# Generated by roxygen2: do not edit by hand

S3method(print,bytes)
S3method(sig_tally,CopyNumber)
S3method(sig_tally,MAF)
S3method(sig_tally,RS)
S3method(subset,CopyNumber)
export("%>%")
export(":=")
export(.data)
export(.env)
export(CopyNumber)
export(MAF)
export(add_h_arrow)
export(add_labels)
export(as_label)
export(as_name)
export(bp_attribute_activity)
export(bp_cluster_iter_list)
export(bp_extract_signatures)
export(bp_extract_signatures_iter)
export(bp_get_clustered_sigs)
export(bp_get_rank_score)
export(bp_get_sig_obj)
export(bp_get_stats)
export(bp_show_survey)
export(bp_show_survey2)
export(cosine)
export(enquo)
export(enquos)
export(enrich_component_strand_bias)
export(expr)
export(get_Aneuploidy_score)
export(get_adj_p)
export(get_bayesian_result)
export(get_cn_freq_table)
export(get_cn_ploidy)
export(get_genome_annotation)
export(get_group_comparison)
export(get_groups)
export(get_intersect_size)
export(get_pLOH_score)
export(get_shannon_diversity_index)
export(get_sig_cancer_type_index)
export(get_sig_db)
export(get_sig_exposure)
export(get_sig_feature_association)
export(get_sig_rec_similarity)
export(get_sig_similarity)
export(get_tidy_association)
export(group_enrichment)
export(group_enrichment2)
export(handle_hyper_mutation)
export(hello)
export(output_bootstrap)
export(output_fit)
export(output_sig)
export(output_tally)
export(read_copynumber)
export(read_copynumber_ascat)
export(read_copynumber_seqz)
export(read_maf)
export(read_maf_minimal)
export(read_sv_as_rs)
export(read_vcf)
export(read_xena_variants)
export(report_bootstrap_p_value)
export(same_size_clustering)
export(scoring)
export(show_catalogue)
export(show_cn_circos)
export(show_cn_components)
export(show_cn_distribution)
export(show_cn_features)
export(show_cn_freq_circos)
export(show_cn_group_profile)
export(show_cn_profile)
export(show_cor)
export(show_cosmic)
export(show_cosmic_sig_profile)
export(show_group_comparison)
export(show_group_distribution)
export(show_group_enrichment)
export(show_group_mapping)
export(show_groups)
export(show_sig_bootstrap_error)
export(show_sig_bootstrap_exposure)
export(show_sig_bootstrap_stability)
export(show_sig_consensusmap)
export(show_sig_exposure)
export(show_sig_feature_corrplot)
export(show_sig_fit)
export(show_sig_number_survey)
export(show_sig_number_survey2)
export(show_sig_profile)
export(show_sig_profile_heatmap)
export(show_sig_profile_loop)
export(sig_attrs)
export(sig_auto_extract)
export(sig_convert)
export(sig_estimate)
export(sig_exposure)
export(sig_extract)
export(sig_fit)
export(sig_fit_bootstrap)
export(sig_fit_bootstrap_batch)
export(sig_modify_names)
export(sig_names)
export(sig_number)
export(sig_signature)
export(sig_tally)
export(sig_unify_extract)
export(sigprofiler_extract)
export(sigprofiler_import)
export(sigprofiler_reorder)
export(simulate_catalogue)
export(simulate_catalogue_matrix)
export(simulate_signature)
export(sym)
export(syms)
export(transform_seg_table)
export(use_color_style)
exportClasses(CopyNumber)
exportClasses(MAF)
import(NMF)
import(cli)
import(ggplot2)
import(methods)
importClassesFrom(data.table,data.table)
importFrom(Rcpp,sourceCpp)
importFrom(dplyr,progress_estimated)
importFrom(furrr,future_pmap)
importFrom(future,plan)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graphics,hist)
importFrom(magrittr,"%>%")
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,.env)
importFrom(rlang,as_label)
importFrom(rlang,as_name)
importFrom(rlang,enquo)
importFrom(rlang,enquos)
importFrom(rlang,expr)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(stats,as.formula)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,kmeans)
importFrom(stats,pairwise.table)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(utils,data)
importFrom(utils,download.file)
importFrom(utils,head)
importFrom(utils,packageDescription)
useDynLib(sigminer, .registration = TRUE)
