTypeofData)
export(Get_AllComparisons)
export(GlobalQuantileAlignment)
export(GraphPepProt)
export(LH0)
export(LH0.lm)
export(LH1)
export(LH1.lm)
export(LOESS)
export(MeanCentering)
export(MetaCellFiltering)
export(MetacellFilteringScope)
export(Metacell_generic)
export(Metacell_maxquant)
export(Metacell_proline)
export(NumericalFiltering)
export(NumericalgetIndicesOfLinesToRemove)
export(QuantileCentering)
export(SetCC)
export(SetMatAdj)
export(Set_POV_MEC_tags)
export(StringBasedFiltering)
export(StringBasedFiltering2)
export(SumByColumns)
export(SymFilteringOperators)
export(UpdateMetacell)
export(aggregateIter)
export(aggregateIterParallel)
export(aggregateMean)
export(aggregateSum)
export(aggregateTopn)
export(averageIntensities)
export(barplotEnrichGO_HC)
export(barplotGroupGO_HC)
export(boxPlotD_HC)
export(buildGraph)
export(check.conditions)
export(check.design)
export(checkClusterability)
export(classic1wayAnova)
export(compareNormalizationD_HC)
export(compute_t_tests)
export(corrMatrixD_HC)
export(createMSnset)
export(dapar_hc_ExportMenu)
export(dapar_hc_chart)
export(deleteLinesFromIndices)
export(densityPlotD_HC)
export(diffAnaComputeFDR)
export(diffAnaGetSignificant)
export(diffAnaSave)
export(diffAnaVolcanoplot)
export(diffAnaVolcanoplot_rCharts)
export(display.CC.visNet)
export(enrich_GO)
export(finalizeAggregation)
export(findMECBlock)
export(formatPHResults)
export(fudge2LRT)
export(get.pep.prot.cc)
export(getIndicesConditions)
export(getIndicesOfLinesToRemove)
export(getListNbValuesInLines)
export(getNumberOf)
export(getNumberOfEmptyLines)
export(getPourcentageOfMV)
export(getProcessingInfo)
export(getProteinsStats)
export(getQuantile4Imp)
export(getTextForAggregation)
export(getTextForAnaDiff)
export(getTextForFiltering)
export(getTextForGOAnalysis)
export(getTextForHypothesisTest)
export(getTextForNewDataset)
export(getTextForNormalization)
export(getTextForpeptideImputation)
export(getTextForproteinImputation)
export(group_GO)
export(hc_logFC_DensityPlot)
export(hc_mvTypePlot2)
export(heatmapD)
export(heatmapForMissingValues)
export(histPValue_HC)
export(impute.pa2)
export(inner.aggregate.iter)
export(limmaCompleteTest)
export(listSheets)
export(make.contrast)
export(make.design)
export(make.design.1)
export(make.design.2)
export(make.design.3)
export(match.metacell)
export(metacell.def)
export(metacellHisto_HC)
export(metacellPerLinesHistoPerCondition_HC)
export(metacellPerLinesHisto_HC)
export(mvImage)
export(my_hc_ExportMenu)
export(my_hc_chart)
export(nonzero)
export(normalizeMethods.dapar)
export(pepa.test)
export(plotJitter)
export(plotJitter_rCharts)
export(plotPCA_Eigen)
export(plotPCA_Eigen_hc)
export(plotPCA_Ind)
export(plotPCA_Var)
export(postHocTest)
export(proportionConRev_HC)
export(rbindMSnset)
export(reIntroduceMEC)
export(readExcel)
export(removeLines)
export(samLRT)
export(saveParameters)
export(scatterplotEnrichGO_HC)
export(search.metacell.tags)
export(splitAdjacencyMat)
export(test.design)
export(translatedRandomBeta)
export(univ_AnnotDbPkg)
export(violinPlotD)
export(visualizeClusters)
export(vsn)
export(wrapper.CVDistD_HC)
export(wrapper.compareNormalizationD_HC)
export(wrapper.corrMatrixD_HC)
export(wrapper.dapar.impute.mi)
export(wrapper.heatmapD)
export(wrapper.impute.KNN)
export(wrapper.impute.detQuant)
export(wrapper.impute.fixedValue)
export(wrapper.impute.mle)
export(wrapper.impute.pa)
export(wrapper.impute.pa2)
export(wrapper.impute.slsa)
export(wrapper.mvImage)
export(wrapper.normalizeD)
export(wrapper.pca)
export(wrapperCalibrationPlot)
export(wrapperClassic1wayAnova)
export(wrapperRunClustering)
export(write.excel)
export(writeMSnsetToCSV)
export(writeMSnsetToExcel)
import(ggplot2)
import(graphics)
import(highcharter)
import(limma)
importFrom(MSnbase,MSnSet)
importFrom(Matrix,"%&%")
importFrom(Matrix,crossprod)
importFrom(RColorBrewer,brewer.pal)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_cols)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,tbl_df)
importFrom(gplots,heatmap.2)
importFrom(grDevices,boxplot.stats)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,heat.colors)
importFrom(graph,connComp)
importFrom(graph,graphAM)
importFrom(graphics,axis)
importFrom(graphics,image)
importFrom(graphics,legend)
importFrom(graphics,mtext)
importFrom(graphics,plot.new)
importFrom(graphics,plot.window)
importFrom(graphics,points)
importFrom(graphics,segments)
importFrom(imp4p,estim.bound)
importFrom(imp4p,estim.mix)
importFrom(imp4p,impute.pa)
importFrom(imp4p,impute.rand)
importFrom(imp4p,mi.mix)
importFrom(imp4p,prob.mcar.tab)
importFrom(limma,normalizeCyclicLoess)
importFrom(methods,is)
importFrom(preprocessCore,normalize.quantiles)
importFrom(reshape2,melt)
importFrom(stats,aov)
importFrom(stats,as.dendrogram)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,formula)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,logLik)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.exclude)
importFrom(stats,na.omit)
importFrom(stats,pchisq)
importFrom(stats,quantile)
importFrom(stats,rbeta)
importFrom(stats,residuals)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stats,var)
importFrom(stringr,str_glue)
importFrom(stringr,str_trim)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_wider)
importFrom(utils,combn)
importFrom(utils,installed.packages)
importFrom(utils,read.table)
importFrom(utils,str)
importFrom(utils,write.csv)
importFrom(utils,zip)