# Generated by roxygen2: do not edit by hand

export(NFRscore)
export(PTscore)
export(TSSEscore)
export(bamQC)
export(distanceDyad)
export(enrichedFragments)
export(estimateLibComplexity)
export(factorFootprints)
export(footprintsScanner)
export(fragSizeDist)
export(plotCorrelation)
export(plotFootprints)
export(prepareBindingSitesList)
export(pseudoPausingIndex)
export(readBamFile)
export(readsDupFreq)
export(saturationPlot)
export(shiftGAlignments)
export(shiftGAlignmentsList)
export(splitBam)
export(splitGAlignmentsByCut)
export(vPlot)
export(writeListOfGAlignments)
import(BiocGenerics)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(S4Vectors)
import(edgeR)
importClassesFrom(GenomicAlignments,GAlignments)
importClassesFrom(GenomicAlignments,GAlignmentsList)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(motifStack,pfm)
importFrom(BSgenome,getSeq)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bptry)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,PWMscoreStartingAt)
importFrom(Biostrings,PhredQuality)
importFrom(Biostrings,letterFrequency)
importFrom(Biostrings,matchPWM)
importFrom(Biostrings,maxScore)
importFrom(ChIPpeakAnno,annotatePeakInBatch)
importFrom(ChIPpeakAnno,estLibSize)
importFrom(ChIPpeakAnno,featureAlignedExtendSignal)
importFrom(ChIPpeakAnno,featureAlignedSignal)
importFrom(ChIPpeakAnno,reCenterPeaks)
importFrom(GenomicAlignments,GAlignments)
importFrom(GenomicAlignments,GAlignmentsList)
importFrom(GenomicAlignments,cigar)
importFrom(GenomicAlignments,cigarNarrow)
importFrom(GenomicAlignments,cigarQNarrow)
importFrom(GenomicAlignments,cigarWidthAlongQuerySpace)
importFrom(GenomicAlignments,coverage)
importFrom(GenomicAlignments,qwidth)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,readGAlignmentsList)
importFrom(GenomicAlignments,sequenceLayer)
importFrom(GenomicAlignments,summarizeOverlaps)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,shift)
importFrom(GenomicScores,gscores)
importFrom(GenomicScores,populations)
importFrom(IRanges,Views)
importFrom(IRanges,viewMeans)
importFrom(KernSmooth,bkde2D)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,`bamTag<-`)
importFrom(Rsamtools,`bamWhich<-`)
importFrom(Rsamtools,asBam)
importFrom(Rsamtools,bamFlagAsBitMatrix)
importFrom(Rsamtools,bamTag)
importFrom(Rsamtools,bamWhich)
importFrom(Rsamtools,countBam)
importFrom(Rsamtools,filterBam)
importFrom(Rsamtools,idxstatsBam)
importFrom(Rsamtools,mergeBam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,testPairedEndBam)
importFrom(S4Vectors,FilterRules)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,smoothScatter)
importFrom(grid,convertX)
importFrom(grid,convertY)
importFrom(grid,gpar)
importFrom(grid,grid.legend)
importFrom(grid,grid.lines)
importFrom(grid,grid.newpage)
importFrom(grid,grid.segments)
importFrom(grid,grid.text)
importFrom(grid,grid.xaxis)
importFrom(grid,grid.yaxis)
importFrom(grid,plotViewport)
importFrom(grid,pushViewport)
importFrom(grid,unit)
importFrom(grid,upViewport)
importFrom(grid,viewport)
importFrom(limma,normalizeBetweenArrays)
importFrom(motifStack,plotMotifLogoA)
importFrom(preseqR,ds.rSAC.bootstrap)
importFrom(randomForest,randomForest)
importFrom(rtracklayer,export)
importFrom(stats,cor.test)
importFrom(stats,heatmap)
importFrom(stats,lm)
importFrom(stats,loess.smooth)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(utils,combn)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.csv)
