# Generated by roxygen2: do not edit by hand

export(calculate_jaccard)
export(clusterwise_DE_analysis)
export(coverage_rate)
export(detection_accuracy)
export(generate_cell_network.wt.loess)
export(get_dropout_rates)
export(get_rooted_membership)
export(identify_scale_parameter)
export(inclusion_rate)
export(iterative_clustering)
export(iterative_clustering.par)
export(load_mtx)
export(msc_workflow)
export(plot_dimred_manual.raw)
export(plot_hierarchy_dot.raw)
export(plot_hierarchy_pie)
export(process_data)
export(prune_hierarchy.compact)
export(run_hierarchical_markers.par)
export(split_network)
import(igraph)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,lfcShrink)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rtsne,Rtsne)
importFrom(Seurat,GetAssayData)
importFrom(SeuratObject,WhichCells)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,sizeFactors)
importFrom(SummarizedExperiment,assay)
importFrom(doParallel,registerDoParallel)
importFrom(foreach,"%dopar%")
importFrom(foreach,getDoParWorkers)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_equal)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_colorbar)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_colour_gradient2)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggraph,geom_edge_diagonal)
importFrom(ggraph,ggraph)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,abline)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,plot.new)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,as_adj)
importFrom(igraph,diameter)
importFrom(igraph,ecount)
importFrom(igraph,edge_betweenness)
importFrom(igraph,edges)
importFrom(igraph,ego)
importFrom(igraph,get.adjacency)
importFrom(igraph,graph.data.frame)
importFrom(igraph,induced_subgraph)
importFrom(igraph,is.connected)
importFrom(igraph,make_ego_graph)
importFrom(igraph,mst)
importFrom(igraph,shortest_paths)
importFrom(igraph,subgraph)
importFrom(igraph,vcount)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(rpart,rpart)
importFrom(rsvd,rsvd)
importFrom(scater,logNormCounts)
importFrom(scater,runTSNE)
importFrom(scater,runUMAP)
importFrom(scatterpie,geom_scatterpie)
importFrom(scran,computeSumFactors)
importFrom(scran,denoisePCA)
importFrom(scran,fixedPCA)
importFrom(scran,getClusteredPCs)
importFrom(scran,getTopHVGs)
importFrom(scran,modelGeneVar)
importFrom(scran,quickCluster)
importFrom(scuttle,logNormCounts)
importFrom(stats,cor)
importFrom(stats,dgamma)
importFrom(stats,dnorm)
importFrom(stats,fisher.test)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,quantile)
importFrom(stats,residuals)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,shapiro.test)
importFrom(stats,weighted.mean)
importFrom(umap,umap)
