# Generated by roxygen2: do not edit by hand

export(SDC)
export(SRD)
export(alignCoor)
export(autoK)
export(availableGeometries)
export(boundaryScore)
export(boundaryScoreTAD)
export(cellClusters)
export(cellDistance)
export(compartment)
export(create3dGenomicSignals)
export(createTADGeometries)
export(extractBackbonePositions)
export(fill_NA)
export(gaussianBlur)
export(hierarchicalClusteringTAD)
export(loopBouquetPlot)
export(mdsPlot)
export(pointCluster)
export(renderthreeJsViewer)
export(rglViewer)
export(smooth3dPoints)
export(spatialDistanceHeatmap)
export(spatialDistanceMatrix)
export(threeJsGeometry)
export(threeJsViewer)
export(threejsOutput)
export(view3dCells)
export(view3dStructure)
exportClasses(threeJsGeometry)
exportMethods("$")
exportMethods("$<-")
import(methods)
importClassesFrom(InteractionSet,GInteractions)
importFrom(BiocGenerics,"end<-")
importFrom(BiocGenerics,"start<-")
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,"width<-")
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,t)
importFrom(BiocGenerics,width)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,letterFrequency)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,slidingWindows)
importFrom(IRanges,IRanges)
importFrom(IRanges,Views)
importFrom(IRanges,countOverlaps)
importFrom(IRanges,coverage)
importFrom(IRanges,distance)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,gaps)
importFrom(IRanges,ranges)
importFrom(IRanges,reduce)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,tile)
importFrom(IRanges,viewMeans)
importFrom(InteractionSet,GInteractions)
importFrom(MASS,isoMDS)
importFrom(Matrix,sparseMatrix)
importFrom(RANN,nn2)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,Pairs)
importFrom(S4Vectors,first)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,second)
importFrom(S4Vectors,subjectHits)
importFrom(Seqinfo,seqnames)
importFrom(aricode,AMI)
importFrom(aricode,ARI)
importFrom(aricode,NID)
importFrom(aricode,NMI)
importFrom(clue,solve_LSAP)
importFrom(cluster,silhouette)
importFrom(dbscan,dbscan)
importFrom(future.apply,future_mapply)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,colors)
importFrom(grDevices,hcl.colors)
importFrom(grDevices,rainbow)
importFrom(grDevices,rgb)
importFrom(graphics,arrows)
importFrom(graphics,axis)
importFrom(graphics,curve)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,segments)
importFrom(graphics,strheight)
importFrom(graphics,text)
importFrom(grid,arrow)
importFrom(grid,convertHeight)
importFrom(grid,convertUnit)
importFrom(grid,convertWidth)
importFrom(grid,convertX)
importFrom(grid,convertY)
importFrom(grid,gpar)
importFrom(grid,grid.circle)
importFrom(grid,grid.draw)
importFrom(grid,grid.lines)
importFrom(grid,grid.newpage)
importFrom(grid,grid.points)
importFrom(grid,grid.segments)
importFrom(grid,grid.text)
importFrom(grid,grobCoords)
importFrom(grid,grobHeight)
importFrom(grid,grobWidth)
importFrom(grid,grobX)
importFrom(grid,grobY)
importFrom(grid,is.unit)
importFrom(grid,linesGrob)
importFrom(grid,popViewport)
importFrom(grid,pushViewport)
importFrom(grid,stringWidth)
importFrom(grid,textGrob)
importFrom(grid,unit)
importFrom(grid,viewport)
importFrom(grid,xsplineGrob)
importFrom(htmlwidgets,createWidget)
importFrom(htmlwidgets,shinyRenderWidget)
importFrom(htmlwidgets,shinyWidgetOutput)
importFrom(igraph,V)
importFrom(igraph,components)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,layout_with_fr)
importFrom(igraph,norm_coords)
importFrom(methods,getPackageName)
importFrom(plotrix,arctext)
importFrom(progressr,progressor)
importFrom(progressr,with_progress)
importFrom(rgl,addNormals)
importFrom(rgl,arrow3d)
importFrom(rgl,bg3d)
importFrom(rgl,cube3d)
importFrom(rgl,cylinder3d)
importFrom(rgl,dodecahedron3d)
importFrom(rgl,icosahedron3d)
importFrom(rgl,lines3d)
importFrom(rgl,octahedron3d)
importFrom(rgl,open3d)
importFrom(rgl,points3d)
importFrom(rgl,polygon3d)
importFrom(rgl,rgl.bringtotop)
importFrom(rgl,rotate3d)
importFrom(rgl,scale3d)
importFrom(rgl,segments3d)
importFrom(rgl,shade3d)
importFrom(rgl,spheres3d)
importFrom(rgl,subdivision3d)
importFrom(rgl,tetrahedron3d)
importFrom(rgl,texts3d)
importFrom(rgl,translate3d)
importFrom(rjson,fromJSON)
importFrom(scales,rescale)
importFrom(stats,as.dist)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,plogis)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,splinefun)
importFrom(stats,var)
importFrom(trackViewer,parseWIG)
importFrom(utils,combn)
importFrom(utils,getFromNamespace)
importFrom(utils,head)
importFrom(utils,tail)
importMethodsFrom(InteractionSet,anchorIds)
importMethodsFrom(InteractionSet,regions)
