# Generated by roxygen2: do not edit by hand

export(FLOSS)
export(PAmotif)
export(assignReadingFrame)
export(codonUsage)
export(countReads)
export(coverageDepth)
export(coverageRates)
export(cvgd)
export(estimatePsite)
export(filterCDS)
export(frameCounts)
export(getFPKM)
export(getORFscore)
export(getPsiteCoordinates)
export(metaPlot)
export(normByRUVs)
export(plotDistance2Codon)
export(plotFrameDensity)
export(plotSpliceEvent)
export(plotTE)
export(plotTranscript)
export(prepareCDS)
export(readsDistribution)
export(readsEndPlot)
export(readsLenToKeep)
export(ribosomeReleaseScore)
export(shiftReadsByFrame)
export(simulateRPF)
export(spliceEvent)
export(strandPlot)
export(summaryReadsLength)
export(translationalEfficiency)
exportClasses(cvgd)
exportMethods(`$<-`)
exportMethods(`$`)
exportMethods(`[[<-`)
exportMethods(`[[`)
exportMethods(show)
import(GenomicRanges)
import(IRanges)
import(methods)
importClassesFrom(GenomicFeatures,TxDb)
importClassesFrom(Rsamtools,BamFile)
importClassesFrom(motifStack,pcm)
importFrom(AnnotationDbi,select)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,table)
importFrom(Biostrings,AA_STANDARD)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,consensusMatrix)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,translate)
importFrom(Biostrings,vmatchPattern)
importFrom(EDASeq,betweenLaneNormalization)
importFrom(EDASeq,counts)
importFrom(EDASeq,newSeqExpressionSet)
importFrom(EDASeq,normCounts)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,`seqlengths<-`)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicAlignments,GAlignments)
importFrom(GenomicAlignments,cigar)
importFrom(GenomicAlignments,cigarNarrow)
importFrom(GenomicAlignments,cigarQNarrow)
importFrom(GenomicAlignments,cigarWidthAlongReferenceSpace)
importFrom(GenomicAlignments,narrow)
importFrom(GenomicAlignments,njunc)
importFrom(GenomicAlignments,qwidth)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,sequenceLayer)
importFrom(GenomicFeatures,cds)
importFrom(GenomicFeatures,cdsBy)
importFrom(GenomicFeatures,coverageByTranscript)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,fiveUTRsByTranscript)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,makeTxDbFromGFF)
importFrom(GenomicFeatures,promoters)
importFrom(GenomicFeatures,threeUTRsByTranscript)
importFrom(GenomicFeatures,transcripts)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,RleList)
importFrom(IRanges,Views)
importFrom(IRanges,disjoin)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,promoters)
importFrom(IRanges,slidingWindows)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,viewApply)
importFrom(IRanges,viewMeans)
importFrom(IRanges,viewSums)
importFrom(RUVSeq,RUVs)
importFrom(RUVSeq,makeGroups)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,getSeq)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsubread,featureCounts)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runLength)
importFrom(S4Vectors,subjectHits)
importFrom(XVector,subseq)
importFrom(cluster,silhouette)
importFrom(ggfittext,geom_bar_text)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotation_logticks)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_label_repel)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,segments)
importFrom(grid,grid.draw)
importFrom(grid,grid.newpage)
importFrom(methods,as)
importFrom(methods,is)
importFrom(motifStack,plotMotifLogo)
importFrom(rtracklayer,export)
importFrom(scales,math_format)
importFrom(scales,trans_breaks)
importFrom(scales,trans_format)
importFrom(stats,cooks.distance)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,p.adjust)
importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,wilcox.test)
importFrom(utils,head)
