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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method("[",congas)
S3method("[",rcongas)
S3method(plot,rcongas)
S3method(print,rcongas)
S3method(summary,rcongas)
export(approx_theta_prior_params)
export(best_cluster)
export(calculate_DE)
export(filter_clusters)
export(filter_genes)
export(filter_quantiles_per_segments)
export(filter_segments_and_return_cnv_table)
export(generate_random_tree)
export(get_DE_table)
export(get_clusters)
export(get_clusters_ploidy)
export(get_clusters_size)
export(get_counts)
export(get_dataset_stats)
export(get_gene_annotations)
export(get_genes_mapped_to_segments)
export(get_input_raw_data)
export(get_input_segmentation)
export(get_k)
export(get_mapped_genes)
export(get_reference_genome)
export(get_segment_ids)
export(get_segment_test_counts)
export(highlights)
export(init)
export(list_models)
export(plot_DE_gw)
export(plot_DE_volcano)
export(plot_chromosome)
export(plot_chromosome_inspection)
export(plot_cohort_statistics)
export(plot_counts_per_segment)
export(plot_counts_rna_segments)
export(plot_dna_pld_vs_rna)
export(plot_gene_counts_on_genome)
export(plot_gene_rank)
export(plot_gw_cna_profiles)
export(plot_highlights)
export(plot_inference_report)
export(plot_latent_variables)
export(plot_mixing_proportions)
export(plot_normalization_factors)
export(plot_raw_data)
export(plot_report_segments)
export(plot_segment_density)
export(recalculate_information_criteria)
export(report_analysis)
export(report_analysis_chromosome)
export(report_analysis_de)
export(report_data)
export(run_inference)
export(run_simulation)
import(ggplot2)
importFrom(CNAqc,plot_segments)
importFrom(cli,cli_rule)
importFrom(cli,cli_text)
importFrom(clisymbols,symbol)
importFrom(crayon,bgYellow)
importFrom(crayon,black)
importFrom(crayon,blue)
importFrom(crayon,bold)
importFrom(crayon,green)
importFrom(crayon,red)
importFrom(crayon,white)
importFrom(crayon,yellow)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,right_join)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(extraDistr,rmvhyper)
importFrom(ggpubr,ggarrange)
importFrom(gtools,mixedorder)
importFrom(gtools,mixedsort)
importFrom(magrittr,"%>%")
importFrom(patchwork,plot_layout)
importFrom(purrr,rbernoulli)
importFrom(tidyr,as_tibble)
importFrom(tidyr,gather)
importFrom(tidyr,spread)
importFrom(tidyr,tibble)
importFrom(tidyr,tribble)