# Generated by roxygen2: do not edit by hand

S3method(lines,hanabi)
S3method(pairs,DataFrame)
S3method(plot,hanabi)
S3method(points,hanabi)
S3method(rowsum,RleDataFrame)
export("CTSScoordinatesGR<-")
export("CTSStagCountSE<-")
export("consensusClustersGR<-")
export("consensusClustersSE<-")
export("genomeName<-")
export("inputFiles<-")
export("inputFilesType<-")
export("sampleLabels<-")
export(.ctss_summary_for_clusters)
export(CAGEexp)
export(CTSS)
export(CTSScoordinatesGR)
export(CTSScumulativesCC)
export(CTSScumulativesTagClusters)
export(CTSSnormalizedTpmDF)
export(CTSSnormalizedTpmGR)
export(CTSStagCountDF)
export(CTSStagCountGR)
export(CTSStagCountSE)
export(CTSStoGenes)
export(CustomConsensusClusters)
export(GeneExpDESeq2)
export(GeneExpSE)
export(TSSlogo)
export(aggregateTagClusters)
export(annotateCTSS)
export(annotateConsensusClusters)
export(annotateTagClusters)
export(consensusClustersDESeq2)
export(consensusClustersGR)
export(consensusClustersSE)
export(consensusClustersTpm)
export(correlationMatrix)
export(cumulativeCTSSdistribution)
export(distclu)
export(exportToTrack)
export(expressionClasses)
export(filterLowExpCTSS)
export(filteredCTSSidx)
export(findStrandInvaders)
export(flagByUpstreamSequences)
export(flagLowExpCTSS)
export(genomeName)
export(getCTSS)
export(getExpressionProfiles)
export(getShiftingPromoters)
export(hanabi)
export(hanabiPlot)
export(importPublicData)
export(inputFiles)
export(inputFilesType)
export(librarySizes)
export(mergeCAGEsets)
export(mergeSamples)
export(normalizeTagCount)
export(paraclu)
export(plotAnnot)
export(plotCorrelation)
export(plotCorrelation2)
export(plotExpressionProfiles)
export(plotInterquantileWidth)
export(plotReverseCumulatives)
export(quantilePositions)
export(removeStrandInvaders)
export(resetCAGEexp)
export(sampleLabels)
export(sampleList)
export(scoreShift)
export(seqNameTotalsSE)
export(setColors)
export(summariseChrExpr)
export(tagClustersGR)
exportClasses(CAGEexp)
exportClasses(CAGEr)
exportClasses(CTSS)
exportMethods(coerce)
exportMethods(findStrandInvaders)
exportMethods(flagByUpstreamSequences)
exportMethods(quickEnhancers)
exportMethods(removeStrandInvaders)
import(BiocGenerics)
import(MultiAssayExperiment)
import(SummarizedExperiment)
import(methods)
importFrom(BSgenome,
  getBSgenome,
  getSeq,
  installed.genomes
)
importFrom(BiocParallel,
  MulticoreParam,
  SerialParam,
  bplapply,
  multicoreWorkers
)
importFrom(Biostrings,consensusMatrix)
importFrom(CAGEfightR,quickEnhancers)
importFrom(GenomicAlignments,
  qwidth,
  readGAlignments
)
importFrom(GenomicFeatures,
  exons,
  genes,
  promoters,
  transcripts
)
importFrom(GenomicRanges,
  GPos,
  GRanges,
  GRangesList,
  countOverlaps,
  findOverlaps,
  from_GPos_to_GRanges,
  granges,
  promoters
)
importFrom(IRanges,
  IRanges,
  IRangesList,
  PartitioningByEnd,
  RleList,
  extractList,
  reduce
)
importFrom(KernSmooth,bkde2D)
importFrom(Matrix,rowSums)
importFrom(Rsamtools,
  "bamFlag<-",
  ScanBamParam,
  scanBamFlag
)
importFrom(S4Vectors,
  "%in%",
  DataFrame,
  List,
  Pairs,
  Rle,
  SimpleList,
  decode,
  endoapply,
  first,
  mcols,
  queryHits,
  runLength,
  runValue,
  second,
  subjectHits,
  unstrsplit
)
importFrom(Seqinfo,
  "genome<-",
  "seqlevels<-",
  bsgenomeName,
  genome,
  seqinfo,
  seqlengths,
  seqlevels,
  seqnames,
  sortSeqlevels
)
importFrom(SummarizedExperiment,
  SummarizedExperiment,
  assay,
  assays
)
importFrom(VGAM,zeta)
importFrom(data.table,
  data.table,
  fread,
  setkeyv,
  setnames
)
importFrom(formula.tools,
  lhs,
  rhs.vars
)
importFrom(ggplot2,
  aes,
  aes_string,
  coord_flip,
  facet_wrap,
  geom_abline,
  geom_bar,
  geom_histogram,
  geom_point,
  geom_segment,
  geom_step,
  geom_vline,
  ggplot,
  ggtitle,
  guide_legend,
  guides,
  labs,
  position_stack,
  scale_color_manual,
  scale_fill_manual,
  scale_x_log10,
  scale_y_log10,
  xlab,
  ylab
)
importFrom(grDevices,
  blues9,
  col2rgb,
  colorRamp,
  colorRampPalette,
  dev.flush,
  dev.hold,
  rainbow,
  rgb,
  xy.coords
)
importFrom(graphics,
  Axis,
  axis,
  box,
  legend,
  lines,
  mtext,
  pairs,
  par,
  points,
  strwidth,
  text
)
importFrom(gtools,mixedorder)
importFrom(memoise,memoise)
importFrom(plyr,ddply)
importFrom(reshape2,melt)
importFrom(rlang,.data)
importFrom(rtracklayer,
  import.bed,
  import.bw
)
importFrom(scales,hue_pal)
importFrom(som,som)
importFrom(stats,
  coefficients,
  cor,
  kmeans,
  lm,
  median,
  p.adjust
)
importFrom(stringdist,stringdist)
importFrom(stringi,stri_sub)
importFrom(utils,
  combn,
  head,
  installed.packages,
  read.table,
  tail
)
importFrom(vegan,rarefy)
