# Generated by roxygen2: do not edit by hand

export(AddImputedScore)
export(AddMetaData)
export(AddSamples)
export(AddSmoothedScore)
export(AssessNodes)
export(AssessSplit)
export(AverageExpression)
export(AveragePCA)
export(BatchGene)
export(BuildClusterTree)
export(BuildRFClassifier)
export(BuildSNN)
export(CalcNoiseModels)
export(CalinskiPlot)
export(CellCorMatrix)
export(CellPlot)
export(ClassifyCells)
export(ClusterAlpha)
export(ColorTSNESplit)
export(DBClustDimension)
export(DBclust_dimension)
export(DiffExpTest)
export(DiffTTest)
export(DimPlot)
export(DoHeatmap)
export(DoKMeans)
export(DotPlot)
export(FeatureHeatmap)
export(FeaturePlot)
export(FetchData)
export(FindAllMarkers)
export(FindAllMarkersNode)
export(FindClusters)
export(FindMarkers)
export(FindMarkersNode)
export(FitGeneK)
export(FitGeneMix)
export(GeneCorMatrix)
export(GenePlot)
export(GenesInCluster)
export(GetCentroids)
export(GetClusters)
export(GetNewScore)
export(HeatmapNode)
export(ICA)
export(ICAPlot)
export(ICHeatmap)
export(ICTopGenes)
export(InitialMapping)
export(JackStraw)
export(JackStrawMC)
export(JackStrawPermutationTest)
export(JackStrawPlot)
export(KClustDimension)
export(KMeansHeatmap)
export(Kclust_dimension)
export(LogNormalize)
export(MakeSparse)
export(MapCell)
export(MarkerTest)
export(MeanVarPlot)
export(MergeNode)
export(MergeSeurat)
export(MultiPlotList)
export(NegBinomDETest)
export(NumberClusters)
export(PCA)
export(PCAFast)
export(PCAPlot)
export(PCASigGenes)
export(PCElbowPlot)
export(PCHeatmap)
export(PCTopCells)
export(PCTopGenes)
export(PlotClusterTree)
export(PlotNoiseModel)
export(PoissonDETest)
export(PosteriorPlot)
export(PrintPCA)
export(ProjectPCA)
export(RefinedMapping)
export(RegressOut)
export(RemovePC)
export(RenameIdent)
export(ReorderIdent)
export(RunDiffusion)
export(RunTSNE)
export(SampleUMI)
export(SaveClusters)
export(SetAllIdent)
export(SetClusters)
export(SetIdent)
export(Setup)
export(StashIdent)
export(SubsetCells)
export(SubsetData)
export(TSNEPlot)
export(TobitTest)
export(ValidateClusters)
export(ValidateSpecificClusters)
export(VizClassification)
export(VizICA)
export(VizPCA)
export(VlnPlot)
export(WhichCells)
export(addImputedScore)
export(addMetaData)
export(addSmoothedScore)
export(add_samples)
export(ainb)
export(anotinb)
export(arrange)
export(average.expression)
export(average.pca)
export(batch.gene)
export(buildClusterTree)
export(bwCols)
export(calc.insitu)
export(calcNoiseModels)
export(calinskiPlot)
export(cell.centroid)
export(cell.centroid.x)
export(cell.centroid.y)
export(cell.cor.matrix)
export(cellPlot)
export(cluster.alpha)
export(cv)
export(diff.t.test)
export(diffExp.test)
export(dim.plot)
export(doHeatMap)
export(doKMeans)
export(dot.plot)
export(exact.cell.centroid)
export(expMean)
export(expSD)
export(expVar)
export(extract_field)
export(feature.heatmap)
export(feature.plot)
export(feature.plot.keynote)
export(fetch.data)
export(find.markers)
export(find.markers.node)
export(findNGene)
export(find_all_markers)
export(fit.gene.k)
export(fit.gene.mix)
export(gene.cor.matrix)
export(genePlot)
export(geneScorePlot)
export(genes.ca.range)
export(genes.in.cluster)
export(get.centroids)
export(getNewScore)
export(getStat)
export(getStat1)
export(getStat2)
export(getStat3)
export(getWeightMatrix)
export(gg.legend.pts)
export(gg.legend.text)
export(gg.xax)
export(gg.yax)
export(gtCut)
export(heatmap2NoKey)
export(humpCt)
export(humpMean)
export(humpVar)
export(icHeatmap)
export(icTopGenes)
export(ica)
export(ica.plot)
export(initial.mapping)
export(jackF)
export(jackRandom)
export(jackStraw)
export(jackStraw.permutation.test)
export(jackStrawF)
export(jackStrawFull)
export(jackStrawMC)
export(jackStrawPlot)
export(kMeansHeatmap)
export(logMeanMinus)
export(logVarDivMean)
export(logVarMinus)
export(logVarMinus2)
export(log_add)
export(map.cell)
export(marker.auc.test)
export(marker.test)
export(mean.var.plot)
export(meanNormFunction)
export(minmax)
export(minusc)
export(minusr)
export(myPalette)
export(no.legend.title)
export(normal.sample)
export(pcHeatmap)
export(pcTopCells)
export(pcTopGenes)
export(pca)
export(pca.plot)
export(pca.sig.genes)
export(plotClusterTree)
export(plotNoiseModel)
export(plotVln)
export(posterior.plot)
export(print.pca)
export(project.pca)
export(project.samples)
export(pyCols)
export(refined.mapping)
export(regulatorScore)
export(removePC)
export(rename.ident)
