import(Biobase)
import(methods)
import(S4Vectors)
importFrom(AnnotationDbi, mget)
import(limma)
import(IRanges)
importFrom(GenomeInfoDb, seqlengths, seqlevelsStyle, mapSeqlevels)
import(GenomicRanges)
import(GenomicFeatures)
importFrom(BSgenome, getSeq, matchPWM)
import(BiocParallel)
importFrom(Gviz, GeneRegionTrack)
importFrom(cleanUpdTSeq, buildFeatureVector, predictTestSet)
importFrom(seqinr, s2c, GC)
importFrom(depmixS4, depmix, fit, posterior, getpars)
importFrom(preprocessCore, colSummarizeAvg, colSummarizeMedian, 
           normalize.quantiles, normalize.quantiles.robust)
exportClass("UTR3eSet")
exportMethods("$", "$<-")
export(coverageFromBedGraph,
       coverageRate,
       CPsites,
       filterRes,
       fisher.exact.test,
       getUTR3eSet,
       inPAS,
       limmaAnalyze,
       prepare4GSEA,
       singleGroupAnalyze,
       singleSampleAnalyze,
       testUsage,
       utr3Annotation,
       utr3UsageEstimation,
       usage4plot
       )
