NAMESPACE

# Generated by roxygen2: do not edit by hand

export(NMFDoubletsDefineModules)
export(NMFDoubletsDetermineCells)
export(NMFDoubletsPlotModuleCombos)
export(NMFDoubletsPlotModuleThresholds)
export(NMFDoubletsPlotModulesInCell)
export(aucprTestAlongTree)
export(aucprTestByFactor)
export(aucprThreshold)
export(batchComBat)
export(binomTestAlongTree)
export(branchpointDetailsPreferenceDist)
export(branchpointDetailsVisitDist)
export(branchpointDetailsVisitTsne)
export(branchpointPreferenceLayout)
export(buildTree)
export(calcDM)
export(calcKNN)
export(calcPCA)
export(calcTsne)
export(cellDistByExpression)
export(cellsAlongLineage)
export(cellsInCluster)
export(clusterCentroids)
export(clusterDE)
export(clusterTipPotential)
export(combineTipVisitation)
export(corner)
export(createURD)
export(cropSmoothFit)
export(cutstring)
export(data.for.plot)
export(deTTest)
export(defaultURDContinuousColors)
export(differentialAUCPR)
export(dsCombineDGE)
export(dsCutoffPlot)
export(dsMetaTrim)
export(dsReadDGE)
export(dsReadStats)
export(edgesFromDM)
export(findVariableGenes)
export(floodBuildTM)
export(floodPseudotime)
export(floodPseudotimeProcess)
export(geneCascadeHeatmap)
export(geneCascadeImpulsePlots)
export(geneCascadeProcess)
export(geneSmoothFit)
export(geneSmoothReduce)
export(getBinaryData)
export(getUPXData)
export(getZData)
export(graphClustering)
export(gridArrangeMulti)
export(groupFromCells)
export(importDM)
export(impulseFit)
export(is.wholenumber)
export(knnOutliers)
export(loadTipCells)
export(logistic)
export(markersAUCPR)
export(markersBinom)
export(matrixReduce)
export(mean.of.logs)
export(mean.of.logs.pos)
export(mean.pos)
export(moduleTestAlongTree)
export(nameSegments)
export(num.mean)
export(pcSDPlot)
export(pcTopGenes)
export(pcaMarchenkoPastur)
export(plotBranchpoint)
export(plotDim)
export(plotDim3D)
export(plotDim3DStoreView)
export(plotDimArray)
export(plotDimDiscretized)
export(plotDimDual)
export(plotDimHighlight)
export(plotDists)
export(plotDot)
export(plotScatter)
export(plotSmoothFit)
export(plotSmoothFitMultiCascade)
export(plotTree)
export(plotTreeDiscretized)
export(plotTreeDual)
export(plotTreeForce)
export(plotTreeForce2D)
export(plotTreeForceDual)
export(plotTreeForceStore3DView)
export(plotViolin)
export(pmax.abs)
export(preference)
export(processRandomWalks)
export(processRandomWalksFromTips)
export(prop.exp)
export(prop.nonexp)
export(pseudotimeDetermineLogistic)
export(pseudotimeMovingWindow)
export(pseudotimePlotStabilityCells)
export(pseudotimePlotStabilityOverall)
export(pseudotimePlotVisits)
export(pseudotimeWeightTransitionMatrix)
export(putativeCellsInSegment)
export(segChildren)
export(segChildrenAll)
export(segParent)
export(segParentAll)
export(segSiblings)
export(segTerminal)
export(seuratToURD)
export(simulateRandomWalk)
export(simulateRandomWalksFromTips)
export(sum.of.logs)
export(tipPotential)
export(translateSegmentNames)
export(treeForceDirectedLayout)
export(treeForcePositionLabels)
export(treeForceRotateCoords)
export(treeForceStretchCoords)
export(treeForceTranslateCoords)
export(treeLayoutCells)
export(treeLayoutDendrogram)
export(treeLayoutElaborate)
export(txCutoffPlot)
export(txReadDGE)
export(txReadsPerCell)
export(urdSubset)
export(whichCells)
exportClasses(URD)
import(Matrix)
import(ggplot2)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(destiny,DiffusionMap)
importFrom(KernSmooth,bkde2D)
importFrom(MASS,fitdistr)
importFrom(Matrix,readMM)
importFrom(Matrix,rowSums)
importFrom(RANN,nn2)
importFrom(RColorBrewer,brewer.pal)
importFrom(ROCR,performance)
importFrom(ROCR,prediction)
importFrom(Rtsne,Rtsne)
importFrom(caTools,trapz)
importFrom(data.table,rbindlist)
importFrom(destiny,DiffusionMap)
importFrom(destiny,find_dm_k)
importFrom(destiny,find_sigmas)
importFrom(diptest,dip.test)
importFrom(gdata,interleave)
importFrom(ggraph,create_layout)
importFrom(gmodels,fast.prcomp)
importFrom(gplots,heatmap.2)
importFrom(gridExtra,grid.arrange)
importFrom(igraph,V)
importFrom(igraph,adjacent_vertices)
importFrom(igraph,as_data_frame)
importFrom(igraph,cluster_infomap)
importFrom(igraph,cluster_louvain)
importFrom(igraph,decompose)
importFrom(igraph,distances)
importFrom(igraph,graph.data.frame)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,graph_from_edgelist)
importFrom(igraph,induced_subgraph)
importFrom(igraph,is_connected)
importFrom(igraph,layout_with_drl)
importFrom(igraph,layout_with_fr)
importFrom(igraph,layout_with_kk)
importFrom(igraph,vcount)
importFrom(methods,new)
importFrom(minpack.lm,nls.lm.control)
importFrom(minpack.lm,nlsLM)
importFrom(plyr,mapvalues)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(scales,cscale)
importFrom(scales,gradient_n_pal)
importFrom(scales,hue_pal)
importFrom(scales,rescale)
importFrom(scales,squish)
importFrom(stats,aggregate)
importFrom(stats,dist)
importFrom(stats,embed)
importFrom(stats,ks.test)
importFrom(stats,lowess)
importFrom(stats,p.adjust)
importFrom(stats,pbinom)
importFrom(stats,quantile)
importFrom(stats,runif)
importFrom(stats,smooth.spline)
importFrom(stats,weighted.mean)
importFrom(utils,combn)