# Generated by roxygen2: do not edit by hand

export(BamFileList)
export(IRanges)
export(RangedData)
export(SRFilterResult)
export(alignData)
export(basename)
export(chastityFilter)
export(chromosomeFilter)
export(compose)
export(locfit)
export(lp)
export(nFilter)
export(naPositionFilter)
export(newCountDataSet)
export(readAligned)
exportClasses(AnnotParam)
exportClasses(AnnotParamCharacter)
exportClasses(AnnotParamObject)
exportClasses(BamFileList)
exportClasses(BamParam)
exportClasses(RNAseq)
exportClasses(RangedData)
exportClasses(RangedSummarizedExperiment)
exportClasses(RnaSeqParam)
exportMethods("chrSize<-")
exportMethods("fileName<-")
exportMethods("geneModel<-")
exportMethods("genomicAnnotation<-")
exportMethods("librarySize<-")
exportMethods("organismName<-")
exportMethods("readCounts<-")
exportMethods("readCoverage<-")
exportMethods("readLength<-")
exportMethods("seqlevels<-")
exportMethods("seqnames<-")
exportMethods("strand<-")
exportMethods(AnnotParam)
exportMethods(BamParam)
exportMethods(RPKM)
exportMethods(RnaSeqParam)
exportMethods(SummarizedExperiment)
exportMethods(annotParam)
exportMethods(assay)
exportMethods(assays)
exportMethods(bamParam)
exportMethods(barcodePlot)
exportMethods(chrSize)
exportMethods(colData)
exportMethods(colnames)
exportMethods(countBy)
exportMethods(createSyntheticTranscripts)
exportMethods(datasource)
exportMethods(demultiplex)
exportMethods(easyRNASeq)
exportMethods(estimateDispersions)
exportMethods(estimateSizeFactors)
exportMethods(exonCounts)
exportMethods(featureCounts)
exportMethods(fetchCoverage)
exportMethods(fileName)
exportMethods(geneCounts)
exportMethods(geneModel)
exportMethods(genomicAnnotation)
exportMethods(getAnnotation)
exportMethods(getBamFileList)
exportMethods(librarySize)
exportMethods(metadata)
exportMethods(multivariateConditions)
exportMethods(organismName)
exportMethods(paired)
exportMethods(parallelize)
exportMethods(plotDispLSD)
exportMethods(plotDispersionEstimates)
exportMethods(plotNormalizationFactors)
exportMethods(precision)
exportMethods(ranges)
exportMethods(readCounts)
exportMethods(readCoverage)
exportMethods(readLength)
exportMethods(reduce)
exportMethods(rowRanges)
exportMethods(seqinfo)
exportMethods(seqlengths)
exportMethods(seqlevels)
exportMethods(seqnames)
exportMethods(simpleRNASeq)
exportMethods(split)
exportMethods(srFilter)
exportMethods(strand)
exportMethods(strandProtocol)
exportMethods(stranded)
exportMethods(transcriptCounts)
exportMethods(type)
exportMethods(unsafeAppend)
exportMethods(validate)
exportMethods(width)
exportMethods(writeFastq)
exportMethods(writeGff3)
exportMethods(yieldSize)
importClassesFrom(Biostrings,DNAStringSet)
importClassesFrom(DESeq,CountDataSet)
importClassesFrom(GenomicAlignments,GAlignmentPairs)
importClassesFrom(GenomicAlignments,GAlignments)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(GenomicRanges,GRangesList)
importClassesFrom(IRanges,RangedData)
importClassesFrom(IRanges,RleList)
importClassesFrom(Rsamtools,BamFile)
importClassesFrom(Rsamtools,BamFileList)
importClassesFrom(S4Vectors,Annotated)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,SimpleList)
importClassesFrom(S4Vectors,Vector)
importClassesFrom(ShortRead,AlignedRead)
