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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(CellChat_theme_opts)
export(StackedVlnPlot)
export(addMeta)
export(addReduction)
export(aggregateNet)
export(barPlot)
export(barplot_internal)
export(buildSNN)
export(checkGeneSymbol)
export(colorRamp3)
export(compareInteractions)
export(computeAveExpr)
export(computeCellDistance)
export(computeCommunProb)
export(computeCommunProbPathway)
export(computeEigengap)
export(computeEnrichmentScore)
export(computeExprGroup_agonist)
export(computeExprGroup_antagonist)
export(computeExpr_LR)
export(computeExpr_agonist)
export(computeExpr_antagonist)
export(computeExpr_complex)
export(computeExpr_coreceptor)
export(computeLaplacian)
export(computeNetD_structure)
export(computeNetSimilarity)
export(computeNetSimilarityPairwise)
export(computeRegionDistance)
export(createCellChat)
export(dotPlot)
export(extractEnrichedLR)
export(extractGene)
export(extractGeneSubset)
export(extractGeneSubsetFromPair)
export(filterCommunication)
export(findEnrichedSignaling)
export(geometricMean)
export(getMaxWeight)
export(ggPalette)
export(identifyCommunicationPatterns)
export(identifyEnrichedInteractions)
export(identifyOverExpressedGenes)
export(identifyOverExpressedInteractions)
export(identifyOverExpressedLigandReceptor)
export(liftCellChat)
export(mergeCellChat)
export(mergeInteractions)
export(netAnalysis_computeCentrality)
export(netAnalysis_contribution)
export(netAnalysis_diff_signalingRole_scatter)
export(netAnalysis_dot)
export(netAnalysis_river)
export(netAnalysis_signalingChanges_scatter)
export(netAnalysis_signalingRole_heatmap)
export(netAnalysis_signalingRole_network)
export(netAnalysis_signalingRole_scatter)
export(netClustering)
export(netEmbedding)
export(netMappingDEG)
export(netVisual)
export(netVisual_aggregate)
export(netVisual_barplot)
export(netVisual_bubble)
export(netVisual_chord_cell)
export(netVisual_chord_cell_internal)
export(netVisual_chord_gene)
export(netVisual_circle)
export(netVisual_diffInteraction)
export(netVisual_embedding)
export(netVisual_embeddingPairwise)
export(netVisual_embeddingPairwiseZoomIn)
export(netVisual_embeddingZoomIn)
export(netVisual_heatmap)
export(netVisual_hierarchy1)
export(netVisual_hierarchy2)
export(netVisual_individual)
export(netVisual_spatial)
export(normalizeData)
export(pieChart)
export(plotGeneExpression)
export(projectData)
export(rankNet)
export(rankNetPairwise)
export(rankSimilarity)
export(runCellChatApp)
export(runPCA)
export(runUMAP)
export(scPalette)
export(scaleData)
export(scaleMat)
export(searchPair)
export(selectK)
export(setIdent)
export(showDatabaseCategory)
export(sketchData)
export(spatialDimPlot)
export(spatialFeaturePlot)
export(subsetCellChat)
export(subsetCommunication)
export(subsetDB)
export(subsetData)
export(triMean)
export(updateCCC_score)
export(updateCellChat)
export(updateCellChatDB)
export(updateClusterLabels)
exportClasses(CellChat)
import(NMF)
import(bslib)
import(dplyr)
import(ggalluvial)
import(ggplot2)
import(reticulate)
import(shiny)
importClassesFrom(Matrix,dgCMatrix)
importFrom(BiocGenerics,as.data.frame)
importFrom(BiocNeighbors,AnnoyParam)
importFrom(BiocNeighbors,queryKNN)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,anno_barplot)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(FNN,get.knn)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,crossprod)
importFrom(Matrix,nnzero)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(NMF,nmf)
importFrom(NMF,nmfEstimateRank)
importFrom(RColorBrewer,brewer.pal)
importFrom(RSpectra,eigs_sym)
importFrom(Rcpp,evalCpp)
importFrom(Rcpp,sourceCpp)
importFrom(circlize,chordDiagram)
importFrom(circlize,circos.clear)
importFrom(circlize,circos.text)
importFrom(circlize,circos.track)
importFrom(circlize,get.cell.meta.data)
importFrom(colorspace,HLS)
importFrom(colorspace,HSV)
importFrom(colorspace,LAB)
importFrom(colorspace,LUV)
importFrom(colorspace,RGB)
importFrom(colorspace,XYZ)
importFrom(colorspace,coords)
importFrom(colorspace,hex)
importFrom(colorspace,sRGB)
importFrom(cowplot,draw_label)
importFrom(cowplot,ggdraw)
importFrom(cowplot,plot_grid)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,desc)
importFrom(dplyr,group_by)
importFrom(dplyr,groups)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,select)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,top_n)
importFrom(future,nbrOfWorkers)
importFrom(future,plan)
importFrom(future.apply,future_sapply)
importFrom(ggnetwork,geom_nodetext_repel)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggpubr,stat_compare_means)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,hcl)
importFrom(grDevices,pdf)
importFrom(grDevices,recordPlot)
importFrom(graphics,symbols)
importFrom(grid,gpar)
importFrom(grid,grid.draw)
importFrom(grid,grid.grabExpr)
importFrom(grid,grid.newpage)
importFrom(grid,popViewport)
importFrom(grid,pushViewport)
importFrom(grid,unit)
importFrom(grid,viewport)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,alpha.centrality)
importFrom(igraph,authority_score)
importFrom(igraph,betweenness)
importFrom(igraph,degree)
importFrom(igraph,eigen_centrality)
importFrom(igraph,ends)
importFrom(igraph,get.edgelist)
importFrom(igraph,graph.complementer)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,hub_score)
importFrom(igraph,in_circle)
importFrom(igraph,layout_)
importFrom(igraph,page_rank)
importFrom(igraph,strength)
importFrom(irlba,irlba)
importFrom(magrittr,"%>%")
importFrom(methods,as)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,slot)
importFrom(patchwork,wrap_plots)
importFrom(pbapply,pbsapply)
importFrom(plyr,mapvalues)
importFrom(reshape2,melt)
importFrom(reticulate,import)
importFrom(scales,percent)
importFrom(shape,Arrows)
importFrom(sna,flowbet)
importFrom(sna,infocent)
importFrom(stats,aggregate)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,wilcox.test)
importFrom(stringr,str_split)
importFrom(stringr,str_split_1)
importFrom(svglite,svglite)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
useDynLib(CellChat, .registration = TRUE)