├── .gitattributes ├── CellChat.Rproj ├── CellChat_Logo.png ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── CellChat-package.R ├── CellChat_class.R ├── RcppExports.R ├── analysis.R ├── app.R ├── data.R ├── database.R ├── modeling.R ├── utilities.R └── visualization.R ├── README.md ├── data ├── CellChatDB.human.rda ├── CellChatDB.mouse.rda ├── CellChatDB.zebrafish.rda ├── PPI.human.rda └── PPI.mouse.rda ├── man ├── AnyMatrix-class.Rd ├── CellChat-class.Rd ├── CellChatDB.human.Rd ├── CellChatDB.mouse.Rd ├── CellChatDB.zebrafish.Rd ├── CellChat_theme_opts.Rd ├── PPI.human.Rd ├── PPI.mouse.Rd ├── StackedVlnPlot.Rd ├── addMeta.Rd ├── addReduction.Rd ├── aggregateNet.Rd ├── alpha_centrality.Rd ├── barPlot.Rd ├── barplot_internal.Rd ├── buildSNN.Rd ├── checkGeneSymbol.Rd ├── colorRamp3.Rd ├── compareInteractions.Rd ├── computeAveExpr.Rd ├── computeCellDistance.Rd ├── computeCentralityLocal.Rd ├── computeCommunProb.Rd ├── computeCommunProbPathway.Rd ├── computeEigengap.Rd ├── computeEnrichmentScore.Rd ├── computeExprGroup_agonist.Rd ├── computeExprGroup_antagonist.Rd ├── computeExpr_LR.Rd ├── computeExpr_agonist.Rd ├── computeExpr_antagonist.Rd ├── computeExpr_complex.Rd ├── computeExpr_coreceptor.Rd ├── computeLaplacian.Rd ├── computeNetD_structure.Rd ├── computeNetSimilarity.Rd ├── computeNetSimilarityPairwise.Rd ├── computeRegionDistance.Rd ├── createCellChat.Rd ├── dotPlot.Rd ├── entropia.Rd ├── extractEnrichedLR.Rd ├── extractEnrichedLR_internal.Rd ├── extractGene.Rd ├── extractGeneSubset.Rd ├── extractGeneSubsetFromPair.Rd ├── extractLRfromGenes.Rd ├── extract_max.Rd ├── filterCommunication.Rd ├── findEnrichedSignaling.Rd ├── geometricMean.Rd ├── getMaxWeight.Rd ├── ggPalette.Rd ├── identifyCommunicationPatterns.Rd ├── identifyEnrichedInteractions.Rd ├── identifyOverExpressedGenes.Rd ├── identifyOverExpressedInteractions.Rd ├── identifyOverExpressedLigandReceptor.Rd ├── l1NormalizeColumns.Rd ├── l1NormalizeRows.Rd ├── liftCellChat.Rd ├── mergeCellChat.Rd ├── mergeInteractions.Rd ├── modify_vlnplot.Rd ├── mycircle.Rd ├── netAnalysis_computeCentrality.Rd ├── netAnalysis_contribution.Rd ├── netAnalysis_diff_signalingRole_scatter.Rd ├── netAnalysis_dot.Rd ├── netAnalysis_river.Rd ├── netAnalysis_signalingChanges_scatter.Rd ├── netAnalysis_signalingRole_heatmap.Rd ├── netAnalysis_signalingRole_network.Rd ├── netAnalysis_signalingRole_scatter.Rd ├── netClustering.Rd ├── netEmbedding.Rd ├── netMappingDEG.Rd ├── netVisual.Rd ├── netVisual_aggregate.Rd ├── netVisual_barplot.Rd ├── netVisual_bubble.Rd ├── netVisual_chord_cell.Rd ├── netVisual_chord_cell_internal.Rd ├── netVisual_chord_gene.Rd ├── netVisual_circle.Rd ├── netVisual_diffInteraction.Rd ├── netVisual_embedding.Rd ├── netVisual_embeddingPairwise.Rd ├── netVisual_embeddingPairwiseZoomIn.Rd ├── netVisual_embeddingZoomIn.Rd ├── netVisual_heatmap.Rd ├── netVisual_hierarchy1.Rd ├── netVisual_hierarchy2.Rd ├── netVisual_individual.Rd ├── netVisual_spatial.Rd ├── nnd.Rd ├── node_distance.Rd ├── normalizeData.Rd ├── pieChart.Rd ├── plotGeneExpression.Rd ├── preProcMultiomics.Rd ├── projectAndRecombine.Rd ├── projectFromNetworkRecombine.Rd ├── projectOnNetwork.Rd ├── randomWalkBySolve.Rd ├── rankNet.Rd ├── rankNetPairwise.Rd ├── rankSimilarity.Rd ├── runCellChatApp.Rd ├── runPCA.Rd ├── runUMAP.Rd ├── scPalette.Rd ├── scaleData.Rd ├── scaleMat.Rd ├── searchPair.Rd ├── selectK.Rd ├── setIdent.Rd ├── show-CellChat-method.Rd ├── showDatabaseCategory.Rd ├── sketchData.Rd ├── smoothData.Rd ├── spatialDimPlot.Rd ├── spatialFeaturePlot.Rd ├── subsetCellChat.Rd ├── subsetCommunication.Rd ├── subsetCommunication_internal.Rd ├── subsetDB.Rd ├── subsetData.Rd ├── thresholdedMean.Rd ├── triMean.Rd ├── updateCCC_score.Rd ├── updateCellChat.Rd ├── updateCellChatDB.Rd └── updateClusterLabels.Rd ├── overview_CellChat.png ├── src ├── CellChat.so ├── CellChat_Rcpp.cpp ├── CellChat_Rcpp.o ├── RcppExports.cpp └── RcppExports.o └── tutorial ├── CellChat-vignette.Rmd ├── CellChat-vignette.html ├── CellChat_analysis_of_multiple_spatial_transcriptomics_datasets.Rmd ├── CellChat_analysis_of_multiple_spatial_transcriptomics_datasets.html ├── CellChat_analysis_of_spatial_multiomics_data.Rmd ├── CellChat_analysis_of_spatial_multiomics_data.html ├── CellChat_analysis_of_spatial_transcriptomics_data.Rmd ├── CellChat_analysis_of_spatial_transcriptomics_data.html ├── Comparison_analysis_of_multiple_datasets.Rmd ├── Comparison_analysis_of_multiple_datasets.html ├── Comparison_analysis_of_multiple_datasets_with_different_cellular_compositions.Rmd ├── Comparison_analysis_of_multiple_datasets_with_different_cellular_compositions.html ├── FAQ_on_applying_CellChat_to_spatial_transcriptomics_data.Rmd ├── FAQ_on_applying_CellChat_to_spatial_transcriptomics_data.html ├── Interface_with_other_single-cell_analysis_toolkits.Rmd ├── Interface_with_other_single-cell_analysis_toolkits.html ├── Update-CellChatDB.Rmd └── Update-CellChatDB.html /.gitattributes: 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