NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(Convert,SingleCellExperiment)
S3method(Convert,anndata.base.AnnData)
S3method(Convert,seurat)
S3method(as.SingleCellExperiment,seurat)
S3method(as.seurat,SingleCellExperiment)
export(AddImputedScore)
export(AddMetaData)
export(AddModuleScore)
export(AddSamples)
export(AddSmoothedScore)
export(AlignSubspace)
export(AssessNodes)
export(AssessSplit)
export(AugmentPlot)
export(AverageDetectionRate)
export(AverageExpression)
export(AveragePCA)
export(BlackAndWhite)
export(BuildClusterTree)
export(BuildRFClassifier)
export(BuildSNN)
export(CalcAlignmentMetric)
export(CalcVarExpRatio)
export(CaseMatch)
export(CellCycleScoring)
export(CellPlot)
export(ClassifyCells)
export(CollapseSpeciesExpressionMatrix)
export(ColorTSNESplit)
export(CombineIdent)
export(Convert)
export(CreateSeuratObject)
export(CustomDistance)
export(CustomPalette)
export(DBClustDimension)
export(DBclust_dimension)
export(DESeq2DETest)
export(DMEmbed)
export(DMPlot)
export(DarkTheme)
export(DiffExpTest)
export(DiffTTest)
export(DimElbowPlot)
export(DimHeatmap)
export(DimPlot)
export(DimTopCells)
export(DimTopGenes)
export(DoHeatmap)
export(DoKMeans)
export(DotPlot)
export(DotPlotOld)
export(ExpMean)
export(ExpSD)
export(ExpVar)
export(ExtractField)
export(FastWhichCells)
export(FeatureHeatmap)
export(FeatureLocator)
export(FeaturePlot)
export(FetchData)
export(FilterCells)
export(FindAllMarkers)
export(FindAllMarkersNode)
export(FindClusters)
export(FindConservedMarkers)
export(FindMarkers)
export(FindMarkersNode)
export(FindVariableGenes)
export(FitGeneK)
export(GenePlot)
export(GenesInCluster)
export(GetAssayData)
export(GetCellEmbeddings)
export(GetCentroids)
export(GetClusters)
export(GetDimReduction)
export(GetGeneLoadings)
export(HTODemux)
export(HTOHeatmap)
export(HeatmapNode)
export(HoverLocator)
export(ICA)
export(ICAEmbed)
export(ICALoad)
export(ICAPlot)
export(ICHeatmap)
export(ICTopCells)
export(ICTopGenes)
export(InitialMapping)
export(JackStraw)
export(JackStrawPlot)
export(JoyPlot)
export(KClustDimension)
export(KMeansHeatmap)
export(Kclust_dimension)
export(LogNormalize)
export(LogVMR)
export(MASTDETest)
export(MakeSparse)
export(MarkerTest)
export(MatrixRowShuffle)
export(MeanVarPlot)
export(MergeNode)
export(MergeSeurat)
export(MetageneBicorPlot)
export(MinMax)
export(NegBinomDETest)
export(NegBinomRegDETest)
export(NormalizeData)
export(NumberClusters)
export(OldDoHeatmap)
export(PCA)
export(PCAEmbed)
export(PCALoad)
export(PCAPlot)
export(PCASigGenes)
export(PCElbowPlot)
export(PCHeatmap)
export(PCTopCells)
export(PCTopGenes)
export(PlotClusterTree)
export(PoissonDETest)
export(PrintAlignSubspaceParams)
export(PrintCCAParams)
export(PrintCalcParams)
export(PrintCalcVarExpRatioParams)
export(PrintDMParams)
export(PrintDim)
export(PrintFindClustersParams)
export(PrintICA)
export(PrintICAParams)
export(PrintPCA)
export(PrintPCAParams)
export(PrintSNNParams)
export(PrintTSNEParams)
export(ProjectDim)
export(ProjectPCA)
export(PurpleAndYellow)
export(Read10X)
export(Read10X_h5)
export(RefinedMapping)
export(RegressOut)
export(RemoveFromTable)
export(RenameCells)
export(RenameIdent)
export(ReorderIdent)
export(RidgePlot)
export(RunCCA)
export(RunDiffusion)
export(RunICA)
export(RunMultiCCA)
export(RunPCA)
export(RunPHATE)
export(RunTSNE)
export(RunUMAP)
export(SampleUMI)
export(SaveClusters)
export(ScaleData)
export(ScaleDataR)
export(SetAllIdent)
export(SetAssayData)
export(SetClusters)
export(SetDimReduction)
export(SetIdent)
export(Shuffle)
export(SplitDotPlotGG)
export(SplitObject)
export(StashIdent)
export(SubsetByPredicate)
export(SubsetColumn)
export(SubsetData)
export(SubsetRow)
export(TSNEPlot)
export(TobitTest)
export(TransferIdent)
export(UpdateSeuratObject)
export(ValidateClusters)
export(ValidateSpecificClusters)
export(VariableGenePlot)
export(VizClassification)
export(VizDimReduction)
export(VizICA)
export(VizPCA)
export(VlnPlot)
export(WhichCells)
export(WilcoxDETest)
export(addImputedScore)
export(addMetaData)
export(addSmoothedScore)
export(add_samples)
export(as.SingleCellExperiment)
export(as.seurat)
export(average.expression)
export(average.pca)
export(batch.gene)
export(buildClusterTree)
export(calc.insitu)
export(calcNoiseModels)
export(calinskiPlot)
export(cell.cor.matrix)
export(cellPlot)
export(cluster.alpha)
export(diffExp.test)
export(doHeatMap)
export(doKMeans)
export(dot.plot)
export(feature.heatmap)
export(feature.plot)
export(feature.plot.keynote)
export(fetch.data)
