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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(TSSenrichment)
export(addAssayToESE)
export(annotateRegions)
export(bam2bw)
export(bamChrChunkApply)
export(breakStrings)
export(bwNormFactors)
export(callPeaks)
export(clusterSignalMatrices)
export(estimateFragSize)
export(formatGenomicDist)
export(frag2bw)
export(fragSizesDist)
export(getCounts)
export(getCovStats)
export(getNormFactors)
export(getSignalMatrices)
export(importBedlike)
export(inject)
export(meltSignals)
export(mergeSignalMatrices)
export(ml2ESE)
export(motifFootprint)
export(plotCorFromCovStats)
export(plotCovStats)
export(plotEnrichedHeatmaps)
export(plotSignalTracks)
export(reduceWithResplit)
export(refragment)
export(regionCAT)
export(regionOverlaps)
export(regionUpset)
export(renormalizeBorders)
export(renormalizeSignalMatrices)
export(resizeMatrix)
export(showTrackInfo)
export(signal2Matrix)
export(tabixChrApply)
export(tileRle)
export(views2Matrix)
exportMethods("[")
exportMethods(score)
import(ComplexHeatmap)
import(EnrichedHeatmap)
import(GenomicRanges)
import(S4Vectors)
import(ggplot2)
import(methods)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(AnnotationFilter,AnnotationFilterList)
importFrom(AnnotationFilter,GeneIdFilter)
importFrom(AnnotationFilter,SymbolFilter)
importFrom(AnnotationFilter,TxIdFilter)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpnworkers)
importFrom(ComplexHeatmap,pheatmap)
importFrom(EnrichedHeatmap,makeWindows)
importFrom(GenomeInfoDb,"seqinfo<-")
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomicAlignments,isProperPair)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicFiles,REDUCEsampler)
importFrom(GenomicFiles,reduceByYield)
importFrom(GenomicRanges,"score<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,disjoin)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,score)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,shift)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,trim)
importFrom(GenomicRanges,width)
importFrom(Gviz,AlignmentsTrack)
importFrom(Gviz,AnnotationTrack)
importFrom(Gviz,DataTrack)
importFrom(Gviz,GeneRegionTrack)
importFrom(Gviz,GenomeAxisTrack)
importFrom(Gviz,OverlayTrack)
importFrom(Gviz,plotTracks)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,IntegerList)
importFrom(IRanges,RleList)
importFrom(IRanges,Views)
importFrom(IRanges,median)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,quantile)
importFrom(IRanges,relist)
importFrom(IRanges,slice)
importFrom(IRanges,viewMaxs)
importFrom(IRanges,viewMeans)
importFrom(IRanges,viewMins)
importFrom(IRanges,viewRangeMaxs)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,TabixFile)
importFrom(Rsamtools,countBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,seqnamesTabix)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,mean.Rle)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,runmean)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(UpSetR,fromList)
importFrom(UpSetR,upset)
importFrom(circlize,colorRamp2)
importFrom(cowplot,get_legend)
importFrom(cowplot,plot_grid)
importFrom(data.table,fread)
importFrom(dplyr,bind_rows)
importFrom(ensembldb,exons)
importFrom(ensembldb,genes)
importFrom(ensembldb,getGeneRegionTrackForGviz)
importFrom(ensembldb,transcripts)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,xlab)
importFrom(grid,gpar)
importFrom(matrixStats,colMedians)
importFrom(matrixStats,colSds)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowMins)
importFrom(matrixStats,rowVars)
importFrom(pbapply,pblapply)
importFrom(rtracklayer,BigWigFile)
importFrom(rtracklayer,BigWigSelection)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.bed)
importFrom(rtracklayer,import.bed15)
importFrom(rtracklayer,import.bw)
importFrom(rtracklayer,import.gff)
importFrom(rtracklayer,path)
importFrom(stats,approx)
importFrom(stats,as.dendrogram)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,ecdf)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,loess)
importFrom(stats,optim)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,ppois)
importFrom(stats,predict)
importFrom(stats,relevel)
importFrom(stats,setNames)
importFrom(viridisLite,inferno)
importFrom(viridisLite,plasma)
importFrom(viridisLite,viridis)