Package index • scGraphVerse

Toy data

adj_truth: Toy adjacency matrix for examples

count_matrices: Toy list of SingleCellExperiment objects

Infer Networks

infer_networks(): Infer Gene Regulatory Networks from Expression Matrices

cutoff_adjacency(): Threshold Adjacency Matrices Based on Shuffled Network Quantiles

generate_adjacency(): Generate Adjacency Matrices from Gene Interaction Tables

earlyj(): Modify Cell Names and Combine Datasets

symmetrize(): Symmetrize a List of Square Matrices

Consensus & Evaluation

create_consensus(): Create a Consensus Adjacency Matrix from Multiple Networks

compare_consensus(): Compare Consensus and Reference Graphs or STRINGdb Networks

community_similarity(): Compare Community Assignments and Topological Properties

plotROC(): Plot ROC Curves for Inferred Networks

pscores(): Compute Performance Scores for Predicted Adjacency Matrices

Simulation & Visualization

zinb_simdata(): Simulate Zero-Inflated Negative Binomial (ZINB) Count Matrices with Sequencing Depth

plotg(): Visualize Graphs from Adjacency Matrices

Data and Utility Functions

download_Atlas(): Download and Load an RDS File from a URL

stringdb_adjacency(): Build Adjacency Matrices for Physical Interactions from STRING (POST API)

edge_mining(): Edge Mining of Gene Interactions Using PubMed

selgene(): Select Top Expressed Genes from Single-Cell Data

community_path(): Community Detection and Pathway Enrichment Analysis

init_py(): Initialize Python Environment for GRNBoost2