# Generated by roxygen2: do not edit by hand

export("parameters<-")
export(HiCDOC)
export(HiCDOCDataSetFromCool)
export(HiCDOCDataSetFromHiC)
export(HiCDOCDataSetFromHiCPro)
export(HiCDOCDataSetFromTabular)
export(chromosomes)
export(compartments)
export(concordances)
export(defaultHiCDOCParameters)
export(detectCompartments)
export(differences)
export(filterSmallChromosomes)
export(filterSparseReplicates)
export(filterWeakPositions)
export(normalizeBiologicalBiases)
export(normalizeDistanceEffect)
export(normalizeTechnicalBiases)
export(parameters)
export(plotCentroids)
export(plotCompartmentChanges)
export(plotCompartments)
export(plotConcordanceDifferences)
export(plotConcordances)
export(plotDistanceEffect)
export(plotInteractions)
export(plotSelfInteractionRatios)
export(reduceHiCDOCDataSet)
export(sampleConditions)
export(sampleReplicates)
exportClasses(HiCDOCDataSet)
exportMethods("parameters<-")
exportMethods(chromosomes)
exportMethods(compartments)
exportMethods(concordances)
exportMethods(differences)
exportMethods(parameters)
exportMethods(sampleConditions)
exportMethods(sampleReplicates)
exportMethods(show)
import(HiCParser)
import(InteractionSet)
import(data.table)
import(ggplot2)
import(methods)
importFrom(BiocGenerics,
  cbind,
  width
)
importFrom(BiocParallel,
  bplapply,
  bpmapply,
  bpparam
)
importFrom(GenomicRanges,
  GRanges,
  distance,
  end,
  match,
  start,
  union
)
importFrom(Rcpp,
  evalCpp,
  sourceCpp
)
importFrom(S4Vectors,
  "%in%",
  DataFrame,
  Rle,
  mcols,
  runLength,
  split
)
importFrom(Seqinfo,
  seqlevels,
  seqnames
)
importFrom(SummarizedExperiment,
  assay,
  colData
)
importFrom(cowplot,
  get_plot_component,
  ggdraw
)
importFrom(grid,
  gpar,
  textGrob
)
importFrom(gridExtra,arrangeGrob)
importFrom(gtools,mixedsort)
importFrom(multiHiCcompare,
  cyclic_loess,
  hic_table,
  make_hicexp
)
importFrom(pbapply,pbmapply)
importFrom(stats,
  ecdf,
  loess,
  loess.control,
  median,
  optimize,
  p.adjust,
  prcomp,
  predict,
  quantile,
  update,
  wilcox.test
)
useDynLib(HiCDOC)
