Cell Communication Analysis for Single Cell RNA Sequencing

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Documentation for package ‘dominoSignal’ version 1.3.0

• 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
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