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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("bootstraps<-")
export("fpkm<-")
export("norm_exprs<-")
export("stand_exprs<-")
export(bootstraps)
export(calcAverage)
export(calculateAverage)
export(calculateCPM)
export(calculateFPKM)
export(calculateQCMetrics)
export(calculateTPM)
export(centreSizeFactors)
export(fpkm)
export(getBMFeatureAnnos)
export(getExplanatoryPCs)
export(getVarianceExplained)
export(isOutlier)
export(librarySizeFactors)
export(multiplot)
export(nexprs)
export(norm_exprs)
export(normalizeCounts)
export(normalizeSCE)
export(plotColData)
export(plotDiffusionMap)
export(plotExplanatoryPCs)
export(plotExplanatoryVariables)
export(plotExpression)
export(plotExprsFreqVsMean)
export(plotExprsVsTxLength)
export(plotHeatmap)
export(plotHighestExprs)
export(plotMDS)
export(plotPCASCE)
export(plotPlatePosition)
export(plotRLE)
export(plotReducedDim)
export(plotRowData)
export(plotScater)
export(plotTSNE)
export(plotUMAP)
export(readSparseCounts)
export(runColDataPCA)
export(runDiffusionMap)
export(runMDS)
export(runTSNE)
export(runUMAP)
export(stand_exprs)
export(sumCountsAcrossCells)
export(sumCountsAcrossFeatures)
export(toSingleCellExperiment)
export(uniquifyFeatureNames)
export(updateSCESet)
exportClasses(SCESet)
exportMethods(bootstraps)
exportMethods(normalize)
exportMethods(plotPCA)
exportMethods(runPCA)
import(SingleCellExperiment)
importClassesFrom(DelayedArray,DelayedMatrix)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(BiocGenerics,"colnames<-")
importFrom(BiocGenerics,"counts<-")
importFrom(BiocGenerics,"rownames<-")
importFrom(BiocGenerics,"sizeFactors<-")
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,normalize)
importFrom(BiocGenerics,plotPCA)
importFrom(BiocGenerics,rownames)
importFrom(BiocGenerics,sizeFactors)
importFrom(BiocNeighbors,KmknnParam)
importFrom(BiocNeighbors,findKNN)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocSingular,ExactParam)
importFrom(BiocSingular,runPCA)
importFrom(DelayedArray,DelayedArray)
importFrom(DelayedArray,sweep)
importFrom(DelayedMatrixStats,colQuantiles)
importFrom(DelayedMatrixStats,colSums2)
importFrom(DelayedMatrixStats,colVars)
importFrom(DelayedMatrixStats,rowMeans2)
importFrom(DelayedMatrixStats,rowMedians)
importFrom(DelayedMatrixStats,rowSums2)
importFrom(DelayedMatrixStats,rowVars)
importFrom(Matrix,rowMeans)
importFrom(Matrix,t)
importFrom(Rcpp,sourceCpp)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"cpm<-")
importFrom(SingleCellExperiment,"logcounts<-")
importFrom(SingleCellExperiment,"normcounts<-")
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,"tpm<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,cpm)
importFrom(SingleCellExperiment,int_colData)
importFrom(SingleCellExperiment,int_elementMetadata)
importFrom(SingleCellExperiment,isSpike)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,normcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,spikeNames)
importFrom(SingleCellExperiment,tpm)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_pointrange)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,position_jitter)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,stat_density)
importFrom(ggplot2,stat_smooth)
importFrom(ggplot2,stat_summary)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grid,grid.layout)
importFrom(grid,grid.newpage)
importFrom(grid,pushViewport)
importFrom(grid,viewport)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(stats,cmdscale)
importFrom(stats,coef)
importFrom(stats,dist)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,nls)
importFrom(stats,runif)
importFrom(utils,head)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(viridis,scale_color_viridis)
importFrom(viridis,scale_fill_viridis)
importFrom(viridis,viridis)
useDynLib(scater, .registration=TRUE, .fixes="cxx_")