# Generated by roxygen2: do not edit by hand

export(addChr2Exclude)
export(addInPASEnsDb)
export(addInPASGenome)
export(addInPASOutputDirectory)
export(addInPASTxDb)
export(addLockName)
export(assemble_allCov)
export(extract_UTR3Anno)
export(filter_testOut)
export(find_minMSEDistr)
export(getChr2Exclude)
export(getInPASEnsDb)
export(getInPASGenome)
export(getInPASOutputDirectory)
export(getInPASSQLiteDb)
export(getInPASTxDb)
export(getLockName)
export(get_UTR3eSet)
export(get_chromosomes)
export(get_lastCDSUTR3)
export(get_regionCov)
export(get_ssRleCov)
export(get_usage4plot)
export(parse_TxDb)
export(plot_utr3Usage)
export(run_coverageQC)
export(run_limmaAnalysis)
export(search_CPs)
export(set_globals)
export(setup_CPsSearch)
export(setup_GSEA)
export(setup_parCPsSearch)
export(setup_sqlitedb)
export(test_dPDUI)
exportClasses(UTR3eSet)
import(BSgenome)
import(Biobase)
import(GenomicFeatures)
import(GenomicRanges)
import(RSQLite)
import(S4Vectors)
import(flock)
import(limma)
import(methods)
import(readr)
importFrom(AnnotationDbi,mapIds)
importFrom(BSgenome,
  getSeq,
  matchPWM
)
importFrom(Biostrings,
  DNAString,
  alphabetFrequency,
  letterFrequencyInSlidingView,
  toString
)
importFrom(GenomeInfoDb,
  mapSeqlevels,
  seqlevelsStyle
)
importFrom(IRanges,
  IRanges,
  Views,
  viewApply,
  viewMeans
)
importFrom(Seqinfo,
  isCircular,
  seqlengths,
  seqlevels,
  seqnames
)
importFrom(batchtools,
  batchMap,
  makeClusterFunctionsInteractive,
  makeClusterFunctionsLSF,
  makeClusterFunctionsMulticore,
  makeClusterFunctionsOpenLava,
  makeClusterFunctionsSGE,
  makeClusterFunctionsSlurm,
  makeClusterFunctionsSocket,
  makeClusterFunctionsTORQUE,
  makeRegistry,
  reduceResultsList,
  submitJobs,
  waitForJobs
)
importFrom(cleanUpdTSeq,
  buildFeatureVector,
  predictTestSet
)
importFrom(depmixS4,
  depmix,
  fit,
  getpars,
  posterior
)
importFrom(dplyr,
  arrange,
  as_tibble,
  bind_cols,
  bind_rows,
  desc,
  filter,
  group_by,
  left_join,
  mutate,
  n,
  pull,
  select,
  summarise,
  syms
)
importFrom(future,
  multicore,
  multisession,
  plan
)
importFrom(future.apply,
  future_lapply,
  future_mapply
)
importFrom(ggplot2,
  aes,
  element_text,
  facet_grid,
  geom_line,
  geom_vline,
  ggplot,
  ggtitle,
  theme,
  vars,
  ylab
)
importFrom(grDevices,
  dev.off,
  pdf,
  rainbow
)
importFrom(graphics,
  abline,
  hist,
  legend,
  lines
)
importFrom(magrittr,"%>%")
importFrom(parallelly,availableCores)
importFrom(plyranges,
  as_granges,
  complement_ranges,
  disjoin_ranges,
  reduce_ranges,
  reduce_ranges_directed,
  remove_names,
  set_genome_info,
  shift_downstream
)
importFrom(preprocessCore,
  colSummarizeAvg,
  colSummarizeMedian,
  normalize.quantiles,
  normalize.quantiles.robust
)
importFrom(reshape2,melt)
importFrom(stats,
  BIC,
  density,
  fft,
  fisher.test,
  loess.smooth,
  model.matrix,
  p.adjust,
  pnorm,
  poisson,
  smooth.spline,
  t.test
)
importFrom(utils,
  packageVersion,
  read.delim,
  write.table
)
