CellPhoneDB             CellPhoneDB subset
PBMC                    PBMC RNAseq data subset
SCENIC                  SCENIC AUC subset
add_rl_column           Adds a column to the RL signaling data frame.
build_domino            Calculate a signaling network for a domino
                        object
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
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
domino-class            The domino class
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-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
plot_differential_linkages
                        Plot differential linkages among domino results
                        ranked by a comparative statistic
print,domino-method     Print domino object
print,linkage_summary-method
                        Print linkage summary object
rename_clusters         Renames clusters in a domino object
show,domino-method      Show domino object information
show,linkage_summary-method
                        Show linkage_summary 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
