# Generated by roxygen2: do not edit by hand

S3method("[",Motif)
S3method(AddMotifObject,Assay)
S3method(AddMotifObject,Seurat)
S3method(BinarizeCounts,Assay)
S3method(BinarizeCounts,Seurat)
S3method(BinarizeCounts,default)
S3method(FindTopFeatures,Assay)
S3method(FindTopFeatures,Seurat)
S3method(FindTopFeatures,default)
S3method(GetMotifData,Assay)
S3method(GetMotifData,Motif)
S3method(GetMotifData,Seurat)
S3method(GetMotifObject,Assay)
S3method(GetMotifObject,Seurat)
S3method(RegionStats,Assay)
S3method(RegionStats,Seurat)
S3method(RegionStats,default)
S3method(RunSVD,Assay)
S3method(RunSVD,Seurat)
S3method(RunSVD,default)
S3method(RunTFIDF,Assay)
S3method(RunTFIDF,Seurat)
S3method(RunTFIDF,default)
S3method(SetMotifData,Assay)
S3method(SetMotifData,Motif)
S3method(SetMotifData,Seurat)
S3method(dim,Motif)
S3method(dimnames,Motif)
S3method(subset,Motif)
export(AddMotifObject)
export(AverageCounts)
export(BinarizeCounts)
export(CellsPerGroup)
export(ClosestFeature)
export(CountsInRegion)
export(CoveragePlot)
export(CreateMotifMatrix)
export(CreateMotifObject)
export(CutMatrix)
export(DepthCor)
export(DownsampleFeatures)
export(Extend)
export(ExtractCell)
export(FRiP)
export(FeatureMatrix)
export(FilterFragments)
export(FindMotifs)
export(FindTopFeatures)
export(FractionCountsInRegion)
export(FragmentHistogram)
export(GRangesToString)
export(GenomeBinMatrix)
export(GetCellsInRegion)
export(GetFragments)
export(GetIntersectingFeatures)
export(GetMotifData)
export(GetMotifObject)
export(GetReadsInRegion)
export(IntersectMatrix)
export(Jaccard)
export(MatchRegionStats)
export(MergeWithRegions)
export(MotifPlot)
export(NucleosomeSignal)
export(RegionStats)
export(RunChromVAR)
export(RunSVD)
export(RunTFIDF)
export(SetFragments)
export(SetMotifData)
export(StringToGRanges)
export(SubsetMatrix)
export(TSSEnrichment)
export(TSSPlot)
export(UnifyPeaks)
exportClasses(Motif)
import(patchwork)
importClassesFrom(Matrix,dgCMatrix)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,width)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,disjoin)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,trim)
importFrom(IRanges,"ranges<-")
importFrom(IRanges,IRanges)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,ranges)
importFrom(IRanges,subsetByOverlaps)
importFrom(Matrix,Diagonal)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,tcrossprod)
importFrom(Rsamtools,TabixFile)
importFrom(Rsamtools,bgzip)
importFrom(Rsamtools,indexTabix)
importFrom(Rsamtools,scanTabix)
importFrom(Rsamtools,seqnamesTabix)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(Seurat,"VariableFeatures<-")
importFrom(Seurat,AddMetaData)
importFrom(Seurat,CreateAssayObject)
importFrom(Seurat,CreateDimReducObject)
importFrom(Seurat,DefaultAssay)
importFrom(Seurat,Embeddings)
importFrom(Seurat,GetAssay)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,Idents)
importFrom(Seurat,Misc)
importFrom(Seurat,SetAssayData)
importFrom(Seurat,VariableFeatures)
importFrom(Seurat,WhichCells)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,rbindlist)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(future,nbrOfWorkers)
importFrom(future.apply,future_lapply)
importFrom(gggenes,geom_gene_arrow)
importFrom(gggenes,geom_gene_label)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_color_identity)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_light)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggseqlogo,ggseqlogo)
importFrom(grid,unit)
importFrom(irlba,irlba)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,setMethod)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(patchwork,wrap_plots)
importFrom(pbapply,pblapply)
importFrom(stats,approx)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,ecdf)
importFrom(stats,median)
importFrom(stats,phyper)
importFrom(stats,sd)
importFrom(tidyr,separate)
importFrom(utils,globalVariables)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(zoo,rollapply)
importMethodsFrom(GenomicRanges,distanceToNearest)
importMethodsFrom(GenomicRanges,end)
importMethodsFrom(GenomicRanges,intersect)
importMethodsFrom(GenomicRanges,seqnames)
importMethodsFrom(GenomicRanges,start)
importMethodsFrom(GenomicRanges,strand)
importMethodsFrom(GenomicRanges,width)
importMethodsFrom(Matrix,t)
