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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(assignCellCycle)
export(assignIdentities)
export(buildReference)
export(cellula)
export(doEmptyDrops)
export(doNormAndReduce)
export(doQC)
export(downsampleCells)
export(downsampleCounts)
export(findTrajectories)
export(integrateSCE)
export(makeGraphsAndClusters)
export(makeMetacells)
export(metaCluster)
export(multipanel_DR)
export(paramSweepUMAP)
export(plotCycle)
export(plotModularity)
export(plotSilhouette)
export(plot_Coldata)
export(plot_UMAP)
export(plot_dots)
export(rebuildModularity)
export(stacked_Violin)
import(SingleCellExperiment)
importFrom(BiocNeighbors,queryKNN)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseVector)
importFrom(Matrix,t)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(batchelor,fastMNN)
importFrom(batchelor,multiBatchNorm)
importFrom(batchelor,regressBatches)
importFrom(bluster,approxSilhouette)
importFrom(bluster,linkClusters)
importFrom(bluster,makeSNNGraph)
importFrom(bluster,pairwiseModularity)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(ggplot2,.data)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,after_stat)
importFrom(ggplot2,arrow)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_label)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_colour_gradientn)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,stat_density_2d)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,unit)
importFrom(ggplot2,vars)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggrepel,geom_label_repel)
importFrom(grDevices,chull)
importFrom(grDevices,palette.colors)
importFrom(grDevices,rainbow)
importFrom(graphics,legend)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,all_shortest_paths)
importFrom(igraph,as_data_frame)
importFrom(igraph,cluster_leiden)
importFrom(igraph,cluster_louvain)
importFrom(igraph,degree)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,groups)
importFrom(igraph,layout_with_fr)
importFrom(igraph,layout_with_lgl)
importFrom(igraph,mst)
importFrom(igraph,subgraph)
importFrom(matrixStats,colMaxs)
importFrom(matrixStats,colMedians)
importFrom(methods,as)
importFrom(methods,formalArgs)
importFrom(methods,is)
importFrom(patchwork,wrap_plots)
importFrom(reshape2,melt)
importFrom(rlang,sym)
importFrom(scater,plotColData)
importFrom(scater,retrieveCellInfo)
importFrom(scater,runPCA)
importFrom(scran,computeSumFactors)
importFrom(scran,getTopHVGs)
importFrom(scran,modelGeneVar)
importFrom(scran,quickCluster)
importFrom(scuttle,isOutlier)
importFrom(scuttle,logNormCounts)
importFrom(scuttle,perCellQCMetrics)
importFrom(scuttle,summarizeAssayByGroup)
importFrom(stats,complete.cases)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,ksmooth)
importFrom(stats,median)
importFrom(stats,optim)
importFrom(stats,rnorm)
importFrom(utils,head)
importFrom(utils,installed.packages)
importFrom(utils,sessionInfo)
importFrom(utils,tail)
importFrom(uwot,umap)