export(reorder.ident)
export(returnTopX)
export(rp)
export(run_diffusion)
export(run_tsne)
export(set.all.ident)
export(set.ident)
export(setup)
export(shuffleMatRow)
export(spatial.de)
export(sub.string)
export(subc)
export(subr)
export(subsetCells)
export(subsetData)
export(tobit.test)
export(tsne.plot)
export(viz.ica)
export(viz.pca)
export(vlnPlot)
export(vminusc)
export(vp.layout)
export(vsubc)
export(which.cells)
export(writ.table)
export(zf.anchor.render)
export(zf.cells.render)
export(zf.insitu.dorsal)
export(zf.insitu.lateral)
export(zf.insitu.side)
export(zf.insitu.vec.lateral)
export(zf.insitu.ventral)
exportClasses(seurat)
exportMethods(AddImputedScore)
exportMethods(AddMetaData)
exportMethods(AddSamples)
exportMethods(AddSmoothedScore)
exportMethods(AssessNodes)
exportMethods(AssessSplit)
exportMethods(AverageExpression)
exportMethods(AveragePCA)
exportMethods(BatchGene)
exportMethods(BuildClusterTree)
exportMethods(BuildRFClassifier)
exportMethods(BuildSNN)
exportMethods(CalcNoiseModels)
exportMethods(CalinskiPlot)
exportMethods(CellCorMatrix)
exportMethods(CellPlot)
exportMethods(ClassifyCells)
exportMethods(ClusterAlpha)
exportMethods(ColorTSNESplit)
exportMethods(DBClustDimension)
exportMethods(DiffExpTest)
exportMethods(DiffTTest)
exportMethods(DimPlot)
exportMethods(DoHeatmap)
exportMethods(DoKMeans)
exportMethods(DotPlot)
exportMethods(FeatureHeatmap)
exportMethods(FeaturePlot)
exportMethods(FetchData)
exportMethods(FindAllMarkers)
exportMethods(FindClusters)
exportMethods(FindMarkers)
exportMethods(FindMarkersNode)
exportMethods(FitGeneK)
exportMethods(FitGeneMix)
exportMethods(GeneCorMatrix)
exportMethods(GenePlot)
exportMethods(GenesInCluster)
exportMethods(GetCentroids)
exportMethods(GetNewScore)
exportMethods(HeatmapNode)
exportMethods(ICA)
exportMethods(ICAPlot)
exportMethods(ICHeatmap)
exportMethods(ICTopGenes)
exportMethods(InitialMapping)
exportMethods(JackStraw)
exportMethods(JackStrawMC)
exportMethods(JackStrawPermutationTest)
exportMethods(JackStrawPlot)
exportMethods(KClustDimension)
exportMethods(KMeansHeatmap)
exportMethods(LogNormalize)
exportMethods(MakeSparse)
exportMethods(MapCell)
exportMethods(MarkerTest)
exportMethods(MeanVarPlot)
exportMethods(MergeNode)
exportMethods(MergeSeurat)
exportMethods(NegBinomDETest)
exportMethods(PCA)
exportMethods(PCAFast)
exportMethods(PCAPlot)
exportMethods(PCASigGenes)
exportMethods(PCElbowPlot)
exportMethods(PCHeatmap)
exportMethods(PCTopCells)
exportMethods(PCTopGenes)
exportMethods(PlotClusterTree)
exportMethods(PlotNoiseModel)
exportMethods(PoissonDETest)
exportMethods(PosteriorPlot)
exportMethods(PrintPCA)
exportMethods(ProjectPCA)
exportMethods(Read10X)
exportMethods(RefinedMapping)
exportMethods(RegressOut)
exportMethods(RemovePC)
exportMethods(RenameIdent)
exportMethods(ReorderIdent)
exportMethods(RunDiffusion)
exportMethods(RunTSNE)
exportMethods(SampleUMI)
exportMethods(ScaleData)
exportMethods(SetAllIdent)
exportMethods(SetIdent)
exportMethods(Setup)
exportMethods(StashIdent)
exportMethods(SubsetCells)
exportMethods(SubsetData)
exportMethods(TSNEPlot)
exportMethods(TobitTest)
exportMethods(ValidateClusters)
exportMethods(ValidateSpecificClusters)
exportMethods(VizClassification)
exportMethods(VizICA)
exportMethods(VizPCA)
exportMethods(VlnPlot)
exportMethods(WhichCells)
exportMethods(show)
import(Matrix)
import(ROCR)
import(Rtsne)
import(VGAM)
import(fastICA)
import(fpc)
import(ggplot2)
import(grid)
import(gridExtra)
import(lars)
import(pbapply)
import(reshape2)
import(stringr)
import(tsne)
importFrom(FNN,get.knn)
importFrom(MASS,glm.nb)
importFrom(MASS,kde2d)
importFrom(Matrix,colSums)
importFrom(Matrix,readMM)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(Rcpp,evalCpp)
importFrom(ape,as.phylo)
importFrom(ape,drop.tip)
importFrom(ape,nodelabels)
importFrom(ape,plot.phylo)
importFrom(caret,train)
importFrom(caret,trainControl)
importFrom(dplyr,"%>%")
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(dplyr,top_n)
importFrom(gdata,drop.levels)
importFrom(gplots,heatmap.2)
importFrom(igraph,E)
importFrom(igraph,graph.adjacency)
importFrom(igraph,graph.adjlist)
importFrom(igraph,plot.igraph)
importFrom(irlba,irlba)
importFrom(mixtools,normalmixEM)
importFrom(pbapply,pbapply)
importFrom(pbapply,pblapply)
importFrom(pbapply,pbsapply)
importFrom(plyr,mapvalues)
importFrom(ranger,ranger)
importFrom(tclust,tkmeans)
useDynLib(Seurat)