NAMESPACE

# Generated by roxygen2: do not edit by hand

export(IDRfilter)
export(addAncestors)
export(addGeneIDs)
export(addMetadata)
export(annoPeaks)
export(annotatePeakInBatch)
export(assignChromosomeRegion)
export(binOverFeature)
export(binOverGene)
export(binOverRegions)
export(condenseMatrixByColnames)
export(convert2EntrezID)
export(countPatternInSeqs)
export(cumulativePercentage)
export(downstreams)
export(egOrgMap)
export(enrichmentPlot)
export(estFragmentLength)
export(estLibSize)
export(featureAlignedDistribution)
export(featureAlignedExtendSignal)
export(featureAlignedHeatmap)
export(featureAlignedSignal)
export(findEnhancers)
export(findMotifsInPromoterSeqs)
export(findOverlappingPeaks)
export(findOverlapsOfPeaks)
export(genomicElementDistribution)
export(genomicElementUpSetR)
export(getAllPeakSequence)
export(getAnnotation)
export(getEnrichedGO)
export(getEnrichedPATH)
export(getGO)
export(getUniqueGOidCount)
export(getVennCounts)
export(hyperGtest)
export(makeVennDiagram)
export(mergePlusMinusPeaks)
export(metagenePlot)
export(oligoFrequency)
export(oligoSummary)
export(peakPermTest)
export(peaksNearBDP)
export(pie1)
export(plotBinOverRegions)
export(preparePool)
export(reCenterPeaks)
export(summarizeOverlapsByBins)
export(summarizePatternInPeaks)
export(tileCount)
export(tileGRanges)
export(toGRanges)
export(translatePattern)
export(write2FASTA)
export(xget)
exportClasses(annoGR)
exportClasses(bindist)
exportClasses(permPool)
exportMethods("$")
exportMethods("$<-")
exportMethods(annoGR)
exportMethods(coerce)
exportMethods(info)
exportMethods(toGRanges)
import(GenomicRanges)
import(IRanges)
import(methods)
importClassesFrom(graph,graphNEL)
importFrom(AnnotationDbi,Definition)
importFrom(AnnotationDbi,Ontology)
importFrom(AnnotationDbi,Term)
importFrom(AnnotationDbi,mappedkeys)
importFrom(AnnotationDbi,mget)
importFrom(AnnotationDbi,select)
importFrom(BiocGenerics,`%in%`)
importFrom(BiocGenerics,dbconn)
importFrom(BiocGenerics,do.call)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,pos)
importFrom(BiocGenerics,score)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,width)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,PDict)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,oligonucleotideFrequency)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,vcountPDict)
importFrom(Biostrings,writeXStringSet)
importFrom(DBI,dbGetQuery)
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,`seqlengths<-`)
importFrom(GenomeInfoDb,`seqlevels<-`)
importFrom(GenomeInfoDb,`seqlevelsStyle<-`)
importFrom(GenomeInfoDb,`seqlevelsStyle`)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicAlignments,Union)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,summarizeOverlaps)
importFrom(GenomicFeatures,cds)
importFrom(GenomicFeatures,cdsBy)
importFrom(GenomicFeatures,exonicParts)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,fiveUTRsByTranscript)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,intronsByTranscript)
importFrom(GenomicFeatures,microRNAs)
importFrom(GenomicFeatures,promoters)
importFrom(GenomicFeatures,tRNAs)
importFrom(GenomicFeatures,threeUTRsByTranscript)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicFeatures,transcriptsBy)
importFrom(InteractionSet,GInteractions)
importFrom(KEGGREST,keggGet)
importFrom(KEGGREST,keggLink)
importFrom(RBGL,connectedComp)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,countBam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,scanBamWhat)
importFrom(Rsamtools,testPairedEndBam)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,aggregate)
importFrom(S4Vectors,elementMetadata)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runLength)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,subjectHits)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(VennDiagram,venn.diagram)
importFrom(biomaRt,getBM)
importFrom(biomaRt,getSequence)
importFrom(data.table,data.table)
importFrom(dplyr,"%>%")
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,pull)
importFrom(dplyr,top_n)
importFrom(ensembldb,EnsDb)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_bin2d)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(grDevices,as.graphicsAnnot)
importFrom(grDevices,boxplot.stats)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.flush)
importFrom(grDevices,dev.hold)
importFrom(grDevices,rgb)
importFrom(graph,ugraph)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,matlines)
importFrom(graphics,matplot)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,plot.new)
importFrom(graphics,plot.window)
importFrom(graphics,polygon)
importFrom(graphics,segments)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(grid,gEdit)
importFrom(grid,gList)
importFrom(grid,gTree)
importFrom(grid,gpar)
importFrom(grid,grid.draw)
importFrom(grid,grid.newpage)
importFrom(grid,grid.pretty)
importFrom(grid,legendGrob)
importFrom(grid,rasterGrob)
importFrom(grid,textGrob)
importFrom(grid,viewport)
importFrom(grid,xaxisGrob)
importFrom(grid,yaxisGrob)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowMins)
importFrom(multtest,mt.rawp2adjp)
importFrom(pwalign,aligned)
importFrom(pwalign,pairwiseAlignment)
importFrom(regioneR,numOverlaps)
importFrom(regioneR,permTest)
importFrom(rtracklayer,import)
importFrom(scales,label_wrap)
importFrom(stats,as.dendrogram)
importFrom(stats,as.formula)
importFrom(stats,binom.test)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,loess.smooth)
importFrom(stats,nobs)
importFrom(stats,phyper)
importFrom(stats,reorder)
importFrom(stats,rexp)
importFrom(stats,setNames)
importFrom(stats,ts)
importFrom(stringr,str_split)
importFrom(tibble,tibble)
importFrom(tidyr,separate_rows)
importFrom(universalmotif,shuffle_sequences)
importFrom(utils,adist)
importFrom(utils,combn)
importFrom(utils,data)
importFrom(utils,installed.packages)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,write.table)
importMethodsFrom(S4Vectors,first)
importMethodsFrom(S4Vectors,second)