Files in sqjin/CellChat

Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

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