# Generated by roxygen2: do not edit by hand

S3method(as_tibble,DataFrame)
S3method(as_tibble,GInteractions)
S3method(as_tibble,GenomicRanges)
S3method(as_tibble,Seqinfo)
S3method(as_tibble,SummarizedExperiment)
S3method(as_tibble,TopTags)
export(addDiffStatus)
export(bestOverlap)
export(centrePeaks)
export(chopMC)
export(colToRanges)
export(collapseGenes)
export(defineRegions)
export(defineSeqinfo)
export(distinctMC)
export(dualFilter)
export(fitAssayDiff)
export(getProfileData)
export(grlToSE)
export(importPeaks)
export(intersectMC)
export(makeConsensus)
export(mapByFeature)
export(mapGrlCols)
export(mergeByCol)
export(mergeByHMP)
export(mergeBySig)
export(partitionRanges)
export(plotAssayDensities)
export(plotAssayHeatmap)
export(plotAssayPCA)
export(plotAssayRle)
export(plotGrlCol)
export(plotHFGC)
export(plotOverlaps)
export(plotPairwise)
export(plotPie)
export(plotProfileHeatmap)
export(plotSplitDonut)
export(propOverlap)
export(reduceMC)
export(setdiffMC)
export(stitchRanges)
export(unionMC)
export(voomWeightsFromCPM)
exportMethods(addDiffStatus)
exportMethods(bestOverlap)
exportMethods(centrePeaks)
exportMethods(colToRanges)
exportMethods(fitAssayDiff)
exportMethods(getProfileData)
exportMethods(grlToSE)
exportMethods(intersectMC)
exportMethods(mergeByCol)
exportMethods(mergeByHMP)
exportMethods(mergeBySig)
exportMethods(partitionRanges)
exportMethods(plotAssayDensities)
exportMethods(plotAssayHeatmap)
exportMethods(plotAssayPCA)
exportMethods(plotAssayRle)
exportMethods(plotOverlaps)
exportMethods(plotPie)
exportMethods(plotProfileHeatmap)
exportMethods(plotSplitDonut)
exportMethods(propOverlap)
exportMethods(setdiffMC)
exportMethods(unionMC)
import(GenomicRanges)
import(SummarizedExperiment)
import(ggplot2)
import(ggside)
import(methods)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(IRanges,CompressedList)
importClassesFrom(IRanges,RleList)
importClassesFrom(IRanges,RleViewsList)
importClassesFrom(Rsamtools,BamFileList)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,HitsList)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importClassesFrom(rtracklayer,BigWigFile)
importClassesFrom(rtracklayer,BigWigFileList)
importFrom(BiocParallel,
  SerialParam,
  bpisup,
  bplapply,
  bpparam,
  bpstart,
  bpstop
)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomicRanges,setdiff)
importFrom(IRanges,
  RleList,
  RleViewsList,
  SplitDataFrameList,
  Views,
  commonColnames,
  overlapsAny,
  subsetByOverlaps,
  viewMaxs,
  viewWhichMaxs
)
importFrom(InteractionSet,anchors)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,
  BamFileList,
  ScanBamParam,
  countBam,
  idxstatsBam
)
importFrom(S4Vectors,
  "mcols<-",
  "metadata<-",
  DataFrame,
  Rle,
  SimpleList,
  endoapply,
  mcols,
  metadata,
  queryHits,
  splitAsList,
  subjectHits,
  subset
)
importFrom(Seqinfo,
  "seqinfo<-",
  Seqinfo,
  genome,
  seqinfo,
  seqlevels,
  seqnames
)
importFrom(csaw,
  combineTests,
  filterWindowsProportion,
  getBestTest,
  getWidths,
  minimalTests,
  readParam,
  reform,
  scaleControlFilter,
  windowCounts
)
importFrom(dplyr,
  across,
  arrange,
  bind_cols,
  bind_rows,
  case_when,
  desc,
  distinct,
  filter,
  group_by,
  inner_join,
  left_join,
  mutate,
  mutate_all,
  n,
  pick,
  select,
  summarise,
  ungroup
)
importFrom(edgeR,
  DGEList,
  cpm,
  estimateDisp,
  glmQLFTest,
  glmQLFit,
  glmTreat,
  normLibSizes,
  topTags
)
importFrom(forcats,
  fct_cross,
  fct_explicit_na,
  fct_inorder,
  fct_na_value_to_level,
  fct_relabel,
  fct_rev
)
importFrom(ggrepel,
  geom_label_repel,
  geom_text_repel
)
importFrom(glue,
  glue,
  glue_collapse
)
importFrom(matrixStats,
  rowMeans2,
  rowMedians,
  rowSds,
  weightedMean
)
importFrom(methods,
  as,
  is,
  new,
  slot,
  slotNames
)
importFrom(patchwork,
  area,
  plot_layout,
  plot_spacer
)
importFrom(rlang,
  "!!!",
  "!!",
  ":=",
  .data,
  as_label,
  enexpr,
  enquo,
  ensym,
  eval_tidy,
  list2,
  quo_is_null,
  quos,
  sym,
  syms
)
importFrom(rtracklayer,
  BigWigFile,
  BigWigFileList,
  import.bw,
  ucscGenomes
)
importFrom(scales,
  comma,
  percent
)
importFrom(stats,
  approxfun,
  as.formula,
  cor,
  density,
  lowess,
  median,
  model.matrix,
  na.omit,
  p.adjust,
  p.adjust.methods,
  prcomp,
  quantile,
  setNames,
  weighted.mean
)
importFrom(stringr,
  str_count,
  str_pad,
  str_replace_all,
  str_replace_na,
  str_sort,
  str_to_title,
  str_trim,
  str_trunc
)
importFrom(tibble,
  as_tibble,
  tibble
)
importFrom(tidyr,
  all_of,
  chop,
  complete,
  nest,
  pivot_longer,
  pivot_wider,
  unite,
  unnest
)
importFrom(tidyselect,
  all_of,
  ends_with,
  everything
)
importFrom(vctrs,vec_proxy)
importMethodsFrom(SummarizedExperiment,'assay<-')
importMethodsFrom(SummarizedExperiment,'colData<-')
importMethodsFrom(SummarizedExperiment,'rowData<-')
importMethodsFrom(SummarizedExperiment,assay)
importMethodsFrom(SummarizedExperiment,colData)
importMethodsFrom(SummarizedExperiment,rowData)
importMethodsFrom(SummarizedExperiment,rowRanges)
useDynLib(extraChIPs, .registration = TRUE)