export(find.markers)
export(find.markers.node)
export(find_all_markers)
export(fit.gene.k)
export(fit.gene.mix)
export(gene.cor.matrix)
export(genePlot)
export(geneScorePlot)
export(genes.in.cluster)
export(get.centroids)
export(getNewScore)
export(icHeatmap)
export(icTopGenes)
export(ica)
export(ica.plot)
export(initial.mapping)
export(jackRandom)
export(jackStraw)
export(jackStraw.permutation.test)
export(jackStrawFull)
export(jackStrawMC)
export(jackStrawPlot)
export(kMeansHeatmap)
export(map.cell)
export(marker.test)
export(minusc)
export(minusr)
export(pcHeatmap)
export(pcTopCells)
export(pcTopGenes)
export(pca)
export(pca.plot)
export(pca.sig.genes)
export(plotClusterTree)
export(plotNoiseModel)
export(posterior.plot)
export(project.pca)
export(project.samples)
export(refined.mapping)
export(regulatorScore)
export(removePC)
export(rename.ident)
export(run_diffusion)
export(run_tsne)
export(set.all.ident)
export(set.ident)
export(spatial.de)
export(subsetCells)
export(subsetData)
export(tobit.test)
export(tsne.plot)
export(viz.ica)
export(viz.pca)
export(vlnPlot)
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)
import(Matrix)
import(RColorBrewer)
import(SDMTools)
import(diffusionMap)
import(doSNOW)
import(fpc)
import(ggplot2)
import(lars)
import(metap)
import(parallel)
import(pbapply)
importFrom(Hmisc,cut2)
importFrom(MASS,glm.nb)
importFrom(MASS,kde2d)
importFrom(MASS,negative.binomial)
importFrom(MASS,theta.ml)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,readMM)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(RANN,nn2)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(ROCR,performance)
importFrom(ROCR,prediction)
importFrom(Rcpp,evalCpp)
importFrom(Rtsne,Rtsne)
importFrom(ape,as.phylo)
importFrom(ape,drop.tip)
importFrom(ape,nodelabels)
importFrom(ape,plot.phylo)
importFrom(cluster,clara)
importFrom(cowplot,get_legend)
importFrom(cowplot,plot_grid)
importFrom(dplyr,"%>%")
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_each)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(dplyr,summarize_each)
importFrom(dplyr,top_n)
importFrom(dplyr,ungroup)
importFrom(dtw,dtw)
importFrom(fitdistrplus,fitdist)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(ggplot2,annotation_raster)
importFrom(ggridges,geom_density_ridges)
importFrom(ggridges,theme_ridges)
importFrom(gplots,heatmap.2)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,colors)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,contour)
importFrom(graphics,hist)
importFrom(graphics,lines)
importFrom(graphics,locator)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,rect)
importFrom(graphics,smoothScatter)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(ica,icafast)
importFrom(ica,icaimax)
importFrom(ica,icajade)
importFrom(igraph,E)
importFrom(igraph,graph.adjacency)
importFrom(igraph,graph.adjlist)
importFrom(igraph,plot.igraph)
importFrom(irlba,irlba)
importFrom(lmtest,lrtest)
importFrom(methods,"slot<-")
importFrom(methods,.hasSlot)
importFrom(methods,as)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setMethod)
importFrom(methods,signature)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(mixtools,normalmixEM)
importFrom(mixtools,plot.mixEM)
importFrom(pbapply,pbapply)
importFrom(pbapply,pblapply)
importFrom(pbapply,pbsapply)
importFrom(reshape2,melt)
importFrom(reticulate,dict)
importFrom(reticulate,import)
importFrom(reticulate,np_array)
importFrom(reticulate,py_module_available)
importFrom(reticulate,py_set_seed)
importFrom(reticulate,py_to_r)
importFrom(reticulate,r_to_py)
importFrom(reticulate,tuple)
importFrom(stats,anova)
importFrom(stats,approx)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,logLik)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,optim)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,pnbinom)
importFrom(stats,poisson)
importFrom(stats,predict)
importFrom(stats,prop.test)
importFrom(stats,qqplot)
importFrom(stats,quantile)
importFrom(stats,qunif)
importFrom(stats,relevel)
importFrom(stats,reorder)
importFrom(stats,residuals)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,smooth.spline)
importFrom(stats,t.test)
importFrom(stats,var)
importFrom(stats,wilcox.test)
importFrom(tidyr,gather)
importFrom(tidyr,separate)
importFrom(tidyr,unite)
importFrom(tsne,tsne)
importFrom(utils,file_test)
importFrom(utils,globalVariables)
importFrom(utils,installed.packages)
importFrom(utils,menu)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
useDynLib(Seurat)