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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("%>%")
export(add_flank_to_variants)
export(add_sample_annotations)
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(combine_predict_grid)
export(compare_cosmic_v2)
export(compare_cosmic_v3)
export(compare_results)
export(cosmic_v2_subtype_map)
export(create_bagel)
export(create_umap)
export(discover_signatures)
export(drop_annotation)
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_sample_annotations)
export(get_sample_names)
export(get_variants)
export(init_sample_annotations)
export(jsd)
export(name_signatures)
export(plot_exposures)
export(plot_exposures_by_annotation)
export(plot_sample_counts)
export(plot_sample_reconstruction_error)
export(plot_signatures)
export(plot_umap)
export(plot_umap_sigs)
export(predict_exposure)
export(rc)
export(select_genome)
export(set_sample_annotations)
export(subset_bagel_by_annotation)
export(subset_bagel_by_counts)
export(subset_variant_by_type)
export(subset_variants_by_samples)
exportClasses(Result)
exportClasses(Result_Grid)
exportClasses(bagel)
exportClasses(count_table)
import(BSgenome)
import(data.table)
importFrom(GenomicFeatures,genes)
importFrom(GenomicRanges,strand)
importFrom(IRanges,IRanges)
importFrom(IRanges,findOverlaps)
importFrom(NMF,nmf)
importFrom(S4Vectors,Rle)
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(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_set)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(magrittr,"%>%")
importFrom(methods,is)
importFrom(rlang,.data)