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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(aggregateData)
export(calcExprFreqs)
export(mmDS)
export(pbDD)
export(pbDS)
export(pbFlatten)
export(pbHeatmap)
export(pbMDS)
export(prepSCE)
export(prepSim)
export(resDS)
export(simData)
export(stagewise_DS_DD)
import(ggplot2)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,columnAnnotation)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,estimateDispersions)
importFrom(DESeq2,results)
importFrom(DESeq2,sizeFactors)
importFrom(DESeq2,varianceStabilizingTransformation)
importFrom(Matrix,colSums)
importFrom(Matrix,qr)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,t)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,as.list)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,split)
importFrom(S4Vectors,unfactor)
importFrom(SingleCellExperiment,"counts<-")
importFrom(SingleCellExperiment,"int_colData<-")
importFrom(SingleCellExperiment,"sizeFactors<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,int_colData)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SingleCellExperiment,sizeFactors)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(blme,bglmer)
importFrom(blme,blmer)
importFrom(data.table,data.table)
importFrom(dplyr,"%>%")
importFrom(dplyr,all_of)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,inner_join)
importFrom(dplyr,last)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,mutate_at)
importFrom(dplyr,mutate_if)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,filterByExpr)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,glmTreat)
importFrom(edgeR,plotMDS.DGEList)
importFrom(edgeR,topTags)
importFrom(glmmTMB,glmmTMB)
importFrom(glmmTMB,nbinom1)
importFrom(grDevices,colorRampPalette)
importFrom(grid,gpar)
importFrom(limma,contrasts.fit)
importFrom(limma,duplicateCorrelation)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(limma,topTreat)
importFrom(limma,treat)
importFrom(limma,voom)
importFrom(lme4,.makeCC)
importFrom(lme4,lmerControl)
importFrom(lmerTest,contest)
importFrom(lmerTest,lmer)
importFrom(matrixStats,colAnys)
importFrom(matrixStats,rowAnyNAs)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowMins)
importFrom(matrixStats,rowQuantiles)
importFrom(matrixStats,rowSds)
importFrom(methods,is)
importFrom(progress,progress_bar)
importFrom(purrr,map)
importFrom(purrr,map_depth)
importFrom(purrr,modify_depth)
importFrom(purrr,negate)
importFrom(purrr,reduce)
importFrom(purrr,set_names)
importFrom(rlang,.data)
importFrom(scales,hue_pal)
importFrom(scater,computeLibraryFactors)
importFrom(scater,isOutlier)
importFrom(sctransform,vst)
importFrom(scuttle,summarizeAssayByGroup)
importFrom(stats,as.formula)
importFrom(stats,coef)
importFrom(stats,df.residual)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,residuals)
importFrom(stats,rgamma)
importFrom(stats,rnbinom)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(variancePartition,dream)
importFrom(variancePartition,getContrast)
importFrom(variancePartition,voomWithDreamWeights)
importFrom(viridis,viridis)