NAMESPACE

# Generated by roxygen2: do not edit by hand

export(CNV_analysis)
export(add_features)
export(add_partitions)
export(adj_outliers_col)
export(apply_CNV_reference)
export(assess_cluster_enrichment)
export(barplot_cluster)
export(boxplot_cluster)
export(boxplot_points)
export(calculate_CNV)
export(calculate_gs_scores)
export(calculate_gs_scores_in_clusters)
export(cel_coocc_partitions)
export(cluster_by_features)
export(cluster_csea)
export(cluster_hyper)
export(cluster_stats)
export(create_scMuffinList)
export(csea)
export(detect_CNV_regions)
export(diff_map)
export(es)
export(extract_cluster_enrichment_table)
export(extract_cluster_enrichment_tags)
export(genes_in_detected_CNV_regions)
export(get_msigdb_geneset)
export(gs_score)
export(gs_scores_in_clusters)
export(heatmap_CNV)
export(inter_dataset_comparison)
export(keep_strongest_representative)
export(ora)
export(overlap_coefficient)
export(overlap_matrix)
export(partitions_to_list)
export(plot_diff_map)
export(plot_heatmap_dataset_comparison)
export(plot_heatmap_features_by_clusters)
export(plot_profile_CNV)
export(plot_umap)
export(plot_umap_colored_features)
export(prepare_cluster_markers_list)
export(prepare_gsls)
export(preprocess_for_heatmap_CNV)
export(preprocess_object_for_CNV)
export(process_GTEx_gene_reads)
export(proliferation_analysis)
export(regions_to_genes)
export(sc_create_null)
export(sc_data_bin)
export(show_tissues)
export(transcr_compl)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,anno_mark)
importFrom(ComplexHeatmap,columnAnnotation)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(Matrix,Matrix)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(Seurat,AddMetaData)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,DimPlot)
importFrom(Seurat,FeaturePlot)
importFrom(Seurat,FetchData)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,RunPCA)
importFrom(Seurat,ScaleData)
importFrom(circlize,colorRamp2)
importFrom(destiny,DPT)
importFrom(destiny,DiffusionMap)
importFrom(destiny,random_root)
importFrom(ggplot2,annotate)
importFrom(ggplot2,cut_interval)
importFrom(ggplot2,cut_number)
importFrom(ggplot2,element_text)
importFrom(ggplot2,theme)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,boxplot.stats)
importFrom(grDevices,dev.off)
importFrom(grDevices,jpeg)
importFrom(grDevices,png)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,boxplot)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,plot.new)
importFrom(graphics,points)
importFrom(graphics,rect)
importFrom(graphics,text)
importFrom(grid,gpar)
importFrom(grid,grid.text)
importFrom(grid,unit)
importFrom(methods,is)
importFrom(msigdbr,msigdbr)
importFrom(org.Hs.eg.db,org.Hs.egCHRLOC)
importFrom(org.Hs.eg.db,org.Hs.egCHRLOCEND)
importFrom(org.Hs.eg.db,org.Hs.egENSEMBL)
importFrom(org.Hs.eg.db,org.Hs.egSYMBOL)
importFrom(pals,alphabet)
importFrom(pals,alphabet2)
importFrom(pals,brewer.accent)
importFrom(pals,brewer.pastel1)
importFrom(pals,brewer.purples)
importFrom(pals,brewer.rdylbu)
importFrom(pals,brewer.ylorrd)
importFrom(parallel,mclapply)
importFrom(plotrix,thigmophobe.labels)
importFrom(qvalue,qvalue)
importFrom(stats,dhyper)
importFrom(stats,glm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,phyper)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stats,wilcox.test)
importFrom(utils,data)
importFrom(utils,read.delim)
importFrom(utils,read.table)