# Generated by roxygen2: do not edit by hand

S3method(arrange,GRanges)
S3method(as.data.frame,csAnno)
S3method(filter,GRanges)
S3method(mutate,GRanges)
S3method(rename,GRanges)
S3method(subset,csAnno)
export(.)
export(annotateSeq)
export(as.GRanges)
export(bmData)
export(combine_csAnno)
export(downloadGEObedFiles)
export(downloadGSMbedFiles)
export(dropAnno)
export(enrichAnnoOverlap)
export(enrichPeakOverlap)
export(getAnnoStat)
export(getBioRegion)
export(getBmMatrix)
export(getGEOInfo)
export(getGEOgenomeVersion)
export(getGEOspecies)
export(getMotifMatrix)
export(getPromoters)
export(getSampleFiles)
export(getTagMatrix)
export(grange2mt)
export(makeBmDataFromData)
export(makeBmDataFromFiles)
export(parse_peak)
export(plotAnnoBar)
export(plotAnnoPie)
export(plotAnnoPie.csAnno)
export(plotBmProf)
export(plotCov)
export(plotDistToTSS)
export(plotGeneTrack)
export(plotMotifProf)
export(plotPeakHeatmap)
export(plotPeakProf)
export(readPeakFile)
export(rel)
export(seq2gene)
export(shuffle)
export(vennpie)
export(vennplot)
export(vennplot.peakfile)
exportClasses(bmData)
exportClasses(csAnno)
exportMethods(getBmMatrix)
exportMethods(makeBmDataFromData)
exportMethods(plotAnnoBar)
exportMethods(plotAnnoPie)
exportMethods(plotDistToTSS)
exportMethods(show)
exportMethods(upsetplot)
exportMethods(vennpie)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(ggplot2)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importFrom(AnnotationDbi,
  get,
  select
)
importFrom(BiocGenerics,
  end,
  start,
  unstrand
)
importFrom(Biostrings,DNAStringSet)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,
  exonsBy,
  fiveUTRsByTranscript,
  genes,
  intronsByTranscript,
  threeUTRsByTranscript,
  transcripts,
  transcriptsBy
)
importFrom(GenomicRanges,
  "mcols<-",
  "strand<-",
  GRanges,
  GRangesList,
  findOverlaps,
  granges,
  makeGRangesFromDataFrame,
  mcols,
  seqnames,
  start,
  strand
)
importFrom(IRanges,
  IRanges,
  subsetByOverlaps
)
importFrom(RSQLite,
  dbConnect,
  dbGetQuery
)
importFrom(S4Vectors,
  SimpleList,
  head,
  metadata,
  queryHits,
  runValue,
  subjectHits,
  tail
)
importFrom(SummarizedExperiment,
  "assays<-",
  SummarizedExperiment,
  assayNames,
  assays
)
importFrom(aplot,
  insert_bottom,
  plot_list,
  xlim2
)
importFrom(boot,
  boot,
  boot.ci
)
importFrom(bsseq,
  BSseq,
  pData
)
importFrom(dplyr,
  arrange,
  filter,
  group_by,
  left_join,
  mutate,
  rename,
  summarise
)
importFrom(enrichplot,upsetplot)
importFrom(ggplot2,
  aes,
  aes_string,
  annotate,
  coord_cartesian,
  coord_fixed,
  coord_flip,
  element_blank,
  element_line,
  element_rect,
  element_text,
  facet_grid,
  geom_bar,
  geom_blank,
  geom_col,
  geom_curve,
  geom_hline,
  geom_line,
  geom_rect,
  geom_ribbon,
  geom_segment,
  geom_text,
  geom_tile,
  geom_vline,
  ggplot,
  ggtitle,
  guide_legend,
  labs,
  rel,
  scale_color_manual,
  scale_fill_brewer,
  scale_fill_distiller,
  scale_fill_gradient2,
  scale_fill_hue,
  scale_fill_manual,
  scale_x_continuous,
  scale_y_continuous,
  theme,
  theme_bw,
  theme_classic,
  theme_minimal,
  xlab,
  xlim,
  ylab
)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,
  layout,
  legend,
  par,
  pie,
  plot.new
)
importFrom(grid,
  popViewport,
  pushViewport,
  viewport
)
importFrom(magrittr,
  "%<>%",
  "%>%"
)
importFrom(methods,
  as,
  is,
  missingArg,
  new,
  setClass,
  setGeneric,
  setMethod,
  show
)
importFrom(parallel,
  detectCores,
  mclapply
)
importFrom(plotrix,floating.pie)
importFrom(rlang,
  .data,
  check_installed,
  quos,
  sym
)
importFrom(rtracklayer,
  import.chain,
  liftOver
)
importFrom(scales,rescale)
importFrom(stats,
  as.formula,
  dist,
  hclust,
  p.adjust,
  phyper,
  reshape
)
importFrom(tidyr,gather)
importFrom(tidyselect,all_of)
importFrom(utils,
  download.file,
  file_test,
  getFromNamespace,
  read.delim,
  setTxtProgressBar,
  txtProgressBar
)
importFrom(yulab.utils,
  get_cache_element,
  get_cache_item,
  initial_cache_item,
  mat2df,
  rm_cache_item,
  update_cache_item,
  yulab_msg
)
