NAMESPACE

# Generated by roxygen2: do not edit by hand

export("graph<-")
export("nhoodAdjacency<-")
export("nhoodCounts<-")
export("nhoodDistances<-")
export("nhoodExpression<-")
export("nhoodGraph<-")
export("nhoodIndex<-")
export("nhoodReducedDim<-")
export("nhoods<-")
export(.calc_distance)
export(.parse_formula)
export(.rEParse)
export(Milo)
export(Satterthwaite_df)
export(annotateNhoods)
export(buildFromAdjacency)
export(buildGraph)
export(buildNhoodGraph)
export(calcNhoodDistance)
export(calcNhoodExpression)
export(checkSeparation)
export(computePvalue)
export(countCells)
export(findNhoodGroupMarkers)
export(findNhoodMarkers)
export(fitGLMM)
export(glmmControl.defaults)
export(graph)
export(graphSpatialFDR)
export(groupNhoods)
export(initialiseG)
export(initializeFullZ)
export(makeNhoods)
export(matrix.trace)
export(nhoodAdjacency)
export(nhoodCounts)
export(nhoodDistances)
export(nhoodExpression)
export(nhoodGraph)
export(nhoodIndex)
export(nhoodReducedDim)
export(nhoods)
export(plotDAbeeswarm)
export(plotNhoodCounts)
export(plotNhoodExpressionDA)
export(plotNhoodExpressionGroups)
export(plotNhoodGraph)
export(plotNhoodGraphDA)
export(plotNhoodGroups)
export(plotNhoodMA)
export(plotNhoodSizeHist)
export(testDiffExp)
export(testNhoods)
exportClasses(Milo)
exportMethods("graph<-")
exportMethods("nhoodAdjacency<-")
exportMethods("nhoodCounts<-")
exportMethods("nhoodDistances<-")
exportMethods("nhoodExpression<-")
exportMethods("nhoodGraph<-")
exportMethods("nhoodIndex<-")
exportMethods("nhoodReducedDim<-")
exportMethods("nhoods<-")
exportMethods(graph)
exportMethods(nhoodAdjacency)
exportMethods(nhoodCounts)
exportMethods(nhoodDistances)
exportMethods(nhoodExpression)
exportMethods(nhoodGraph)
exportMethods(nhoodIndex)
exportMethods(nhoodReducedDim)
exportMethods(nhoods)
exportMethods(show)
import(SingleCellExperiment)
import(ggplot2)
import(ggraph)
import(igraph)
import(methods)
import(patchwork)
importClassesFrom(Matrix,ddiMatrix)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(Matrix,dgTMatrix)
importClassesFrom(Matrix,dgeMatrix)
importClassesFrom(Matrix,dsCMatrix)
importClassesFrom(Matrix,sparseMatrix)
importClassesFrom(S4Vectors,DataFrame)
importFrom(BiocGenerics,which)
importFrom(BiocNeighbors,KmknnParam)
importFrom(BiocNeighbors,findKNN)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpok)
importFrom(BiocParallel,bpoptions)
importFrom(BiocParallel,bpstopOnError)
importFrom(BiocParallel,bptry)
importFrom(BiocSingular,bsparam)
importFrom(Matrix,Matrix)
importFrom(Matrix,colSums)
importFrom(Matrix,crossprod)
importFrom(Matrix,diag)
importFrom(Matrix,kronecker)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,solve)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(Matrix,tcrossprod)
importFrom(Matrix,tril)
importFrom(Matrix,which)
importFrom(MatrixGenerics,colSums2)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rcpp,evalCpp)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,coolcat)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExps)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,colPairs)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SingleCellExperiment,rowData)
importFrom(SingleCellExperiment,rowPairs)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(cowplot,theme_cowplot)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,first)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,percent_rank)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,topTags)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,stat_summary)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(gtools,permutations)
importFrom(igraph,V)
importFrom(igraph,as_ids)
importFrom(igraph,cluster_louvain)
importFrom(igraph,components)
importFrom(igraph,count_triangles)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,induced_subgraph)
importFrom(igraph,is_igraph)
importFrom(igraph,make_graph)
importFrom(igraph,neighborhood)
importFrom(igraph,neighbors)
importFrom(igraph,set_vertex_attr)
importFrom(igraph,simplify)
importFrom(igraph,vertex.attributes)
importFrom(irlba,prcomp_irlba)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTreat)
importFrom(matrixStats,colMedians)
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,slot)
importFrom(numDeriv,jacobian)
importFrom(pracma,pinv)
importFrom(stats,as.formula)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.exclude)
importFrom(stats,na.fail)
importFrom(stats,na.omit)
importFrom(stats,na.pass)
importFrom(stats,pt)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(stringr,str_replace)
importFrom(tibble,has_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,pivot_longer)
importFrom(utils,tail)
importMethodsFrom(Matrix,"%*%")
importMethodsFrom(Matrix,t)
useDynLib(miloR)