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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(assign_neighbourhoods)
export(calc_AUC_per_neighbourhood)
export(convert_de_stat)
export(de_test_neighbourhoods)
export(de_test_single_neighbourhood)
export(estimate_neighbourhood_sizes)
export(filter_neighbourhoods)
export(plot_DE_gene_set)
export(plot_DE_single_gene)
export(plot_beeswarm_gene_set)
export(plot_beeswarm_single_gene)
export(plot_milo_by_single_metric)
export(rank_neighbourhoods_by_DE_magnitude)
export(spatial_pval_adjustment)
import(Augur)
import(Matrix)
import(ggplot2)
importFrom(BiocParallel,bplapply)
importFrom(RColorBrewer,brewer.pal)
importFrom(RcppGreedySetCover,greedySetCover)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,isEmpty)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,distinct)
importFrom(dplyr,mutate)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,filterByExpr)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,topTags)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(ggpubr,ggarrange)
importFrom(ggraph,geom_edge_link)
importFrom(ggraph,geom_edge_link0)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,ggraph)
importFrom(ggraph,scale_edge_width)
importFrom(grDevices,colorRampPalette)
importFrom(igraph,"E<-")
importFrom(igraph,"V<-")
importFrom(igraph,"vertex_attr<-")
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,connect)
importFrom(igraph,count_triangles)
importFrom(igraph,delete.edges)
importFrom(igraph,induced_subgraph)
importFrom(igraph,is_igraph)
importFrom(igraph,neighborhood)
importFrom(igraph,permute)
importFrom(igraph,set_vertex_attr)
importFrom(igraph,simplify)
importFrom(igraph,vertex_attr)
importFrom(limma,makeContrasts)
importFrom(methods,as)
importFrom(methods,is)
importFrom(miloR,"graph<-")
importFrom(miloR,"nhoodGraph<-")
importFrom(miloR,"nhoodIndex<-")
importFrom(miloR,"nhoods<-")
importFrom(miloR,Milo)
importFrom(miloR,buildGraph)
importFrom(miloR,buildNhoodGraph)
importFrom(miloR,graph)
importFrom(miloR,nhoodGraph)
importFrom(miloR,nhoodIndex)
importFrom(miloR,nhoods)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(scuttle,summarizeAssayByGroup)
importFrom(stats,as.formula)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(tibble,rownames_to_column)