# 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(select_optimal_lambda)
export(sidak)
export(signature_fitting)
export(spectra_comparison)
export(spectra_comparison_rpdmm)
export(subtype_dict)
export(subtype_list)
export(write_depth_data)
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,
  getBSgenome,
  installed.genomes
)
importFrom(BiocGenerics,
  end,
  start,
  strand
)
importFrom(Biostrings,
  getSeq,
  matchPattern,
  vcountPattern,
  writeXStringSet
)
importFrom(GenomicRanges,
  GRanges,
  end,
  findOverlaps,
  makeGRangesFromDataFrame,
  start
)
importFrom(IRanges,
  IRanges,
  ranges
)
importFrom(S4Vectors,
  mcols,
  queryHits
)
importFrom(Seqinfo,seqnames)
importFrom(SummarizedExperiment,colData)
importFrom(VariantAnnotation,
  alt,
  asVCF,
  geno,
  info,
  makeVRangesFromGRanges,
  rbind,
  readVcf,
  ref,
  writeVcf
)
importFrom(data.table,":=")
importFrom(dplyr,
  "%>%",
  across,
  all_of,
  anti_join,
  arrange,
  bind_rows,
  case_when,
  desc,
  distinct,
  ends_with,
  filter,
  first,
  group_by,
  if_else,
  left_join,
  mutate,
  n,
  n_distinct,
  pull,
  relocate,
  rename,
  row_number,
  select,
  starts_with,
  summarise,
  summarize,
  tally,
  ungroup,
  where
)
importFrom(ggplot2,
  aes,
  element_blank,
  element_line,
  element_rect,
  element_text,
  facet_wrap,
  geom_bar,
  geom_errorbar,
  geom_line,
  geom_point,
  geom_segment,
  geom_text,
  ggplot,
  ggsave,
  ggtitle,
  guides,
  labs,
  position_dodge,
  scale_color_manual,
  scale_fill_manual,
  scale_size_continuous,
  scale_x_continuous,
  theme,
  theme_minimal,
  xlab,
  ylab
)
importFrom(grDevices,
  colorRampPalette,
  dev.cur,
  dev.list,
  dev.new,
  dev.off,
  png,
  rainbow,
  recordPlot,
  svg
)
importFrom(graphics,
  abline,
  boxplot,
  hist,
  layout,
  legend,
  lines,
  mtext,
  par,
  plot,
  points,
  text,
  title
)
importFrom(here,here)
importFrom(magrittr,"%>%")
importFrom(methods,is)
importFrom(plyranges,
  find_overlaps,
  join_overlap_left,
  join_overlap_left_directed,
  join_overlap_left_within_directed
)
importFrom(rlang,
  .data,
  sym
)
importFrom(stats,
  as.dist,
  as.formula,
  dist,
  glm,
  hclust,
  lm,
  median,
  model.matrix,
  na.omit,
  optimize,
  pchisq,
  pf,
  pnorm,
  qnorm,
  qqline,
  qqnorm,
  qt,
  r2dtable,
  relevel,
  reshape,
  residuals,
  rgamma,
  rmultinom,
  sd,
  setNames,
  uniroot,
  var
)
importFrom(stringr,
  str_c,
  str_count,
  str_extract,
  str_length,
  str_sub
)
importFrom(tibble,column_to_rownames)
importFrom(tidyr,
  crossing,
  pivot_longer,
  pivot_wider
)
importFrom(utils,
  head,
  install.packages,
  menu,
  modifyList,
  read.delim,
  read.table,
  write.table
)
