# Generated by roxygen2: do not edit by hand

export(annotate_interactions)
export(digest_genome)
export(distance_summary)
export(export_interactions)
export(getByBaits)
export(getByRegions)
export(getParameters)
export(interactionsByBaits)
export(interactionsByRegions)
export(intersect_interactions)
export(load_interactions)
export(peakmatrix2list)
export(plot_distance_summary)
exportClasses(HiCaptuRe)
exportMethods(as.data.frame)
exportMethods(getByBaits)
exportMethods(getByRegions)
exportMethods(getParameters)
import(GenomicInteractions)
import(InteractionSet)
importFrom(BSgenome,getBSgenome)
importFrom(BiocGenerics,as.data.frame)
importFrom(Biostrings,
  DNAStringSet,
  matchPattern,
  replaceAt
)
importFrom(GenomeInfoDb,
  bsgenomeName,
  seqlevels,
  seqlevelsStyle,
  seqnames
)
importFrom(GenomicInteractions,
  GenomicInteractions,
  anchorOne,
  anchorTwo,
  annotateInteractions,
  annotateRegions,
  calculateDistances,
  export.igraph,
  is.cis,
  resetAnnotations
)
importFrom(GenomicRanges,
  findOverlaps,
  makeGRangesFromDataFrame,
  mcols,
  seqnames,
  split
)
importFrom(IRanges,
  IRanges,
  countOverlaps,
  mergeByOverlaps,
  overlapsAny,
  pintersect,
  subsetByOverlaps
)
importFrom(InteractionSet,
  anchorIds,
  regions
)
importFrom(S4Vectors,
  elementMetadata,
  subjectHits,
  width
)
importFrom(UpSetR,
  fromList,
  upset
)
importFrom(data.table,
  fread,
  fwrite,
  rbindlist
)
importFrom(dplyr,
  arrange,
  as_tibble,
  bind_rows,
  coalesce,
  filter,
  full_join,
  group_by,
  mutate,
  n,
  reframe,
  rename,
  select,
  slice,
  tibble
)
importFrom(ggVennDiagram,ggVennDiagram)
importFrom(ggplot2,
  aes,
  element_text,
  geom_bar,
  ggplot,
  labs,
  theme,
  theme_minimal
)
importFrom(ggpubr,theme_classic2)
importFrom(gplots,venn)
importFrom(igraph,
  as_edgelist,
  simplify
)
importFrom(methods,
  as,
  callNextMethod,
  is,
  new,
  slot,
  slotNames
)
importFrom(stats,setNames)
importFrom(stringr,
  str_replace_all,
  str_split
)
importFrom(tibble,add_column)
importFrom(tidyr,
  separate,
  separate_rows
)
