# Generated by roxygen2: do not edit by hand

S3method("Annotation<-",ChromatinAssay)
S3method("Annotation<-",Seurat)
S3method("Cells<-",Fragment)
S3method("Fragments<-",ChromatinAssay)
S3method("Fragments<-",Seurat)
S3method("LayerData<-",ChromatinAssay)
S3method("Links<-",ChromatinAssay)
S3method("Links<-",Seurat)
S3method("Motifs<-",ChromatinAssay)
S3method("Motifs<-",Seurat)
S3method("[",Motif)
S3method(AddMotifs,Assay)
S3method(AddMotifs,ChromatinAssay)
S3method(AddMotifs,Seurat)
S3method(AddMotifs,StdAssay)
S3method(AddMotifs,default)
S3method(AggregateTiles,ChromatinAssay)
S3method(AggregateTiles,Seurat)
S3method(AggregateTiles,default)
S3method(AlleleFreq,Assay)
S3method(AlleleFreq,Seurat)
S3method(AlleleFreq,StdAssay)
S3method(AlleleFreq,default)
S3method(Annotation,ChromatinAssay)
S3method(Annotation,Seurat)
S3method(BinarizeCounts,Assay)
S3method(BinarizeCounts,Seurat)
S3method(BinarizeCounts,default)
S3method(CallPeaks,ChromatinAssay)
S3method(CallPeaks,Fragment)
S3method(CallPeaks,Seurat)
S3method(CallPeaks,default)
S3method(Cells,Fragment)
S3method(ConvertMotifID,Assay)
S3method(ConvertMotifID,ChromatinAssay)
S3method(ConvertMotifID,Motif)
S3method(ConvertMotifID,Seurat)
S3method(ConvertMotifID,StdAssay)
S3method(ConvertMotifID,default)
S3method(FindTopFeatures,Assay)
S3method(FindTopFeatures,Seurat)
S3method(FindTopFeatures,StdAssay)
S3method(FindTopFeatures,default)
S3method(Footprint,ChromatinAssay)
S3method(Footprint,Seurat)
S3method(Fragments,ChromatinAssay)
S3method(Fragments,Seurat)
S3method(GetAssayData,ChromatinAssay)
S3method(GetMotifData,ChromatinAssay)
S3method(GetMotifData,Motif)
S3method(GetMotifData,Seurat)
S3method(IdentifyVariants,Assay)
S3method(IdentifyVariants,Seurat)
S3method(IdentifyVariants,StdAssay)
S3method(IdentifyVariants,default)
S3method(InsertionBias,ChromatinAssay)
S3method(InsertionBias,Seurat)
S3method(LayerData,ChromatinAssay)
S3method(Links,ChromatinAssay)
S3method(Links,Seurat)
S3method(Motifs,ChromatinAssay)
S3method(Motifs,Seurat)
S3method(RegionMatrix,ChromatinAssay)
S3method(RegionMatrix,Seurat)
S3method(RegionMatrix,default)
S3method(RegionStats,ChromatinAssay)
S3method(RegionStats,Seurat)
S3method(RegionStats,default)
S3method(RenameCells,ChromatinAssay)
S3method(RenameCells,Fragment)
S3method(RunChromVAR,ChromatinAssay)
S3method(RunChromVAR,Seurat)
S3method(RunSVD,Assay)
S3method(RunSVD,Seurat)
S3method(RunSVD,StdAssay)
S3method(RunSVD,default)
S3method(RunTFIDF,Assay)
S3method(RunTFIDF,Seurat)
S3method(RunTFIDF,StdAssay)
S3method(RunTFIDF,default)
S3method(SetAssayData,ChromatinAssay)
S3method(SetMotifData,ChromatinAssay)
S3method(SetMotifData,Motif)
S3method(SetMotifData,Seurat)
S3method(as.ChromatinAssay,Assay)
S3method(dim,Motif)
S3method(dimnames,Motif)
S3method(head,Fragment)
S3method(merge,ChromatinAssay)
S3method(subset,ChromatinAssay)
S3method(subset,Fragment)
S3method(subset,Motif)
export("Annotation<-")
export("Cells<-")
export("Fragments<-")
export("Links<-")
export("Motifs<-")
export(AccessiblePeaks)
export(AddChromatinModule)
export(AddMotifs)
export(AggregateTiles)
export(AlleleFreq)
export(Annotation)
export(AnnotationPlot)
export(AverageCounts)
export(BigwigTrack)
export(BinarizeCounts)
export(CallPeaks)
export(Cells)
export(CellsPerGroup)
export(ClosestFeature)
export(ClusterClonotypes)
export(CombineTracks)
export(ConnectionsToLinks)
export(ConvertMotifID)
export(CountFragments)
export(CountsInRegion)
export(CoverageBrowser)
export(CoveragePlot)
export(CreateChromatinAssay)
export(CreateFragmentObject)
export(CreateMotifMatrix)
export(CreateMotifObject)
