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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(composition_barplot)
export(composition_boxplot)
export(feature_corr_plot)
export(get_aggregated_profile)
export(get_aggregated_signature)
export(get_celltype_composition)
export(get_cluster_score)
export(global_corr_plots)
export(merge_scoot_objects)
export(nas_per_sample)
export(read_objs)
export(save_objs)
export(scoot)
export(summarize_cluster_scores)
export(summarized_scores_barplot)
import(SeuratObject)
importFrom(BiocGenerics,counts)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,bplapply)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,vst)
importFrom(Hotelling,clr)
importFrom(Matrix,Matrix)
importFrom(Matrix,rowSums)
importFrom(MatrixGenerics,rowMins)
importFrom(MatrixGenerics,rowVars)
importFrom(RColorBrewer,brewer.pal)
importFrom(Seurat,AggregateExpression)
importFrom(Seurat,AverageExpression)
importFrom(Seurat,FindVariableFeatures)
importFrom(SummarizedExperiment,assay)
importFrom(cluster,pam)
importFrom(data.table,rbindlist)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,bind_rows)
importFrom(dplyr,coalesce)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,mutate_if)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,select_if)
importFrom(dplyr,summarize)
importFrom(dplyr,summarize_at)
importFrom(dplyr,ungroup)
importFrom(dplyr,where)
importFrom(factoextra,fviz_nbclust)
importFrom(factoextra,fviz_pca)
importFrom(fastcluster,hclust)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_equal)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_jitterdodge)
importFrom(ggplot2,set_last_plot)
importFrom(ggplot2,sym)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggplotify,as.ggplot)
importFrom(ggpubr,as_ggplot)
importFrom(ggpubr,get_legend)
importFrom(ggpubr,ggboxplot)
importFrom(ggpubr,stat_compare_means)
importFrom(ggraph,geom_edge_link)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,ggraph)
importFrom(grDevices,colorRampPalette)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(igraph,V)
importFrom(igraph,gorder)
importFrom(igraph,layout_nicely)
importFrom(igraph,modularity)
importFrom(igraph,set_vertex_attr)
importFrom(igraph,strength)
importFrom(mclust,Mclust)
importFrom(mclust,adjustedRandIndex)
importFrom(mclust,mclustBIC)
importFrom(metap,sumlog)
importFrom(metap,sumz)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,slot)
importFrom(parallelly,availableCores)
importFrom(patchwork,plot_annotation)
importFrom(patchwork,plot_layout)
importFrom(patchwork,plot_spacer)
importFrom(patchwork,wrap_elements)
importFrom(patchwork,wrap_plots)
importFrom(pheatmap,pheatmap)
importFrom(purrr,map_df)
importFrom(rrapply,rrapply)
importFrom(scran,buildKNNGraph)
importFrom(stats,cor)
importFrom(stats,formula)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,reformulate)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stringr,str_remove_all)
importFrom(stringr,str_split)
importFrom(stringr,str_to_title)
importFrom(tibble,column_to_rownames)
importFrom(tibble,remove_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,separate)