NAMESPACE

# Generated by roxygen2: do not edit by hand

export(assignGeneID)
export(assignMissingID)
export(assignTxID)
export(assignTxType)
export(balanceBC)
export(balanceD)
export(bwCommonGenome)
export(bwGenomeCompatibility)
export(bwValid)
export(calcBidirectionality)
export(calcComposition)
export(calcPooled)
export(calcShape)
export(calcSupport)
export(calcTPM)
export(calcTotalTags)
export(checkCTSSs)
export(checkPeaked)
export(checkPooled)
export(clusterBidirectionally)
export(clusterUnidirectionally)
export(combineClusters)
export(convertBAM2BigWig)
export(convertBED2BedGraph)
export(convertBED2BigWig)
export(convertBedGraph2BED)
export(convertBedGraph2BigWig)
export(convertBigWig2BED)
export(convertBigWig2BedGraph)
export(convertGRanges2GPos)
export(findLinks)
export(findStretches)
export(quantifyCTSSs)
export(quantifyClusters)
export(quantifyGenes)
export(quickEnhancers)
export(quickGenes)
export(quickTSSs)
export(shapeEntropy)
export(shapeIQR)
export(shapeMean)
export(subsetByBidirectionality)
export(subsetByComposition)
export(subsetBySupport)
export(swapRanges)
export(swapScores)
export(trackBalance)
export(trackCTSS)
export(trackClusters)
export(trackLinks)
export(trimToPeak)
export(trimToPercentiles)
export(tuneTagClustering)
export(utilsAggregateRows)
export(utilsDeStrand)
export(utilsScoreOverlaps)
export(utilsSimplifyTxDb)
exportMethods(calcBidirectionality)
exportMethods(combineClusters)
exportMethods(quantifyCTSSs)
exportMethods(subsetByBidirectionality)
exportMethods(trackBalance)
exportMethods(trackCTSS)
exportMethods(trackClusters)
exportMethods(utilsAggregateRows)
import(BiocGenerics)
import(GenomeInfoDb)
import(GenomicFeatures)
import(GenomicRanges)
import(Gviz)
import(IRanges)
import(S4Vectors)
import(SummarizedExperiment)
import(assertthat)
import(rtracklayer)
importClassesFrom(GenomicAlignments,GAlignments)
importClassesFrom(Matrix,dgCMatrix)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setRefClass)