# Generated by roxygen2: do not edit by hand

export("%>%")
export(BS_org_map)
export(bmd_proast)
export(calculate_mf)
export(check_required_columns)
export(classify_variation)
export(context_list)
export(denominator_dict)
export(filter_mut)
export(find_BS_genome)
export(get_binom_ci)
export(get_seq)
export(import_mut_data)
export(import_vcf_data)
export(load_regions_file)
export(model_mf)
export(op)
export(plot_bubbles)
export(plot_ci)
export(plot_lollipop)
export(plot_mean_mf)
export(plot_mf)
export(plot_model_mf)
export(plot_radar)
export(plot_spectra)
export(plot_trinucleotide)
export(plot_trinucleotide_heatmap)
export(rename_columns)
export(render_report)
export(sidak)
export(signature_fitting)
export(spectra_comparison)
export(subtype_dict)
export(subtype_list)
export(write_excel)
export(write_mutation_calling_file)
export(write_mutational_matrix)
export(write_reference_fasta)
export(write_vcf_from_mut)
import(ggdendro)
import(ggplot2)
import(stringr)
importFrom(BSgenome,available.genomes)
importFrom(BSgenome,getBSgenome)
importFrom(BSgenome,installed.genomes)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,matchPattern)
importFrom(Biostrings,vcountPattern)
importFrom(Biostrings,writeXStringSet)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,start)
importFrom(IRanges,IRanges)
importFrom(IRanges,ranges)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(Seqinfo,seqnames)
importFrom(SummarizedExperiment,colData)
importFrom(VariantAnnotation,alt)
importFrom(VariantAnnotation,asVCF)
importFrom(VariantAnnotation,geno)
importFrom(VariantAnnotation,info)
importFrom(VariantAnnotation,makeVRangesFromGRanges)
importFrom(VariantAnnotation,rbind)
importFrom(VariantAnnotation,readVcf)
importFrom(VariantAnnotation,ref)
importFrom(VariantAnnotation,writeVcf)
importFrom(data.table,":=")
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,ends_with)
importFrom(dplyr,filter)
importFrom(dplyr,first)
importFrom(dplyr,group_by)
importFrom(dplyr,if_else)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,pull)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,tally)
importFrom(dplyr,ungroup)
importFrom(dplyr,where)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.cur)
importFrom(grDevices,dev.list)
importFrom(grDevices,dev.new)
importFrom(grDevices,dev.off)
importFrom(grDevices,png)
importFrom(grDevices,recordPlot)
importFrom(grDevices,svg)
importFrom(graphics,abline)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(here,here)
importFrom(magrittr,"%>%")
importFrom(methods,is)
importFrom(plyranges,find_overlaps)
importFrom(plyranges,join_overlap_left)
importFrom(plyranges,join_overlap_left_directed)
importFrom(plyranges,join_overlap_left_within_directed)
importFrom(rlang,.data)
importFrom(rlang,sym)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,dist)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,pchisq)
importFrom(stats,pf)
importFrom(stats,pnorm)
importFrom(stats,qnorm)
importFrom(stats,qqline)
importFrom(stats,qqnorm)
importFrom(stats,qt)
importFrom(stats,r2dtable)
importFrom(stats,relevel)
importFrom(stats,reshape)
importFrom(stats,residuals)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,uniroot)
importFrom(stats,var)
importFrom(stringr,str_c)
importFrom(stringr,str_count)
importFrom(stringr,str_extract)
importFrom(stringr,str_length)
importFrom(stringr,str_sub)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(utils,install.packages)
importFrom(utils,menu)
importFrom(utils,modifyList)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.table)
