File: NAMESPACE

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r-bioc-dexseq 1.38.0%2Bdfsg-1
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import(
  Biobase,
  BiocGenerics, 
  hwriter, 
  methods, 
  stringr, 
  statmod, 
  biomaRt, 
  GenomicRanges,
  S4Vectors,
  IRanges, 
  Rsamtools,
  DESeq2,
  BiocParallel,
  geneplotter,
  genefilter,
  SummarizedExperiment
)

importFrom(AnnotationDbi,select)
importFrom(RColorBrewer,brewer.pal)
importFrom(grDevices, colorRamp, colorRampPalette,
           dev.off, rgb, svg)
importFrom(graphics, abline, axis, hist,
           layout, mtext, par, plot.new,
           plot.window, rect, segments)
importFrom(stats, as.formula,
           coefficients, model.matrix,
           runif, terms, weighted.mean)
importFrom(utils, read.delim, read.table)
importFrom(stats, relevel)


exportClasses( 
  "DEXSeqDataSet",
  "DEXSeqResults"
)

exportMethods(
  estimateDispersions,
  plotMA,
  counts,
  estimateSizeFactors,
  subsetByOverlaps,
  findOverlaps,
  "[",
  "$<-",
  "colData<-"
)

export(
  geneIDs, "geneIDs<-",
  groupIDs, "groupIDs<-",
  exonIDs, "exonIDs<-",
  featureIDs, "featureIDs<-",
  DEXSeqHTML,
  plotDEXSeq,
  testForDEU,
  featureCounts,
  perGeneQValue,
### NEW FUNCTIONS
  DEXSeqDataSet,
  DEXSeqDataSetFromSE,
  DEXSeqDataSetFromHTSeq,
  DEXSeqResults,
  estimateExonFoldChanges,
  DEXSeq,
  sampleAnnotation
)