# Generated by roxygen2: do not edit by hand

export(bamQC)
export(enrichedFragments)
export(factorFootprints)
export(fragSizeDist)
export(readBamFile)
export(shiftGAlignmentsList)
export(splitBam)
export(splitGAlignmentsByCut)
export(writeListOfGAlignments)
import(BiocGenerics)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(S4Vectors)
importClassesFrom(motifStack,pfm)
importFrom(BSgenome,getSeq)
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,featureAlignedExtendSignal)
importFrom(ChIPpeakAnno,featureAlignedSignal)
importFrom(ChIPpeakAnno,reCenterPeaks)
importFrom(GenomicAlignments,cigar)
importFrom(GenomicAlignments,cigarNarrow)
importFrom(GenomicAlignments,cigarQNarrow)
importFrom(GenomicAlignments,coverage)
importFrom(GenomicAlignments,qwidth)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,readGAlignmentsList)
importFrom(GenomicAlignments,sequenceLayer)
importFrom(GenomicScores,scores)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,bamFlagAsBitMatrix)
importFrom(Rsamtools,countBam)
importFrom(Rsamtools,filterBam)
importFrom(Rsamtools,idxstatsBam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,testPairedEndBam)
importFrom(S4Vectors,FilterRules)
importFrom(graphics,axis)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(grid,convertX)
importFrom(grid,convertY)
importFrom(grid,gpar)
importFrom(grid,grid.legend)
importFrom(grid,grid.lines)
importFrom(grid,grid.newpage)
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(randomForest,randomForest)
importFrom(rtracklayer,export)
importFrom(stats,cor.test)
importFrom(stats,predict)
