NAMESPACE

# Generated by roxygen2: do not edit by hand

export("cellPairwiseDistances<-")
export("minSpanningTree<-")
export("reducedDimA<-")
export(BEAM)
export(addCellType)
export(branchTest)
export(buildBranchCellDataSet)
export(calABCs)
export(calILRs)
export(calculateMarkerSpecificity)
export(cellPairwiseDistances)
export(classifyCells)
export(clusterCells)
export(clusterGenes)
export(compareModels)
export(detectBifurcationPoint)
export(detectGenes)
export(differentialGeneTest)
export(dispersionTable)
export(estimate_t)
export(exportCDS)
export(fitModel)
export(genSmoothCurves)
export(get_classic_muscle_markers)
export(importCDS)
export(load_HSMM)
export(load_HSMM_markers)
export(load_cellranger_data)
export(load_lung)
export(markerDiffTable)
export(mcesApply)
export(minSpanningTree)
export(newCellDataSet)
export(newCellTypeHierarchy)
export(orderCells)
export(plot_cell_clusters)
export(plot_cell_trajectory)
export(plot_clusters)
export(plot_complex_cell_trajectory)
export(plot_genes_branched_heatmap)
export(plot_genes_branched_pseudotime)
export(plot_genes_in_pseudotime)
export(plot_genes_jitter)
export(plot_genes_positive_cells)
export(plot_genes_violin)
export(plot_multiple_branches_heatmap)
export(plot_multiple_branches_pseudotime)
export(plot_ordering_genes)
export(plot_pc_variance_explained)
export(plot_pseudotime_heatmap)
export(plot_rho_delta)
export(plot_spanning_tree)
export(reduceDimension)
export(reducedDimA)
export(reducedDimK)
export(reducedDimS)
export(reducedDimW)
export(relative2abs)
export(responseMatrix)
export(selectTopMarkers)
export(setOrderingFilter)
export(vstExprs)
exportClasses(CellDataSet)
exportClasses(CellType)
exportClasses(CellTypeHierarchy)
import(DDRTree)
import(HSMMSingleCell)
import(Matrix)
import(Rtsne)
import(VGAM)
import(ggplot2)
import(grid)
import(irlba)
import(methods)
import(pheatmap)
import(slam)
importFrom(Biobase,"exprs<-")
importFrom(Biobase,"fData<-")
importFrom(Biobase,"pData<-")
importFrom(Biobase,ExpressionSet)
importFrom(Biobase,annotatedDataFrameFrom)
importFrom(Biobase,assayDataNew)
importFrom(Biobase,esApply)
importFrom(Biobase,exprs)
importFrom(Biobase,fData)
importFrom(Biobase,multiassign)
importFrom(Biobase,pData)
importFrom(BiocGenerics,"sizeFactors<-")
importFrom(BiocGenerics,clusterApply)
importFrom(BiocGenerics,clusterCall)
importFrom(BiocGenerics,estimateDispersions)
importFrom(BiocGenerics,estimateSizeFactors)
importFrom(BiocGenerics,parCapply)
importFrom(BiocGenerics,parRapply)
importFrom(BiocGenerics,sizeFactors)
importFrom(Matrix,readMM)
importFrom(RANN,nn2)
importFrom(cluster,pam)
importFrom(combinat,permn)
importFrom(densityClust,densityClust)
importFrom(densityClust,findClusters)
importFrom(dplyr,"%>%")
importFrom(dplyr,do)
importFrom(dplyr,group_by_)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,sample_n)
importFrom(dplyr,select_)
importFrom(dplyr,slice)
importFrom(dplyr,top_n)
importFrom(fastICA,ica.R.def)
importFrom(fastICA,ica.R.par)
importFrom(ggplot2,Position)
importFrom(grDevices,rgb)
importFrom(igraph,"V<-")
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,as.undirected)
importFrom(igraph,bfs)
importFrom(igraph,cluster_louvain)
importFrom(igraph,degree)
importFrom(igraph,delete.vertices)
importFrom(igraph,ecount)
importFrom(igraph,edge)
importFrom(igraph,get.all.shortest.paths)
importFrom(igraph,get.diameter)
importFrom(igraph,get.edgelist)
importFrom(igraph,get.shortest.paths)
importFrom(igraph,graph.adjacency)
importFrom(igraph,graph.data.frame)
importFrom(igraph,graph.dfs)
importFrom(igraph,graph.empty)
importFrom(igraph,graph.neighborhood)
importFrom(igraph,induced.subgraph)
importFrom(igraph,layout_as_tree)
importFrom(igraph,membership)
importFrom(igraph,minimum.spanning.tree)
importFrom(igraph,modularity)
importFrom(igraph,shortest.paths)
importFrom(igraph,shortest_paths)
importFrom(igraph,subcomponent)
importFrom(igraph,vertex)
importFrom(limma,removeBatchEffect)
importFrom(matrixStats,rowSds)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(parallel,mcmapply)
importFrom(parallel,splitIndices)
importFrom(parallel,stopCluster)
importFrom(plyr,.)
importFrom(plyr,ddply)
importFrom(qlcMatrix,rowMax)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(stats,Gamma)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,cooks.distance)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,ecdf)
importFrom(stats,glm)
importFrom(stats,lowess)
importFrom(stats,median)
importFrom(stats,optim)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,qnorm)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(stringr,str_c)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_trim)
importFrom(tibble,rownames_to_column)
importFrom(utils,data)
importFrom(viridis,scale_color_viridis)
useDynLib(monocle)