export(DensityScatter)
export(DepthCor)
export(DownsampleFeatures)
export(ExpressionPlot)
export(Extend)
export(FRiP)
export(FeatureMatrix)
export(FilterCells)
export(FindClonotypes)
export(FindMotifs)
export(FindTopFeatures)
export(Footprint)
export(FractionCountsInRegion)
export(FragmentHistogram)
export(Fragments)
export(GRangesToString)
export(GeneActivity)
export(GenomeBinMatrix)
export(GetCellsInRegion)
export(GetFootprintData)
export(GetFragmentData)
export(GetGRangesFromEnsDb)
export(GetIntersectingFeatures)
export(GetLinkedGenes)
export(GetLinkedPeaks)
export(GetMotifData)
export(GetTSSPositions)
export(IdentifyVariants)
export(InsertionBias)
export(IntersectMatrix)
export(Jaccard)
export(LinkPeaks)
export(LinkPlot)
export(Links)
export(LookupGeneCoords)
export(MatchRegionStats)
export(MotifCounts)
export(MotifPlot)
export(Motifs)
export(NucleosomeSignal)
export(PeakPlot)
export(PlotFootprint)
export(ReadMGATK)
export(RegionHeatmap)
export(RegionMatrix)
export(RegionPlot)
export(RegionStats)
export(RunChromVAR)
export(RunSVD)
export(RunTFIDF)
export(SetMotifData)
export(SortIdents)
export(SplitFragments)
export(StringToGRanges)
export(SubsetMatrix)
export(TSSEnrichment)
export(TSSPlot)
export(TilePlot)
export(UnifyPeaks)
export(UpdatePath)
export(ValidateCells)
export(ValidateFragments)
export(ValidateHash)
export(VariantPlot)
export(as.ChromatinAssay)
export(corSparse)
export(theme_browser)
exportClasses(ChromatinAssay)
exportClasses(Fragment)
exportClasses(Motif)
exportMethods("genome<-")
exportMethods("isCircular<-")
exportMethods("seqinfo<-")
exportMethods("seqlengths<-")
exportMethods("seqlevels<-")
exportMethods("seqnames<-")
exportMethods(coverage)
exportMethods(disjoin)
exportMethods(disjointBins)
exportMethods(distance)
exportMethods(distanceToNearest)
exportMethods(findOverlaps)
exportMethods(follow)
exportMethods(gaps)
exportMethods(genome)
exportMethods(granges)
exportMethods(isCircular)
exportMethods(isDisjoint)
exportMethods(nearest)
exportMethods(precede)
exportMethods(range)
exportMethods(reduce)
exportMethods(seqinfo)
exportMethods(seqlengths)
exportMethods(seqlevels)
exportMethods(seqnames)
import(data.table)
import(patchwork)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(SeuratObject,Assay)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,width)
importFrom(GenomeInfoDb,"genome<-")
importFrom(GenomeInfoDb,"isCircular<-")
importFrom(GenomeInfoDb,"seqinfo<-")
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,"seqnames<-")
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,dropSeqlevels)
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,isCircular)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,disjoin)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,isDisjoint)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,trim)
importFrom(GenomicRanges,union)
importFrom(GenomicRanges,width)
importFrom(IRanges,"ranges<-")
importFrom(IRanges,IRanges)
importFrom(IRanges,countOverlaps)
importFrom(IRanges,coverage)
importFrom(IRanges,disjoin)
importFrom(IRanges,disjointBins)
importFrom(IRanges,distance)
importFrom(IRanges,distanceToNearest)
importFrom(IRanges,end)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,follow)
importFrom(IRanges,gaps)
importFrom(IRanges,isDisjoint)
importFrom(IRanges,narrow)
importFrom(IRanges,nearest)
importFrom(IRanges,precede)
importFrom(IRanges,ranges)
importFrom(IRanges,reduce)
importFrom(IRanges,start)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,width)
importFrom(Matrix,Diagonal)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,crossprod)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,summary)
