# Generated by roxygen2: do not edit by hand

export(IDRfilter)
export(addAncestors)
export(addGeneIDs)
export(addMetadata)
export(annoPeaks)
export(annotatePeakInBatch)
export(assignChromosomeRegion)
export(binOverFeature)
export(binOverGene)
export(binOverRegions)
export(condenseMatrixByColnames)
export(convert2EntrezID)
export(countPatternInSeqs)
export(cumulativePercentage)
export(downstreams)
export(egOrgMap)
export(enrichmentPlot)
export(estFragmentLength)
export(estLibSize)
export(featureAlignedDistribution)
export(featureAlignedExtendSignal)
export(featureAlignedHeatmap)
export(featureAlignedSignal)
export(findEnhancers)
export(findMotifsInPromoterSeqs)
export(findOverlappingPeaks)
export(findOverlapsOfPeaks)
export(genomicElementDistribution)
export(genomicElementUpSetR)
export(getAllPeakSequence)
export(getAnnotation)
export(getEnrichedGO)
export(getEnrichedPATH)
export(getGO)
export(getUniqueGOidCount)
export(getVennCounts)
export(hyperGtest)
export(makeVennDiagram)
export(mergePlusMinusPeaks)
export(metagenePlot)
export(oligoFrequency)
export(oligoSummary)
export(peakPermTest)
export(peaksNearBDP)
export(pie1)
export(plotBinOverRegions)
export(preparePool)
export(reCenterPeaks)
export(summarizeOverlapsByBins)
export(summarizePatternInPeaks)
export(tileCount)
export(tileGRanges)
export(toGRanges)
export(translatePattern)
export(write2FASTA)
export(xget)
exportClasses(annoGR)
exportClasses(bindist)
exportClasses(permPool)
exportMethods("$")
exportMethods("$<-")
exportMethods(annoGR)
exportMethods(coerce)
exportMethods(info)
exportMethods(toGRanges)
import(GenomicRanges)
import(IRanges)
import(methods)
importClassesFrom(graph,graphNEL)
importFrom(AnnotationDbi,
  Definition,
  Ontology,
  Term,
  keytypes,
  mappedkeys,
  mget,
  select
)
importFrom(BiocGenerics,
  "%in%",
  dbconn,
  do.call,
  end,
  pos,
  score,
  start,
  strand,
  width
)
importFrom(Biostrings,
  DNAString,
  DNAStringSet,
  PDict,
  getSeq,
  oligonucleotideFrequency,
  readDNAStringSet,
  reverseComplement,
  vcountPDict,
  writeXStringSet
)
importFrom(DBI,dbGetQuery)
importFrom(GenomeInfoDb,
  "seqlengths<-",
  "seqlevels<-",
  "seqlevelsStyle<-",
  Seqinfo,
  keepSeqlevels,
  seqinfo,
  seqlengths,
  seqlevels,
  seqlevelsStyle,
  seqnames
)
importFrom(GenomicAlignments,
  Union,
  readGAlignmentPairs,
  readGAlignments,
  summarizeOverlaps
)
importFrom(GenomicFeatures,
  cds,
  cdsBy,
  exonicParts,
  exons,
  exonsBy,
  fiveUTRsByTranscript,
  genes,
  intronsByTranscript,
  promoters,
  tRNAs,
  threeUTRsByTranscript,
  transcripts,
  transcriptsBy
)
importFrom(InteractionSet,GInteractions)
importFrom(KEGGREST,
  keggGet,
  keggLink
)
importFrom(RBGL,connectedComp)
importFrom(Rsamtools,
  ScanBamParam,
  countBam,
  scanBam,
  scanBamFlag,
  scanBamHeader,
  scanBamWhat,
  testPairedEndBam
)
importFrom(S4Vectors,
  DataFrame,
  Rle,
  SimpleList,
  aggregate,
  elementMetadata,
  elementNROWS,
  mcols,
  queryHits,
  runLength,
  runValue,
  subjectHits
)
importFrom(SummarizedExperiment,
  SummarizedExperiment,
  assay,
  assays,
  colData
)
importFrom(VennDiagram,venn.diagram)
importFrom(biomaRt,
  getBM,
  getSequence
)
importFrom(data.table,data.table)
importFrom(dplyr,
  "%>%",
  filter,
  group_by,
  left_join,
  pull,
  top_n
)
importFrom(ensembldb,EnsDb)
importFrom(ggplot2,
  aes,
  aes_string,
  coord_flip,
  coord_polar,
  element_text,
  expansion,
  facet_grid,
  facet_wrap,
  geom_bar,
  geom_bin2d,
  geom_col,
  geom_point,
  geom_rect,
  geom_text,
  ggplot,
  guide_legend,
  scale_fill_manual,
  scale_x_discrete,
  scale_y_continuous,
  theme,
  theme_bw,
  theme_classic,
  theme_void,
  xlab,
  xlim,
  ylab
)
importFrom(grDevices,
  as.graphicsAnnot,
  boxplot.stats,
  col2rgb,
  colorRampPalette,
  dev.flush,
  dev.hold,
  rgb
)
importFrom(graph,ugraph)
importFrom(graphics,
  abline,
  axis,
  hist,
  legend,
  lines,
  matlines,
  matplot,
  par,
  plot,
  plot.new,
  plot.window,
  polygon,
  segments,
  text,
  title
)
importFrom(grid,
  gEdit,
  gList,
  gTree,
  gpar,
  grid.draw,
  grid.newpage,
  grid.pretty,
  legendGrob,
  rasterGrob,
  textGrob,
  viewport,
  xaxisGrob,
  yaxisGrob
)
importFrom(matrixStats,
  rowMaxs,
  rowMins
)
importFrom(multtest,mt.rawp2adjp)
importFrom(pwalign,
  aligned,
  pairwiseAlignment
)
importFrom(regioneR,
  numOverlaps,
  permTest
)
importFrom(rtracklayer,import)
importFrom(scales,label_wrap)
importFrom(stats,
  as.dendrogram,
  as.formula,
  binom.test,
  fisher.test,
  hclust,
  kmeans,
  loess.smooth,
  nobs,
  phyper,
  reorder,
  rexp,
  setNames,
  ts
)
importFrom(stringr,str_split)
importFrom(tibble,tibble)
importFrom(tidyr,separate_rows)
importFrom(universalmotif,shuffle_sequences)
importFrom(utils,
  adist,
  combn,
  data,
  installed.packages,
  read.csv,
  read.table,
  write.table
)
importMethodsFrom(S4Vectors,first)
importMethodsFrom(S4Vectors,second)
