Package index • tkoi

Main Functions

Core methods for network-based transcriptomic analysis

run_tkoi(): Run tKOI Analysis

run_gene_enrichment(): Run Gene Enrichment and Compare with TKOI Data

get_neighboring_nodes(): Retrieve Neighboring Nodes in a Knowledge Graph

make_gene_exploration_plot(): Create Gene Exploration Plot

export_gene_exploration_data(): Export Gene Exploration Data

export_network_summary_statistics(): Export Network Summary Statistics from tKOI Result

visualize_topn(): Visualize Top Network Enrichment Statistics

plot_network(): Plot a Local Network Around a Target Node from tKOI Results

compute_network_enrichment(): Compute Z-Score and P-Value for Node Pagerank

Data and Annotations

Annotation datasets used for node interpretation

tkoi_net: Human-Specific Heterogeneous Network

anatomy_annotation: Anatomical Entity Annotations from UBERON

celltype_annotation: Cell Type Ontology Annotations (CL)

clinicallab_annotation: Clinical Laboratory Measurement Annotations (LOINC)

complex_annotation: Protein and Molecular Complex Annotations

compound_annotation: Chemical Compound Annotations

disease_annotation: Disease Ontology (DO) Annotations

ec_annotation: Enzyme Commission (EC) Number Annotations

go_annotation: Gene Ontology (GO) Term Annotations

mirna_annotation: Human miRNA Annotations (miRBase-style)

pathway_annotation: Pathway Annotations (WikiPathways)

protein_annotation: Protein Annotations (UniProt-Based)

proteindomain_annotation: Protein Domain Annotations (Pfam)

proteinfamily_annotation: Protein Family Annotations (Pfam Clans)

pwgroup_annotation: Pathway Group Annotations (Reactome Interaction Sets)

reaction_annotation: Biochemical Reaction Annotations (KEGG-Based)

genes: Gene Metadata

human_metabolites: human_metabolites: Parsed Human Metabolite Metadata from HMDB