importClassesFrom(ShortRead,ShortReadQ)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importClassesFrom(edgeR,DGEList)
importClassesFrom(genomeIntervals,Genome_intervals)
importClassesFrom(genomeIntervals,Genome_intervals_stranded)
importClassesFrom(methods,"function")
importClassesFrom(methods,ANY)
importClassesFrom(methods,character)
importClassesFrom(methods,integer)
importClassesFrom(methods,list)
importClassesFrom(methods,matrix)
importClassesFrom(methods,missing)
importClassesFrom(methods,numeric)
importClassesFrom(methods,vector)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(Biostrings,DNAStringSet)
importFrom(DESeq,fitInfo)
importFrom(DESeq,newCountDataSet)
importFrom(GenomicAlignments,GAlignments)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,LogicalList)
importFrom(IRanges,RangedData)
importFrom(IRanges,RleList)
importFrom(IRanges,SplitDataFrameList)
importFrom(LSD,heatscatter)
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,bamFlagTest)
importFrom(Rsamtools,index)
importFrom(Rsamtools,scanBamFlag)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,queryHits)
importFrom(ShortRead,SRFilterResult)
importFrom(ShortRead,alignData)
importFrom(ShortRead,chromosomeFilter)
importFrom(ShortRead,compose)
importFrom(ShortRead,nFilter)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listDatasets)
importFrom(biomaRt,useDataset)
importFrom(biomaRt,useMart)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateCommonDisp)
importFrom(edgeR,estimateTagwiseDisp)
importFrom(edgeR,maPlot)
importFrom(edgeR,plotBCV)
importFrom(edgeR,plotMDS.DGEList)
importFrom(edgeR,plotMeanVar)
importFrom(genomeIntervals,getGffAttribute)
importFrom(genomeIntervals,parseGffAttributes)
importFrom(graphics,abline)
importFrom(graphics,axTicks)
importFrom(graphics,axis)
importFrom(graphics,boxplot)
importFrom(graphics,grid)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,rect)
importFrom(locfit,locfit)
importFrom(locfit,lp)
importFrom(methods,as)
importFrom(methods,extends)
importFrom(methods,is)
importFrom(methods,new)
importFrom(parallel,makePSOCKcluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(stats,aggregate)
importFrom(stats,na.omit)
importFrom(utils,combn)
importFrom(utils,packageVersion)
importFrom(utils,str)
importMethodsFrom(Biobase,fData)
importMethodsFrom(Biobase,varMetadata)
importMethodsFrom(BiocGenerics,"strand<-")
importMethodsFrom(BiocGenerics,annotation)
importMethodsFrom(BiocGenerics,cbind)
importMethodsFrom(BiocGenerics,clusterApply)
importMethodsFrom(BiocGenerics,colnames)
importMethodsFrom(BiocGenerics,counts)
importMethodsFrom(BiocGenerics,duplicated)
importMethodsFrom(BiocGenerics,estimateDispersions)
importMethodsFrom(BiocGenerics,estimateSizeFactors)
importMethodsFrom(BiocGenerics,eval)
importMethodsFrom(BiocGenerics,fileName)
importMethodsFrom(BiocGenerics,get)
importMethodsFrom(BiocGenerics,intersect)
importMethodsFrom(BiocGenerics,lapply)
importMethodsFrom(BiocGenerics,match)
importMethodsFrom(BiocGenerics,order)
importMethodsFrom(BiocGenerics,paste)
importMethodsFrom(BiocGenerics,path)
importMethodsFrom(BiocGenerics,pmax)
importMethodsFrom(BiocGenerics,rbind)
importMethodsFrom(BiocGenerics,rownames)
importMethodsFrom(BiocGenerics,sapply)
importMethodsFrom(BiocGenerics,strand)
importMethodsFrom(BiocGenerics,table)
importMethodsFrom(BiocGenerics,unique)
