NAMESPACE

# Generated by roxygen2: do not edit by hand

export(aggregateNonCountSignal)
export(aggregateToPseudoBulk)
export(aggregateVar)
export(as.dreamletResult)
export(buildClusterTreeFromPB)
export(cellCounts)
export(cellTypeSpecificity)
export(coefNames)
export(compositePosteriorTest)
export(computeCellCounts)
export(computeLogCPM)
export(computeNormCounts)
export(details)
export(dreamlet)
export(dreamletCompareClusters)
export(dropRedundantTerms)
export(extractData)
export(fitVarPart)
export(meta_analysis)
export(outlier)
export(outlierByAssay)
export(plotBeeswarm)
export(plotCellComposition)
export(plotForest)
export(plotGeneHeatmap)
export(plotHeatmap)
export(plotProjection)
export(plotViolin)
export(plotVolcano)
export(plotVoom)
export(processAssays)
export(removeConstantTerms)
export(run_mash)
export(seeErrors)
export(stackAssays)
exportClasses(cellSpecificityValues)
exportClasses(dreamletProcessedData)
exportClasses(dreamletResult)
exportClasses(dreamlet_mash_result)
exportClasses(vpDF)
exportMethods("[")
exportMethods("colData<-")
exportMethods(assay)
exportMethods(assayNames)
exportMethods(coefNames)
exportMethods(colData)
exportMethods(details)
exportMethods(dreamlet)
exportMethods(extractData)
exportMethods(fitVarPart)
exportMethods(getTreat)
exportMethods(metadata)
exportMethods(plotCellComposition)
exportMethods(plotForest)
exportMethods(plotHeatmap)
exportMethods(plotPCA)
exportMethods(plotPercentBars)
exportMethods(print)
exportMethods(residuals)
exportMethods(seeErrors)
exportMethods(show)
exportMethods(sortCols)
exportMethods(topTable)
exportMethods(zenith_gsa)
import(Rcpp)
import(ggplot2)
importClassesFrom(SparseArray,SparseArray)
importClassesFrom(limma,EList)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(DelayedArray,colsum)
importFrom(DelayedArray,defaultAutoGrid)
importFrom(DelayedArray,getAutoBlockSize)
importFrom(DelayedArray,setAutoBlockSize)
importFrom(DelayedMatrixStats,colSums2)
importFrom(GSEABase,geneIds)
importFrom(IRanges,ranges)
importFrom(MASS,cov.rob)
importFrom(Matrix,colSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,summary)
importFrom(Matrix,t)
importFrom(MatrixGenerics,colMeans2)
importFrom(MatrixGenerics,colVars)
importFrom(MatrixGenerics,rowCounts)
importFrom(MatrixGenerics,rowMeans2)
importFrom(MatrixGenerics,rowMedians)
importFrom(MatrixGenerics,rowSds)
importFrom(MatrixGenerics,rowSums2)
importFrom(MatrixGenerics,rowVars)
importFrom(Rdpack,reprompt)
importFrom(S4Arrays,read_block)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,as.data.frame)
importFrom(S4Vectors,coolcat)
importFrom(S4Vectors,extractROWS)
importFrom(S4Vectors,merge)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,selfmatch)
importFrom(S4Vectors,wmsg)
importFrom(SingleCellExperiment,"int_colData<-")
importFrom(SingleCellExperiment,"reducedDims<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,int_colData)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"metadata<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(ashr,get_lfsr)
importFrom(ashr,get_pm)
importFrom(ashr,get_psd)
importFrom(broom,tidy)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(dplyr,`%>%`)
importFrom(dplyr,across)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_rows)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,filter_at)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,group_modify)
importFrom(dplyr,inner_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,summarise_at)
importFrom(dplyr,summarize)
importFrom(dplyr,sym)
importFrom(dplyr,tibble)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,filterByExpr)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(ggrepel,geom_text_repel)
importFrom(gtools,smartbind)
importFrom(irlba,prcomp_irlba)
importFrom(limma,cameraPR)
importFrom(limma,ids2indices)
importFrom(lme4,findbars)
importFrom(lme4,nobars)
importFrom(lme4,subbars)
importFrom(mashr,cov_canonical)
importFrom(mashr,mash_estimate_corr_em)
importFrom(mashr,mash_set_data)
importFrom(metafor,rma)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(purrr,map)
importFrom(remaCor,RE2C)
importFrom(reshape2,melt)
importFrom(rlang,sym)
importFrom(scattermore,geom_scattermore)
importFrom(stats,as.formula)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,mahalanobis)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,prcomp)
importFrom(stats,qnorm)
importFrom(stats,reformulate)
importFrom(stats,terms)
importFrom(stats,update.formula)
importFrom(stats,var)
importFrom(tidyr,complete)
importFrom(utils,head)
importFrom(utils,tail)
importFrom(variancePartition,augmentPriorCount)
importFrom(variancePartition,dream)
importFrom(variancePartition,eBayes)
importFrom(variancePartition,fitExtractVarPartModel)
importFrom(variancePartition,getContrast)
importFrom(variancePartition,getTreat)
importFrom(variancePartition,ggColorHue)
importFrom(variancePartition,makeContrastsDream)
importFrom(variancePartition,plotPercentBars)
importFrom(variancePartition,topTable)
importFrom(variancePartition,voomWithDreamWeights)
importFrom(zenith,zenith)
importMethodsFrom(BiocGenerics,residuals)
importMethodsFrom(GSEABase,details)
importMethodsFrom(variancePartition,sortCols)
useDynLib(dreamlet)