# Generated by roxygen2: do not edit by hand

export(alignmentStats)
export(preprocessReads)
export(qAlign)
export(qCount)
export(qExportWig)
export(qMeth)
export(qProfile)
export(qProjectUpdate)
export(qQCReport)
exportClasses(qProject)
exportMethods("[")
exportMethods(alignments)
exportMethods(auxiliaries)
exportMethods(genome)
exportMethods(length)
exportMethods(show)
import(Rbowtie)
importFrom(AnnotationDbi,loadDb)
importFrom(BSgenome,available.genomes)
importFrom(BSgenome,getSeq)
importFrom(Biobase,createPackage)
importFrom(Biobase,testBioCConnection)
importFrom(BiocGenerics,as.vector)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,match)
importFrom(BiocGenerics,setdiff)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,unlist)
importFrom(BiocGenerics,which)
importFrom(BiocGenerics,width)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(BiocParallel,bpworkers)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,alphabetFrequency)
importFrom(Biostrings,chartr)
importFrom(Biostrings,dinucleotideFrequency)
importFrom(Biostrings,fasta.seqlengths)
importFrom(Biostrings,injectHardMask)
importFrom(Biostrings,masks)
importFrom(Biostrings,quality)
importFrom(Biostrings,replaceLetterAt)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,trimLRPatterns)
importFrom(Biostrings,writeXStringSet)
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,bsgenomeName)
importFrom(GenomeInfoDb,commonName)
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,organism)
importFrom(GenomeInfoDb,provider)
importFrom(GenomeInfoDb,releaseDate)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,makeTxDbFromGFF)
importFrom(GenomicFeatures,promoters)
importFrom(GenomicFiles,REDUCEsampler)
importFrom(GenomicFiles,reduceByYield)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,seqnames)
importFrom(IRanges,IRanges)
importFrom(IRanges,breakInChunks)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,ranges)
importFrom(IRanges,reverse)
importFrom(Rbowtie,SpliceMap)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,asBam)
importFrom(Rsamtools,getSeq)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,indexFa)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,scanFa)
importFrom(Rsamtools,scanFaIndex)
importFrom(Rsamtools,sortBam)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,active)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,evalSeparately)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runLength)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,split)
importFrom(S4Vectors,subjectHits)
importFrom(ShortRead,FastqSampler)
importFrom(ShortRead,FastqStreamer)
importFrom(ShortRead,SRFilterResult)
importFrom(ShortRead,ShortReadQ)
importFrom(ShortRead,alphabetByCycle)
importFrom(ShortRead,nFilter)
importFrom(ShortRead,narrow)
importFrom(ShortRead,qa)
importFrom(ShortRead,readFasta)
importFrom(ShortRead,srFilter)
importFrom(ShortRead,sread)
importFrom(ShortRead,tables)
importFrom(ShortRead,width)
importFrom(ShortRead,writeFastq)
importFrom(ShortRead,yield)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.cur)
importFrom(grDevices,dev.new)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,box)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,matplot)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,rect)
importFrom(graphics,strheight)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(methods,.hasSlot)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,show)
importFrom(parallel,clusterApplyLB)
importFrom(parallel,clusterCall)
importFrom(parallel,clusterEvalQ)
importFrom(parallel,clusterMap)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,splitIndices)
importFrom(parallel,stopCluster)
importFrom(rtracklayer,wigToBigWig)
importFrom(stats,aggregate)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(tools,file_ext)
importFrom(tools,file_path_as_absolute)
importFrom(tools,file_path_sans_ext)
importFrom(tools,md5sum)
importFrom(utils,flush.console)
importFrom(utils,install.packages)
importFrom(utils,installed.packages)
importFrom(utils,packageVersion)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.table)
useDynLib(QuasR, .registration=TRUE)