importMethodsFrom(Biostrings,type)
importMethodsFrom(DESeq,estimateDispersions)
importMethodsFrom(DESeq,estimateSizeFactors)
importMethodsFrom(GenomeInfoDb,"seqlengths<-")
importMethodsFrom(GenomeInfoDb,"seqlevels<-")
importMethodsFrom(GenomeInfoDb,"seqnames<-")
importMethodsFrom(GenomeInfoDb,seqinfo)
importMethodsFrom(GenomeInfoDb,seqlengths)
importMethodsFrom(GenomeInfoDb,seqlevels)
importMethodsFrom(GenomeInfoDb,seqnames)
importMethodsFrom(GenomicAlignments,cigar)
importMethodsFrom(GenomicAlignments,summarizeOverlaps)
importMethodsFrom(GenomicRanges,grglist)
importMethodsFrom(IRanges,"colnames<-")
importMethodsFrom(IRanges,"end<-")
importMethodsFrom(IRanges,"rownames<-")
importMethodsFrom(IRanges,"start<-")
importMethodsFrom(IRanges,as.list)
importMethodsFrom(IRanges,as.matrix)
importMethodsFrom(IRanges,countOverlaps)
importMethodsFrom(IRanges,coverage)
importMethodsFrom(IRanges,end)
importMethodsFrom(IRanges,findOverlaps)
importMethodsFrom(IRanges,gsub)
importMethodsFrom(IRanges,mean)
importMethodsFrom(IRanges,median)
importMethodsFrom(IRanges,narrow)
importMethodsFrom(IRanges,nchar)
importMethodsFrom(IRanges,ranges)
importMethodsFrom(IRanges,reduce)
importMethodsFrom(IRanges,rev)
importMethodsFrom(IRanges,space)
importMethodsFrom(IRanges,start)
importMethodsFrom(IRanges,sub)
importMethodsFrom(IRanges,tolower)
importMethodsFrom(IRanges,unlist)
importMethodsFrom(IRanges,values)
importMethodsFrom(IRanges,which)
importMethodsFrom(IRanges,width)
importMethodsFrom(Rsamtools,"asMates<-")
importMethodsFrom(Rsamtools,"yieldSize<-")
importMethodsFrom(Rsamtools,ScanBamParam)
importMethodsFrom(Rsamtools,asMates)
importMethodsFrom(Rsamtools,countBam)
importMethodsFrom(Rsamtools,scanBam)
importMethodsFrom(Rsamtools,scanBamHeader)
importMethodsFrom(Rsamtools,yieldSize)
importMethodsFrom(S4Vectors,"%in%")
importMethodsFrom(S4Vectors,"elementMetadata<-")
importMethodsFrom(S4Vectors,"metadata<-")
importMethodsFrom(S4Vectors,Rle)
importMethodsFrom(S4Vectors,as.table)
importMethodsFrom(S4Vectors,elementMetadata)
importMethodsFrom(S4Vectors,elementNROWS)
importMethodsFrom(S4Vectors,levels)
importMethodsFrom(S4Vectors,mcols)
importMethodsFrom(S4Vectors,metadata)
importMethodsFrom(S4Vectors,runLength)
importMethodsFrom(S4Vectors,runValue)
importMethodsFrom(S4Vectors,runsum)
importMethodsFrom(S4Vectors,split)
importMethodsFrom(S4Vectors,substr)
importMethodsFrom(ShortRead,chromosome)
importMethodsFrom(ShortRead,id)
importMethodsFrom(ShortRead,position)
importMethodsFrom(ShortRead,readAligned)
importMethodsFrom(ShortRead,srFilter)
importMethodsFrom(ShortRead,srdistance)
importMethodsFrom(ShortRead,sread)
importMethodsFrom(ShortRead,writeFastq)
importMethodsFrom(SummarizedExperiment,"assays<-")
importMethodsFrom(SummarizedExperiment,"colData<-")
importMethodsFrom(SummarizedExperiment,"rowRanges<-")
importMethodsFrom(SummarizedExperiment,SummarizedExperiment)
importMethodsFrom(SummarizedExperiment,assay)
importMethodsFrom(SummarizedExperiment,assays)
importMethodsFrom(SummarizedExperiment,colData)
importMethodsFrom(SummarizedExperiment,rowRanges)
importMethodsFrom(genomeIntervals,readGff3)
importMethodsFrom(genomeIntervals,writeGff3)
importMethodsFrom(methods,coerce)
importMethodsFrom(methods,initialize)
importMethodsFrom(methods,show)
