# Generated by roxygen2: do not edit by hand

export("%>%")
export("credible_intervals<-")
export("exposures<-")
export("hyperparameter<-")
export("metrics<-")
export("modality<-")
export("model_id<-")
export("num_signatures<-")
export("other_parameters<-")
export("parameter<-")
export("result_list<-")
export("samp_annot<-")
export("signatures<-")
export("tables<-")
export("umap<-")
export("variants<-")
export(add_flank_to_variants)
export(add_result)
export(annotate_replication_strand)
export(annotate_transcript_strand)
export(annotate_variant_length)
export(annotate_variant_type)
export(auto_predict_grid)
export(build_custom_table)
export(build_standard_table)
export(built_tables)
export(cluster_exposure)
export(combine_count_tables)
export(combine_predict_grid)
export(compare_cosmic_v2)
export(compare_cosmic_v3)
export(compare_k_vals)
export(compare_results)
export(cosmic_v2_subtype_map)
export(create_musica_from_counts)
export(create_musica_from_variants)
export(create_umap)
export(credible_intervals)
export(discover_signatures)
export(drop_annotation)
export(exposure_differential_analysis)
export(exposures)
export(extract_count_tables)
export(extract_variants)
export(extract_variants_from_maf)
export(extract_variants_from_maf_file)
export(extract_variants_from_matrix)
export(extract_variants_from_vcf)
export(extract_variants_from_vcf_file)
export(generate_result_grid)
export(get_count_table)
export(get_modality)
export(get_model)
export(get_result_list_entry)
export(hyperparameter)
export(k_select)
export(metrics)
export(modality)
export(model_id)
export(musicatk)
export(name_signatures)
export(num_signatures)
export(other_parameters)
export(parameter)
export(plot_cluster)
export(plot_differential_analysis)
export(plot_exposures)
export(plot_heatmap)
export(plot_k_comparison)
export(plot_sample_counts)
export(plot_sample_reconstruction_error)
export(plot_signatures)
export(plot_umap)
export(predict_exposure)
export(rc)
export(result_list)
export(samp_annot)
export(sample_names)
export(select_genome)
export(signatures)
export(subset_musica_by_annotation)
export(subset_musica_by_counts)
export(subset_variant_by_type)
export(subset_variants_by_samples)
export(table_selected)
export(tables)
export(umap)
export(variants)
exportClasses(count_table)
exportClasses(musica)
exportClasses(result_collection)
exportClasses(result_model)
import(dplyr)
import(ggplot2)
import(tidyr)
import(tidyverse)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(GenomicFeatures,genes)
importFrom(GenomicRanges,strand)
importFrom(IRanges,IRanges)
importFrom(IRanges,findOverlaps)
importFrom(MASS,glm.nb)
importFrom(NMF,nmf)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,decode)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg19.knownGene)
importFrom(TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene)
importFrom(cluster,silhouette)
importFrom(cluster,sortSilhouette)
importFrom(data.table,data.table)
importFrom(dplyr,any_vars)
importFrom(dplyr,filter_all)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(magrittr,"%>%")
importFrom(matrixTests,row_kruskalwallis)
importFrom(methods,is)
importFrom(rlang,.data)
importFrom(scales,pretty_breaks)
importFrom(utils,capture.output)
