Package index • inferCSN

Inferring cell-specific gene regulatory network

inferCSN-package: Inferring Cell-Specific Gene Regulatory Network

infercsn_logo(): The logo of inferCSN

inferCSN(): inferring cell-type specific gene regulatory network

Network processing

network_sift(): Sifting network

weight_sift(): Weight sift

Network evaluation

calculate_metrics(): Calculate Network Prediction Performance Metrics

calculate_accuracy(): Calculate Accuracy

calculate_auc(): Calculate AUC Metrics

calculate_auroc(): Calculate AUROC Metric

calculate_auprc(): Calculate AUPRC Metric

calculate_precision(): Calculate Precision Metric

calculate_recall(): Calculate Recall Metric

calculate_f1(): Calculate F1 Score

calculate_si(): Calculate Set Intersection

calculate_ji(): Calculate Jaccard Index

Network visualization

plot_contrast_networks(): Plot contrast networks

plot_dynamic_networks(): Plot dynamic networks

plot_network_heatmap(): Plot network heatmap

plot_static_networks(): Plot dynamic networks

Plotting functions

plot_coefficient(): Plot coefficients

plot_coefficients(): Plot coefficients for multiple targets

plot_edges_comparison(): Network Edge Comparison Visualization

plot_embedding(): Plot embedding

plot_histogram(): Plot histogram

plot_scatter(): Plot expression data in a scatter plot

Calculate gene rank

calculate_gene_rank(): Rank TFs and genes in network

Sparse regression model

single_network(): Construct network for single target gene

fit_srm(): Sparse regression model

Utils functions

filter_sort_matrix(): Filter and sort matrix

meta_cells(): Detection of metacells from single-cell gene expression matrix

network_format(): Format network table

print(<infercsn_logo>): Print logo

subsampling(): Subsampling function

Example data

example_matrix: Example matrix data

example_meta_data: Example meta data

example_ground_truth: Example ground truth data