# Generated by roxygen2: do not edit by hand

export(Pagoda2)
export(armaCor)
export(basicP2proc)
export(basicP2web)
export(buildWijMatrix)
export(calcMulticlassified)
export(cellsPerSelectionGroup)
export(collapse.aspect.clusters)
export(compareClusterings)
export(extendedP2proc)
export(factorFromP2Selection)
export(factorListToMetadata)
export(factorToP2selection)
export(gene.vs.molecule.cell.filter)
export(generateClassificationAnnotation)
export(get.control.geneset)
export(get.de.geneset)
export(getCellsInSelections)
export(getClusterLabelsFromSelection)
export(getColorsFromP2Selection)
export(getIntExtNamesP2Selection)
export(hierDiffToGenesets)
export(make.p2.app)
export(minMaxScale)
export(namedNames)
export(p2.generate.dr.go)
export(p2.generate.go)
export(p2.generate.human.go)
export(p2.generate.mouse.go)
export(p2.make.pagoda1.app)
export(p2.metadata.from.factor)
export(p2.toweb.hdea)
export(p2ViewPagodaApp)
export(pagoda.reduce.loading.redundancy)
export(pagoda.reduce.redundancy)
export(pathway.pc.correlation.distance)
export(plotMulticlassified)
export(plotOneWithValues)
export(plotSelectionOverlaps)
export(projectKNNs)
export(read.10x.matrices)
export(read10xMatrix)
export(readPagoda2SelectionAsFactor)
export(readPagoda2SelectionFile)
export(removeSelectionOverlaps)
export(score.cells.nb0)
export(score.cells.puram)
export(sgdBatches)
export(show.app)
export(subsetSignatureToData)
export(tp2c.view.pathways)
export(validateSelectionsObject)
export(webP2proc)
export(winsorize.matrix)
export(writeGenesAsPagoda2Selection)
export(writePagoda2SelectionFile)
exportClasses(pagoda2WebApp)
import(MASS)
import(Matrix)
import(R.utils)
import(R6)
import(RMTstat)
import(Rook)
import(drat)
import(igraph)
import(rjson)
import(sccore)
importFrom(N2R,Knn)
importFrom(Rcpp,evalCpp)
importFrom(Rcpp,sourceCpp)
importFrom(Rtsne,Rtsne)
importFrom(dendsort,dendsort)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,colors)
importFrom(grDevices,dev.size)
importFrom(grDevices,rainbow)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,hist)
importFrom(graphics,layout)
importFrom(graphics,lcm)
importFrom(graphics,legend)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(irlba,irlba)
importFrom(magrittr,"%>%")
importFrom(methods,as)
importFrom(methods,new)
importFrom(mgcv,gam)
importFrom(parallel,mclapply)
importFrom(rjson,fromJSON)
importFrom(rjson,toJSON)
importFrom(rlang,.data)
importFrom(stats,aggregate)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,dendrapply)
importFrom(stats,dist)
importFrom(stats,is.leaf)
importFrom(stats,na.omit)
importFrom(stats,order.dendrogram)
importFrom(stats,phyper)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,qnorm)
importFrom(stats,qt)
importFrom(stats,quantile)
importFrom(stats,reorder)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(urltools,url_decode)
importFrom(utils,browseURL)
importFrom(utils,read.delim)
useDynLib(pagoda2)
