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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(`%in%`)
export(check_format_cluster_set)
export(clust_names)
export(clust_size)
export(cluster_set_from_matrix)
export(cluster_set_from_seurat)
export(cluster_set_report)
export(cluster_set_to_xls)
export(cluster_stats)
export(col_names)
export(colors_for_gradient)
export(compare_genesets)
export(construct_new_graph)
export(create_3_rnd_clust)
export(create_4_rnd_clust)
export(create_rand_str)
export(discrete_palette)
export(display_hull)
export(enrich_go)
export(filter_by_dot_prod)
export(filter_cluster_sd)
export(filter_cluster_size)
export(filter_nb_supporting_cells)
export(gene_cluster)
export(gene_clustering)
export(getFlippedTissueCoordinates)
export(get_data_for_scigenex)
export(get_genes)
export(get_verbosity)
export(grep_clust)
export(install_mcl)
export(keep_dbf_graph)
export(load_example_dataset)
export(mcl_system_cmd)
export(module_quality_scores)
export(nclust)
export(plot_clust_enrichments)
export(plot_cluster_stats)
export(plot_cmp_genesets)
export(plot_dist)
export(plot_ggheatmap)
export(plot_heatmap)
export(plot_markers_to_clusters)
export(plot_profiles)
export(plot_spatial)
export(plot_spatial_panel)
export(plot_stratum)
export(print_msg)
export(print_stat)
export(rename_clust)
export(reorder_clust)
export(reorder_genes)
export(row_names)
export(select_genes)
export(set_verbosity)
export(show)
export(show_methods)
export(stratify_seurat)
export(top_by_go)
export(top_genes)
export(viz_enrich)
export(which_clust)
exportClasses(ClusterSet)
exportMethods(clust_size)
exportMethods(plot_markers_to_clusters)
import(SeuratObject)
import(ggplot2)
import(org.Hs.eg.db)
import(org.Mm.eg.db)
importFrom(AnnotationDbi,select)
importFrom(DT,datatable)
importFrom(Matrix,rowSums)
importFrom(Seurat,AddModuleScore)
importFrom(Seurat,DimPlot)
importFrom(Seurat,NoAxes)
importFrom(Seurat,NoLegend)
importFrom(Seurat,SpatialDimPlot)
importFrom(SeuratObject,GetAssayData)
importFrom(SparseM,t)
importFrom(WriteXLS,WriteXLS)
importFrom(amap,Dist)
importFrom(amap,hcluster)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listDatasets)
importFrom(biomaRt,useMart)
importFrom(clValid,connectivity)
importFrom(clValid,dunn)
importFrom(cluster,silhouette)
importFrom(clusterProfiler,enrichGO)
importFrom(dplyr,distinct)
importFrom(dplyr,group_by)
importFrom(dplyr,summarise)
importFrom(enrichplot,dotplot)
importFrom(ggforce,geom_mark_hull)
importFrom(ggh4x,elem_list_rect)
importFrom(ggh4x,facet_grid2)
importFrom(ggh4x,strip_themed)
importFrom(ggplot2,.data)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_equal)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_colourbar)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_size_area)
importFrom(ggplot2,scale_size_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,stat_density)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggstar,geom_star)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,hcl)
importFrom(graphics,barplot)
importFrom(grid,unit)
importFrom(igraph,as_adj)
importFrom(igraph,graph_from_data_frame)
importFrom(iheatmapr,add_col_annotation)
importFrom(iheatmapr,add_col_dendro)
importFrom(iheatmapr,add_col_labels)
importFrom(iheatmapr,add_col_title)
importFrom(iheatmapr,add_row_labels)
importFrom(iheatmapr,add_row_title)
importFrom(iheatmapr,main_heatmap)
importFrom(iheatmapr,modify_layout)
importFrom(magrittr,"%>%")
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,showMethods)
importFrom(methods,signature)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(patchwork,plot_layout)
importFrom(pheatmap,pheatmap)
importFrom(plotly,layout)
importFrom(qlcMatrix,corSparse)
importFrom(qlcMatrix,cosSparse)
importFrom(reshape2,melt)
importFrom(scales,hue_pal)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,heatmap)
importFrom(stats,median)
importFrom(stats,phyper)
importFrom(stats,pnorm)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(testthat,expect_equal)
importFrom(utils,capture.output)
importFrom(utils,download.file)
importFrom(utils,object.size)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,write.table)
importMethodsFrom(methods,show)