NAMESPACE

import(
  Biobase,
  BiocGenerics, 
  hwriter, 
  methods, 
  stringr, 
  statmod, 
  biomaRt, 
  GenomicRanges,
  IRanges, 
  Rsamtools,
  DESeq2,
  BiocParallel,
  geneplotter,
  genefilter,
  RColorBrewer
)

exportClasses( 
  "ExonCountSet",
  "DEXSeqDataSet",
  "DEXSeqResults"
)

exportMethods(
  estimateDispersions,
  plotMA,
  counts,
  estimateSizeFactors,
  subsetByOverlaps,
  findOverlaps,
### TO DEPRECATE
  plotDispEsts
)

export(
  geneIDs, "geneIDs<-",
  groupIDs, "groupIDs<-",
  exonIDs, "exonIDs<-",
  featureIDs, "featureIDs<-",
  DEXSeqHTML,
  plotDEXSeq,
  testForDEU,
  featureCounts,
  perGeneQValue,
### NEW FUNCTIONS
  DEXSeqDataSet,
  DEXSeqDataSetFromSE,
  DEXSeqDataSetFromHTSeq,
  DEXSeqResults,
  estimateExonFoldChanges,
  DEXSeq,
  sampleAnnotation,
### DEPRECATE
  newExonCountSet,
  subsetByGenes,
  geneCountTable,
  countTableForGene,
  modelFrameForGene,
  estimateExonDispersionsForModelFrame_BM,
  fitDispersionFunction,
  read.HTSeqCounts,
  DEUresultTable,
  estimatelog2FoldChanges,
  doCompleteDEUAnalysis,
  makeCompleteDEUAnalysis_BM,
  constructModelFrame,
  estimateDispersions_BM,
  testGeneForDEU_BM,
  testForDEU_BM,
  buildExonCountSet,
### DEFUNCT
  countReadsForDEXSeq,
  prepareAnnotationForDEXSeq
)