# Generated by roxygen2: do not edit by hand

export(heatmaps_karioCaS)
export(import_karioCaS)
export(optimize_CS)
export(reads_per_taxa)
export(retrieve_selected_taxa)
export(taxa_resolution)
export(taxa_retention)
export(upset_kariocas)
importFrom(S4Vectors,DataFrame)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(TreeSummarizedExperiment,TreeSummarizedExperiment)
importFrom(UpSetR,upset)
importFrom(dplyr,"%>%")
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,lag)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice_head)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(forcats,fct_inorder)
importFrom(forcats,fct_reorder)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,guide_colorbar)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,unit)
importFrom(ggtext,element_markdown)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grid,gpar)
importFrom(grid,grid.text)
importFrom(methods,is)
importFrom(patchwork,plot_annotation)
importFrom(patchwork,plot_layout)
importFrom(readr,read_rds)
importFrom(readr,write_delim)
importFrom(readr,write_rds)
importFrom(readr,write_tsv)
importFrom(rlang,":=")
importFrom(scales,breaks_pretty)
importFrom(scales,cut_short_scale)
importFrom(scales,label_number)
importFrom(scales,log_trans)
importFrom(scales,percent)
importFrom(stats,as.dendrogram)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,reorder)
importFrom(stats,resid)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract)
importFrom(stringr,str_match)
importFrom(stringr,str_remove)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,complete)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(utils,head)
importFrom(utils,read.table)
