# Cell Communication Analysis for Single Cell RNA Sequencing

## Documentation for package ‘dominoSignal’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
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
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