scGraphVerse: A Gene Network Analysis Package

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Documentation for package ‘scGraphVerse’ version 1.0.0

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

Help Pages

build_network_se	Create a SummarizedExperiment for Network Storage
classify_edges	Classify Edges as TP, FP, or FN
community_path	Community Detection and Pathway Enrichment Analysis
community_similarity	Compare Community Assignments and Topological Properties
compare_consensus	Compare Consensus and Reference Graphs or STRINGdb Networks
compute_community_metrics	Compute Community Assignment Similarity Metrics
compute_topology_metrics	Compute Network Topological Properties
create_consensus	Create a Consensus Adjacency Matrix from Multiple Networks
create_mae	Create MultiAssayExperiment from Multiple Single-Cell Datasets
cutoff_adjacency	Threshold Adjacency Matrices Based on Shuffled Network Quantiles
download_Atlas	Download and Load an RDS File from a URL
earlyj	Modify Cell Names and Combine Datasets
edge_mining	Edge Mining of Gene Interactions Using PubMed
generate_adjacency	Generate Adjacency Matrices from Gene Interaction Tables
infer_networks	Infer Gene Regulatory Networks from Expression Matrices
init_py	Initialize Python Environment for GRNBoost2
PCzinb	Structure learning for count data using PC algorithms
plotg	Visualize Graphs from Adjacency Matrices
plotROC	Plot ROC Curves for Inferred Networks
plot_community_comparison	Visualize Community and Topology Comparison
plot_network_comparison	Visualize Network Comparison
pscores	Compute Performance Scores for Predicted Adjacency Matrices
selgene	Select Top Expressed Genes from Single-Cell Data
stringdb_adjacency	Build Adjacency Matrices for Physical Interactions from STRING (POST API)
symmetrize	Symmetrize Adjacency Matrices in a SummarizedExperiment
toy_adj_matrix	Toy adjacency matrix for examples
toy_counts	Toy MultiAssayExperiment for Network Inference
zinb_simdata	Simulate Zero-Inflated Negative Binomial (ZINB) Count Matrices with Sequencing Depth