NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(addBmatToSnap,default)
S3method(addGmatToSnap,default)
S3method(addPmatToSnap,default)
S3method(barcodeInSnapFile,default)
S3method(boxPlotFeature,default)
S3method(calBmatCor,default)
S3method(createGmatFromMat,default)
S3method(createSnap,default)
S3method(createSnapFromBmat,default)
S3method(createSnapFromGmat,default)
S3method(createSnapFromPmat,default)
S3method(exportMetaData,default)
S3method(filterBins,default)
S3method(filterCells,default)
S3method(findDAR,default)
S3method(isSnapFile,default)
S3method(makeBinary,default)
S3method(plotBarcode,default)
S3method(plotBinCoverage,default)
S3method(plotDimReductElbow,default)
S3method(plotDimReductPW,default)
S3method(plotFeatureSingle,default)
S3method(plotGene,default)
S3method(plotViz,default)
S3method(readMetaData,default)
S3method(rmBmatFromSnap,default)
S3method(rmGmatFromSnap,default)
S3method(rmPmatFromSnap,default)
S3method(runCluster,default)
S3method(runDimReduct,default)
S3method(runHarmony,default)
S3method(runHomer,default)
S3method(runJaccard,default)
S3method(runKNN,default)
S3method(runNormJaccard,default)
S3method(runSnapAddPmat,default)
S3method(runViz,default)
S3method(scaleCountMatrix,default)
S3method(showBinSizes,default)
export(addBmatToSnap)
export(addGmatToSnap)
export(addPmatToSnap)
export(barcodeInSnapFile)
export(boxPlotFeature)
export(calBmatCor)
export(createGmatFromMat)
export(createPmat)
export(createSnap)
export(createSnapFromBmat)
export(createSnapFromGmat)
export(createSnapFromPmat)
export(exportMetaData)
export(extractReads)
export(filterBins)
export(filterCells)
export(findDAR)
export(isSnapFile)
export(makeBinary)
export(newSnap)
export(plotBarcode)
export(plotBinCoverage)
export(plotDimReductElbow)
export(plotDimReductPW)
export(plotFeatureSingle)
export(plotGene)
export(plotViz)
export(predictGenePeakPair)
export(readMetaData)
export(rmBmatFromSnap)
export(rmGmatFromSnap)
export(rmPmatFromSnap)
export(runChromVAR)
export(runCluster)
export(runDiffusionMaps)
export(runDiffusionMapsExtension)
export(runDimReduct)
export(runHarmony)
export(runHomer)
export(runJaccard)
export(runKNN)
export(runLDA)
export(runLSA)
export(runMACS)
export(runMACSForAll)
export(runMagic)
export(runNormJaccard)
export(runSnapAddPmat)
export(runViz)
export(scaleCountMatrix)
export(showBinSizes)
export(snapRbind)
export(snapToSeurat)
exportClasses(snap)
exportMethods("[")
exportMethods(colMeans)
exportMethods(colSums)
exportMethods(is.snap)
exportMethods(nrow)
exportMethods(rowMeans)
exportMethods(rowSums)
exportMethods(summarySnap)
import(Matrix)
import(doSNOW)
import(parallel)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,reduce)
importFrom(IRanges,IRanges)
importFrom(Matrix,sparseMatrix)
importFrom(RANN,nn2)
importFrom(RColorBrewer,brewer.pal)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(Rtsne,Rtsne)
importFrom(bigmemory,as.big.matrix)
importFrom(bigmemory,attach.big.matrix)
importFrom(doParallel,registerDoParallel)
importFrom(doSNOW,registerDoSNOW)
importFrom(edgeR,DGEList)
importFrom(edgeR,exactTest)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,glmQLFit)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,xy.coords)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,strheight)
importFrom(graphics,stripchart)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(igraph,E)
importFrom(igraph,arpack)
importFrom(igraph,cluster_louvain)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_edgelist)
importFrom(igraph,similarity)
importFrom(irlba,irlba)
importFrom(irlba,prcomp_irlba)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,setMethod)
importFrom(methods,slot)
importFrom(parallel,clusterEvalQ)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(parallel,stopCluster)
importFrom(plot3D,scatter2D)
importFrom(plyr,count)
importFrom(plyr,laply)
importFrom(plyr,llply)
importFrom(rhdf5,h5ls)
importFrom(rhdf5,h5read)
importFrom(scales,alpha)
importFrom(stats,approxfun)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,glm)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(utils,file_test)
importFrom(utils,installed.packages)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,write.table)
importFrom(viridis,viridis)