Cell Communication Analysis for Single Cell RNA Sequencing

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Documentation for package ‘dominoSignal’ version 1.7.1

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

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 clusters 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
DominoObjects	Example domino objects
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_signalling	Access signaling
dom_tf_activation	Access transcription factor activity scores
dom_to_df	Turn domino object signaling information into a data frame
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
incoming_signalling_heatmap	Create a cluster incoming signaling heatmap
LinkageSummary	Example linkage summary
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
PBMC	PBMC scRNAseq data subset
plot_differential_linkages	Plot differential linkages among domino results ranked by a comparative statistic
print-method	Print domino object
print-method	Print linkage summary object
rename_clusters	Renames clusters in a 'domino()' object
SCENIC	SCENIC example subset
show-method	Show domino object information
show-method	Show linkage_summary object information
signaling_heatmap	Create a network heatmap
signaling_network	Create a cluster to cluster signaling network diagram
signalling_heatmap	Create a network heatmap
signalling_network	Create a cluster to cluster signaling network diagram
subset-method	Subset a linkage_summary object
summarise_linkages	Summarize linkages from multiple domino objects
summarize_linkages	Summarize linkages from multiple domino objects
test_differential_linkages	Statistical test for differential linkages across multiple domino results