# Generated by roxygen2: do not edit by hand

export(CIS_grubbs)
export(CIS_grubbs_overtime)
export(CIS_volcano_plot)
export(HSC_population_plot)
export(HSC_population_size_estimate)
export(NGSdataExplorer)
export(aggregate_metadata)
export(aggregate_values_by_key)
export(annotation_IS_vars)
export(annotation_issues)
export(as_sparse_matrix)
export(association_file_columns)
export(available_outlier_tests)
export(available_tags)
export(blood_lineages_default)
export(circos_genomic_density)
export(clinical_relevant_suspicious_genes)
export(comparison_matrix)
export(compute_abundance)
export(compute_near_integrations)
export(cumulative_count_union)
export(cumulative_is)
export(date_formats)
export(default_af_transform)
export(default_iss_file_prefixes)
export(default_meta_agg)
export(default_rec_agg_lambdas)
export(default_report_path)
export(default_stats)
export(enable_progress_bars)
export(export_ISA_settings)
export(fisher_scatterplot)
export(gene_frequency_fisher)
export(generate_Vispa2_launch_AF)
export(generate_blank_association_file)
export(generate_default_folder_structure)
export(import_ISA_settings)
export(import_Vispa2_stats)
export(import_association_file)
export(import_parallel_Vispa2Matrices)
export(import_parallel_Vispa2Matrices_auto)
export(import_parallel_Vispa2Matrices_interactive)
export(import_single_Vispa2Matrix)
export(inspect_tags)
export(integration_alluvial_plot)
export(is_sharing)
export(iss_source)
export(iss_stats_specs)
export(known_clinical_oncogenes)
export(mandatory_IS_vars)
export(matching_options)
export(matrix_file_suffixes)
export(outlier_filter)
export(outliers_by_pool_fragments)
export(pcr_id_column)
export(purity_filter)
export(quantification_types)
export(realign_after_collisions)
export(reduced_AF_columns)
export(refGene_table_cols)
export(remove_collisions)
export(reset_af_columns_def)
export(reset_annotation_IS_vars)
export(reset_dyn_vars_config)
export(reset_iss_stats_specs)
export(reset_mandatory_IS_vars)
export(reset_matrix_file_suffixes)
export(sample_statistics)
export(separate_quant_matrices)
export(set_af_columns_def)
export(set_annotation_IS_vars)
export(set_iss_stats_specs)
export(set_mandatory_IS_vars)
export(set_matrix_file_suffixes)
export(sharing_heatmap)
export(sharing_venn)
export(threshold_filter)
export(top_abund_tableGrob)
export(top_cis_overtime_heatmap)
export(top_integrations)
export(top_targeted_genes)
export(transform_columns)
export(unzip_file_system)
import(bslib)
import(datamods)
import(ggplot2)
import(lifecycle)
import(shiny)
import(shinyWidgets)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_keys)
importFrom(dplyr,group_modify)
importFrom(dplyr,group_split)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,rename_with)
importFrom(dplyr,select)
importFrom(dplyr,slice_head)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(fs,as_fs_path)
importFrom(fs,dir_create)
importFrom(fs,dir_exists)
importFrom(fs,dir_ls)
importFrom(fs,is_dir)
importFrom(fs,path)
importFrom(fs,path_ext)
importFrom(fs,path_ext_set)
importFrom(fs,path_home)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,labs)
importFrom(ggplot2,rel)
importFrom(ggplot2,scale_alpha_continuous)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_viridis_d)
importFrom(ggplot2,sym)
importFrom(ggplot2,theme)
importFrom(lifecycle,deprecate_warn)
importFrom(lubridate,today)
importFrom(purrr,detect_index)
importFrom(purrr,is_empty)
importFrom(purrr,list_c)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map2_lgl)
importFrom(purrr,map_chr)
importFrom(purrr,map_lgl)
importFrom(purrr,pluck)
importFrom(purrr,pmap_chr)
importFrom(purrr,pmap_lgl)
importFrom(purrr,reduce)
importFrom(purrr,set_names)
importFrom(purrr,walk)
importFrom(purrr,walk2)
importFrom(readr,cols)
importFrom(readr,problems)
importFrom(readr,read_delim)
importFrom(rlang,.data)
importFrom(rlang,`!!!`)
importFrom(rlang,`:=`)
importFrom(rlang,abort)
importFrom(rlang,arg_match)
importFrom(rlang,as_function)
importFrom(rlang,call2)
importFrom(rlang,current_env)
importFrom(rlang,dots_list)
importFrom(rlang,enexpr)
importFrom(rlang,eval_tidy)
importFrom(rlang,exec)
importFrom(rlang,expr)
importFrom(rlang,fn_fmls_names)
importFrom(rlang,inform)
importFrom(rlang,is_formula)
importFrom(rlang,is_function)
importFrom(rlang,is_installed)
importFrom(rlang,list2)
importFrom(rlang,parse_expr)
importFrom(rlang,sym)
importFrom(rlang,warn)
importFrom(stats,dt)
importFrom(stats,setNames)
importFrom(stats,shapiro.test)
importFrom(stringr,str_detect)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_to_upper)
importFrom(tibble,add_column)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tibble,tibble_row)
importFrom(tibble,tribble)
importFrom(tidyr,nest)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(tools,file_path_sans_ext)
importFrom(utils,read.delim)
importFrom(utils,tail)