importFrom(Matrix,tcrossprod)
importFrom(Rcpp,evalCpp)
importFrom(RcppRoll,roll_mean)
importFrom(RcppRoll,roll_sum)
importFrom(Rsamtools,TabixFile)
importFrom(Rsamtools,bgzip)
importFrom(Rsamtools,indexTabix)
importFrom(Rsamtools,scanTabix)
importFrom(Rsamtools,seqnamesTabix)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,split)
importFrom(S4Vectors,subjectHits)
importFrom(SeuratObject,"Idents<-")
importFrom(SeuratObject,"Key<-")
importFrom(SeuratObject,"LayerData<-")
importFrom(SeuratObject,"VariableFeatures<-")
importFrom(SeuratObject,AddMetaData)
importFrom(SeuratObject,Assays)
importFrom(SeuratObject,Cells)
importFrom(SeuratObject,CheckFeaturesNames)
importFrom(SeuratObject,CreateAssayObject)
importFrom(SeuratObject,CreateDimReducObject)
importFrom(SeuratObject,CreateSeuratObject)
importFrom(SeuratObject,DefaultAssay)
importFrom(SeuratObject,Embeddings)
importFrom(SeuratObject,GetAssayData)
importFrom(SeuratObject,Idents)
importFrom(SeuratObject,Key)
importFrom(SeuratObject,LayerData)
importFrom(SeuratObject,Layers)
importFrom(SeuratObject,Project)
importFrom(SeuratObject,RenameCells)
importFrom(SeuratObject,RowMergeSparseMatrices)
importFrom(SeuratObject,SetAssayData)
importFrom(SeuratObject,VariableFeatures)
importFrom(SeuratObject,WhichCells)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,slice_sample)
importFrom(dplyr,summarize)
importFrom(dplyr,top_n)
importFrom(dplyr,ungroup)
importFrom(fastmatch,fmatch)
importFrom(future,nbrOfWorkers)
importFrom(future.apply,future_lapply)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
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_label)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_gradient2)
importFrom(ggplot2,scale_color_grey)
importFrom(ggplot2,scale_color_identity)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_color_viridis_c)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_grey)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_fill_viridis_c)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,scale_y_reverse)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_light)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(grid,arrow)
importFrom(irlba,irlba)
importFrom(lifecycle,deprecated)
importFrom(lifecycle,is_present)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,callGeneric)
importFrom(methods,hasArg)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,setMethod)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(patchwork,guide_area)
importFrom(patchwork,plot_layout)
importFrom(patchwork,wrap_plots)
importFrom(pbapply,pblapply)
importFrom(rlang,.data)
importFrom(scales,comma)
importFrom(scales,hue_pal)
importFrom(stats,approx)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,ecdf)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,phyper)
importFrom(stats,pnorm)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stringi,stri_split_fixed)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,separate)
importFrom(tidyselect,all_of)
importFrom(tools,file_ext)
importFrom(tools,md5sum)
importFrom(utils,globalVariables)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importMethodsFrom(GenomicRanges,distanceToNearest)
importMethodsFrom(GenomicRanges,end)
importMethodsFrom(GenomicRanges,intersect)
importMethodsFrom(GenomicRanges,seqnames)
importMethodsFrom(GenomicRanges,start)
importMethodsFrom(GenomicRanges,strand)
importMethodsFrom(GenomicRanges,width)
importMethodsFrom(Matrix,colMeans)
importMethodsFrom(Matrix,mean)
importMethodsFrom(Matrix,t)
useDynLib(Signac)
