# Generated by roxygen2: do not edit by hand

export("ConnectedComp<-")
export("DifferentialAnalysis<-")
export("HypothesisTest<-")
export("analysis<-")
export("design_qf<-")
export("filename<-")
export("idcol<-")
export("names_metacell<-")
export("paramshistory<-")
export("parentProtId<-")
export("qMetacell<-")
export("typeDataset<-")
export("version<-")
export(Add2History)
export(Add_Aggregated_rowData)
export(Add_Item_to_Dataset)
export(AdjMatFilters)
export(BuildAdjacencyMatrix)
export(BuildColumnToProteinDataset)
export(BuildMetacell)
export(Children)
export(CleanRowData)
export(ConvertListToHtml)
export(CountPep)
export(ExtendPalette)
export(ExtractUniquePeptides)
export(FunctionFilter)
export(GetColorsForConditions)
export(GetDetailedNbPeptides)
export(GetDetailedNbPeptidesUsed)
export(GetHistory)
export(GetIndices_BasedOnConditions)
export(GetIndices_FunFiltering)
export(GetIndices_WholeLine)
export(GetIndices_WholeMatrix)
export(GetMetacellTags)
export(GetMetadataSlot)
export(GetNbPeptidesUsed)
export(GetNbTags)
export(GetSoftAvailables)
export(GlobalQuantileAlignment)
export(GraphPepProt)
export(InitializeHistory)
export(Keep_Items_from_Dataset)
export(LH0)
export(LH0_lm)
export(LH1)
export(LH1_lm)
export(LOESS)
export(MeanCentering)
export(MetacellFilteringScope)
export(Metacell_DIA_NN)
export(Metacell_generic)
export(Metacell_maxquant)
export(Metacell_proline)
export(NAIsZero)
export(OWAnova)
export(Parent)
export(Pipelines)
export(QFeaturesFromSE)
export(QuantileCentering)
export(ReplaceSpecialChars)
export(RunAggregation)
export(SetHistory)
export(Set_POV_MEC_tags)
export(Set_POV_MEC_tags2)
export(SumByColumns)
export(SymFilteringOperators)
export(WriteHistory)
export(Write_RowData)
export(Write_SamplesData_to_Excel)
export(aggQmetacell)
export(aggregateMethods)
export(allPeptides)
export(applyAnovasOnProteins)
export(buildGraph)
export(checkConditions)
export(checkDesign)
export(classic1wayAnova)
export(compareNormalizationD_HC)
export(compute_t_tests)
export(createQFeatures)
export(custom_metacell_colors)
export(diffAnaComputeAdjustedPValues)
export(diffAnaComputeFDR)
export(diffAnaVolcanoplot_rCharts)
export(displayCCvisNet)
export(findMECBlock)
export(formatPHResults)
export(fudge2LRT)
export(getDesignLevel)
export(getListNbValuesInLines)
export(getNumberOfEmptyLines)
export(getPepProtCC)
export(getProteinsStats)
export(getQuantile4Imp)
export(globalAdjPval)
export(hc_logFC_DensityPlot)
export(hc_mvTypePlot2)
export(heatmapForMissingValues)
export(histPValue_HC)
export(imputePA2)
export(innerAggregateIter)
export(innerMean)
export(innerMedian)
export(innerMedianpolish)
export(innerRobustsummary)
export(innerSum)
export(isDifferential)
export(isOfType)
export(isSubset)
export(last_assay)
export(limmaCompleteTest)
export(listSheets)
export(mainAssay)
export(makeContrast)
export(makeDesign)
export(makeDesign1)
export(makeDesign2)
export(makeDesign3)
export(matchMetacell)
export(metacellDef)
export(metacellHisto_HC)
export(metacellPerLinesHistoPerCondition_HC)
export(metacellPerLinesHisto_HC)
export(metacell_agg)
export(metacombine)
export(mvImage)
export(nEmptyLines)
export(n_assays_in_qf)
export(nonzero)
export(normalizeFunction)
export(normalizeMethods)
export(pepaTest)
export(pkgsRequire)
export(plotCompareAssays)
export(plotJitter)
export(plotJitter_rCharts)
export(postHocTest)
export(pushpvalue)
export(qMetacellFilteringScope)
export(qMetacellOnConditions)
export(qMetacellWholeLine)
export(qMetacellWholeMatrix)
export(reIntroduceMEC)
export(readExcel)
export(samLRT)
export(searchMetacellTags)
export(select_topn)
export(separateAdjPval)
export(sharedPeptides)
export(specPeptides)
export(splitAdjacencyMat)
export(subAdjMat_sharedPeptides)
export(subAdjMat_specificPeptides)
export(subAdjMat_topnPeptides)
export(testAnovaModels)
export(testDesign)
export(topnFunctions)
export(topnPeptides)
export(translatedRandomBeta)
export(vsn)
export(wrapperCalibrationPlot)
export(wrapperClassic1wayAnova)
export(wrapperDaparImputeMI)
export(wrapperImputeDetQuant)
export(wrapperImputeFixedValue)
export(wrapperImputeKNN)
export(wrapperImputeMLE)
export(wrapperImputePA)
export(wrapperImputePA2)
export(wrapperImputeSLSA)
export(wrapperMVImage)
export(wrapperPirat)
export(writeExcel)
export(write_Assay_To_Excel)
exportClasses(FunctionFilter)
exportMethods(ConnectedComp)
exportMethods(DifferentialAnalysis)
exportMethods(GetMetacellTags)
exportMethods(GetUniqueTags)
exportMethods(HypothesisTest)
exportMethods(UpdateMetacellAfterImputation)
exportMethods(aggregateFeatures4Prostar)
exportMethods(aggregateRedistribution)
exportMethods(analysis)
exportMethods(design_qf)
exportMethods(filename)
exportMethods(filterFeaturesOneSE)
exportMethods(idcol)
exportMethods(names_metacell)
exportMethods(paramshistory)
exportMethods(parentProtId)
exportMethods(qMetacell)
exportMethods(typeDataset)
exportMethods(version)
exportMethods(write2excel)
import(AnnotationFilter)
import(QFeatures)
import(SummarizedExperiment)
import(dplyr)
import(grDevices)
import(openxlsx)
import(plotly)
importFrom(BiocGenerics,t)
importFrom(Matrix,Matrix)
importFrom(Matrix,crossprod)
importFrom(MsCoreUtils,robustSummary)
importFrom(QFeatures,addAssay)
importFrom(QFeatures,addAssayLink)
importFrom(QFeatures,adjacencyMatrix)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,sort)
importFrom(graph,connComp)
importFrom(graph,graphAM)
importFrom(graphics,barplot)
importFrom(graphics,hist)
importFrom(graphics,par)
importFrom(igraph,components)
importFrom(igraph,graph.adjacency)
importFrom(matrixStats,colMedians)
importFrom(matrixStats,rowMedians)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(preprocessCore,normalize.quantiles)
importFrom(stats,TukeyHSD)
importFrom(stats,aov)
importFrom(stats,density)
importFrom(stats,formula)
importFrom(stats,lm)
importFrom(stats,logLik)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,model.matrix)
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(stringr,str_trim)
importFrom(tibble,as_tibble)
importFrom(utils,combn)
importFrom(utils,installed.packages)
importFrom(utils,read.table)
importFrom(utils,stack)
importFrom(utils,str)
