import(Biobase, hwriter, methods, stringr, statmod, biomaRt, GenomicRanges, Rsamtools)

exportClasses( "ExonCountSet" )

exportMethods(
  counts, "counts<-",
  sizeFactors, "sizeFactors<-",
  design, "design<-",
  estimateSizeFactors,
  estimateDispersions
)

export(
  newExonCountSet,
  geneIDs, "geneIDs<-",
  exonIDs, "exonIDs<-",
  subsetByGenes,
  geneCountTable,
  countTableForGene,
  modelFrameForGene,
  estimateExonDispersionsForModelFrame,
  fitDispersionFunction,
  testGeneForDEU,
  testForDEU,
  read.HTSeqCounts,
  DEXSeqHTML,
  DEUresultTable,
  plotDEXSeq,
  estimatelog2FoldChanges,
  makeCompleteDEUAnalysis,
  modelFrameForTRT,
  estimateDispersionsTRT,
  testForDEUTRT,
  perGeneQValue,
  prepareAnnotationForDEXSeq,
  countReadsForDEXSeq,
  buildExonCountSet
)


