| add_rl_column | Adds a column to the RL signaling data frame. |
| build_domino | Calculate a signaling network for a domino object |
| CellPhoneDB | CellPhoneDB subset |
| circos_ligand_receptor | Plot expression of a receptor's ligands by other cell types as a chord plot |
| cor_heatmap | Create a heatmap of correlation between receptors and transcription factors |
| cor_scatter | Create a correlation plot between TF and receptor |
| count_linkage | Count occurrences of linkages across multiple domino results from a linkage summary |
| create_domino | Create a domino object and prepare it for network construction |
| create_regulon_list_scenic | Create a list of genes in regulons inferred by SCENIC |
| create_rl_map_cellphonedb | Create a receptor - ligand map from a CellPhoneDB signaling database |
| domino | The domino class |
| domino-class | The domino class |
| dom_clusters | Access clusters |
| dom_correlations | Access correlations |
| dom_counts | Access counts |
| dom_database | Access database |
| dom_de | Access differential expression |
| dom_info | Access build information |
| dom_linkages | Access linkages |
| dom_network_items | Access all features, receptors, or ligands present in a signaling network. |
| dom_signaling | Access signaling |
| dom_tf_activation | Access transcription factor activation |
| dom_zscores | Access z-scores |
| feat_heatmap | Create a heatmap of features organized by cluster |
| gene_network | Create a gene association network |
| incoming_signaling_heatmap | Create a cluster incoming signaling heatmap |
| linkage_summary | The domino linkage summary class |
| linkage_summary-class | The domino linkage summary class |
| mean_ligand_expression | Calculate mean ligand expression as a data frame for plotting in circos plot |
| mock_linkage_summary | Create a mock linkage summary object |
| obtain_circos_expression | Obtain Circos Expression |
| PBMC | PBMC RNAseq data subset |
| plot_differential_linkages | Plot differential linkages among domino results ranked by a comparative statistic |
| print-method | Print domino object |
| rename_clusters | Renames clusters in a domino object |
| render_circos_ligand_receptor | Render Circos Ligand Receptor Plot |
| SCENIC | SCENIC AUC subset |
| show-method | Show domino object information |
| signaling_heatmap | Create a network heatmap |
| signaling_network | Create a cluster to cluster signaling network diagram |
| summarize_linkages | Summarize linkages from multiple domino objects |
| test_differential_linkages | Statistical test for differential linkages across multiple domino results |