# Generated by roxygen2: do not edit by hand

export(.logBH)
export(DM)
export(bootstrapCluster)
export(buildKNNGraph)
export(buildSNNGraph)
export(calculateSumFactors)
export(clusterCells)
export(clusterKNNGraph)
export(clusterModularity)
export(clusterPurity)
export(clusterSNNGraph)
export(coassignProb)
export(combineBlocks)
export(combineCV2)
export(combineMarkers)
export(combinePValues)
export(combineVar)
export(computeMinRank)
export(computeSumFactors)
export(connectClusterMST)
export(convertTo)
export(correlateGenes)
export(correlateNull)
export(correlatePairs)
export(createClusterMST)
export(cyclone)
export(decideTestsPerLabel)
export(decomposeVar)
export(denoisePCA)
export(denoisePCANumber)
export(doubletCells)
export(doubletCluster)
export(doubletRecovery)
export(findMarkers)
export(fitTrendCV2)
export(fitTrendPoisson)
export(fitTrendVar)
export(fixedPCA)
export(getClusteredPCs)
export(getDenoisedPCs)
export(getMarkerEffects)
export(getTopHVGs)
export(getTopMarkers)
export(improvedCV2)
export(makeTechTrend)
export(modelGeneCV2)
export(modelGeneCV2WithSpikes)
export(modelGeneVar)
export(modelGeneVarByPoisson)
export(modelGeneVarWithSpikes)
export(multiBlockNorm)
export(multiBlockVar)
export(multiMarkerStats)
export(orderClusterMST)
export(overlapExprs)
export(pairwiseBinom)
export(pairwiseTTests)
export(pairwiseWilcox)
export(parallelPCA)
export(pseudoBulkDGE)
export(pseudoBulkSpecific)
export(quickCluster)
export(quickPseudotime)
export(quickSubCluster)
export(rhoToPValue)
export(sandbag)
export(scaledColRanks)
export(scoreMarkers)
export(summarizeTestsPerLabel)
export(summaryMarkerStats)
export(technicalCV2)
export(testLinearModel)
export(testPseudotime)
export(testVar)
export(trendVar)
exportMethods(buildKNNGraph)
exportMethods(buildSNNGraph)
exportMethods(correlatePairs)
exportMethods(cyclone)
exportMethods(findMarkers)
exportMethods(getDenoisedPCs)
exportMethods(modelGeneCV2)
exportMethods(modelGeneCV2WithSpikes)
exportMethods(modelGeneVar)
exportMethods(modelGeneVarByPoisson)
exportMethods(modelGeneVarWithSpikes)
exportMethods(pairwiseBinom)
exportMethods(pairwiseTTests)
exportMethods(pairwiseWilcox)
exportMethods(pseudoBulkDGE)
exportMethods(pseudoBulkSpecific)
exportMethods(quickCluster)
exportMethods(quickSubCluster)
exportMethods(sandbag)
exportMethods(scoreMarkers)
exportMethods(summaryMarkerStats)
exportMethods(testLinearModel)
import(SingleCellExperiment)
import(methods)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(Matrix,sparseMatrix)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,List)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(BiocGenerics,"sizeFactors<-")
importFrom(BiocGenerics,as.data.frame)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,sizeFactors)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bpisup)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocParallel,bpstart)
importFrom(BiocParallel,bpstop)
importFrom(BiocSingular,LowRankMatrix)
importFrom(BiocSingular,bsdeferred)
importFrom(BiocSingular,bsparam)
importFrom(BiocSingular,runSVD)
importFrom(DelayedArray,DelayedArray)
importFrom(DelayedArray,currentViewport)
importFrom(DelayedArray,getAutoBPPARAM)
importFrom(DelayedArray,makeNindexFromArrayViewport)
importFrom(DelayedArray,setAutoBPPARAM)
importFrom(DelayedMatrixStats,colAnyNAs)
importFrom(DelayedMatrixStats,colMins)
importFrom(DelayedMatrixStats,colRanks)
importFrom(DelayedMatrixStats,colVars)
importFrom(DelayedMatrixStats,rowMaxs)
importFrom(DelayedMatrixStats,rowMedians)
importFrom(DelayedMatrixStats,rowMins)
importFrom(DelayedMatrixStats,rowRanks)
importFrom(DelayedMatrixStats,rowSds)
importFrom(DelayedMatrixStats,rowVars)
importFrom(DelayedMatrixStats,rowWeightedMeans)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,t)
importFrom(Matrix,which)
importFrom(Rcpp,sourceCpp)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,I)
importFrom(S4Vectors,List)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,match)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,selfmatch)
importFrom(S4Vectors,splitAsList)
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExp)
importFrom(SingleCellExperiment,colLabels)
importFrom(SingleCellExperiment,reduced.dim.matrix)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(beachmat,colBlockApply)
importFrom(beachmat,realizeFileBackedMatrix)
importFrom(beachmat,rowBlockApply)
importFrom(bluster,HclustParam)
importFrom(bluster,NNGraphParam)
importFrom(bluster,clusterRows)
importFrom(bluster,makeKNNGraph)
importFrom(bluster,makeSNNGraph)
importFrom(dqrng,generateSeedVectors)
importFrom(edgeR,"[.DGEList")
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,filterByExpr)
importFrom(edgeR,getOffset)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,glmTreat)
importFrom(edgeR,scaleOffset)
importFrom(edgeR,scaleOffset.DGEList)
importFrom(edgeR,topTags)
importFrom(igraph,E)
importFrom(igraph,cluster_walktrap)
importFrom(igraph,modularity)
importFrom(limma,classifyTestsF)
importFrom(limma,contrastAsCoef)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(limma,treat)
importFrom(limma,voom)
importFrom(limma,voomWithQualityWeights)
importFrom(limma,weighted.median)
importFrom(limma,weightedLowess)
importFrom(metapod,averageParallelStats)
importFrom(metapod,combineParallelPValues)
importFrom(metapod,parallelStouffer)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,selectMethod)
importFrom(scuttle,.assignIndicesToWorkers)
importFrom(scuttle,.bpNotSharedOrUp)
importFrom(scuttle,.guessMinMean)
importFrom(scuttle,.ranksafeQR)
importFrom(scuttle,.splitVectorByWorkers)
importFrom(scuttle,.subset2index)
importFrom(scuttle,.unpackLists)
importFrom(scuttle,calculateAverage)
importFrom(scuttle,computePooledFactors)
importFrom(scuttle,correctGroupSummary)
importFrom(scuttle,fitLinearModel)
importFrom(scuttle,librarySizeFactors)
importFrom(scuttle,logNormCounts)
importFrom(scuttle,normalizeCounts)
importFrom(scuttle,numDetectedAcrossCells)
importFrom(scuttle,pooledSizeFactors)
importFrom(scuttle,sumCountsAcrossCells)
importFrom(scuttle,summarizeAssayByGroup)
importFrom(statmod,glmgam.fit)
importFrom(stats,approx)
importFrom(stats,approxfun)
importFrom(stats,coef)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,fitted)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,nls)
importFrom(stats,nls.control)
importFrom(stats,p.adjust)
importFrom(stats,pbinom)
importFrom(stats,pf)
importFrom(stats,pnorm)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,rnbinom)
importFrom(stats,rpois)
importFrom(stats,runmed)
importFrom(stats,var)
importFrom(utils,head)
importFrom(utils,tail)
importMethodsFrom(S4Vectors,"%in%")
useDynLib(scran)
