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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("clusterAnalysis<-")
export("colInfo<-")
export("controls<-")
export("progressLog<-")
export("regcounts<-")
export("rowInfo<-")
export(EMSet)
export(addGeneLabel)
export(calcGeoMeansDense)
export(calcGeoMeansSparse)
export(calcNormFactorDense)
export(calcNormFactorSparse)
export(calculateCV)
export(calculateQC)
export(clusterAnalysis)
export(colInfo)
export(controls)
export(convert)
export(convertGeneID)
export(convertSparse)
export(excludeControl)
export(filterByControl)
export(filterByOutliers)
export(filterLowAbundanceGenes)
export(func_DESeq)
export(loadCellRanger)
export(normaliseBatches)
export(normaliseByRLE)
export(plotAverageGeneCount)
export(plotBatchNormQC)
export(plotControlHist)
export(plotControlPctPerSample)
export(plotDendrogram)
export(plotFeatureHist)
export(plotGeneNumber)
export(plotGeneralQC)
export(plotLibsizeBoxplot)
export(plotLibsizeHist)
export(plotLibsizePerSample)
export(plotMDS)
export(plotNormQC)
export(plotPCA)
export(plotPCAVariance)
export(plotSmoothScatter)
export(plotStability)
export(plotStabilityDendro)
export(plotTSNE)
export(plotTopGenesBoxplot)
export(plotTopGenesPerSample)
export(plotUMAP)
export(plotVariableGenes)
export(plotVolcano)
export(progressLog)
export(regcounts)
export(regressConfoundingFactors)
export(rowInfo)
export(runCORE)
export(runDESeq)
export(runDESeq2)
export(runDiffExpression)
export(runPCA)
export(runSCTransform)
export(runTSNE)
export(runUMAP)
export(scranCellCycle)
export(scranNormalise)
export(subsetCondition)
export(useVariableGenes)
export(validateEMSet)
exportClasses(EMSet)
exportMethods(show)
exportMethods(updateObject)
import(RcppArmadillo)
import(SingleCellExperiment)
import(SummarizedExperiment)
import(methods)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,rownames)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocParallel,bpparam)
importFrom(BiocParallel,bpvec)
importFrom(MASS,kde2d)
importFrom(Matrix,rowSums)
importFrom(Matrix,t)
importFrom(Rcpp,sourceCpp)
importFrom(Rtsne,Rtsne)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,merge)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,isSpike)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,normcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SingleCellExperiment,rowData)
importFrom(SingleCellExperiment,sizeFactors)
importFrom(SingleCellExperiment,spikeNames)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(data.table,as.data.table)
importFrom(dendextend,"%>%")
importFrom(dendextend,branches_attr_by_clusters)
importFrom(dendextend,colored_bars)
importFrom(dendextend,get_leaves_branches_attr)
importFrom(dendextend,get_leaves_branches_col)
importFrom(dendextend,set)
importFrom(dendextend,sort_levels_values)
importFrom(dplyr,bind_rows)
importFrom(dplyr,id)
importFrom(dplyr,intersect)
importFrom(dplyr,left_join)
importFrom(dplyr,semi_join)
importFrom(dynamicTreeCut,cutreeDynamic)
importFrom(fastcluster,hclust)
importFrom(fields,interp.surface)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,qplot)
importFrom(ggplot2,scale_alpha)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(graphics,legend)
importFrom(graphics,smoothScatter)
importFrom(gridExtra,grid.arrange)
importFrom(irlba,prcomp_irlba)
importFrom(methods,is)
importFrom(reshape2,melt)
importFrom(stats,as.dendrogram)
importFrom(stats,cmdscale)
importFrom(stats,dist)
importFrom(stats,median)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,reorder)
importFrom(stats,setNames)
importFrom(tidyr,gather)
importFrom(umap,umap)
useDynLib(ascend)