INDRA CoGEx Client

The INDRA CoGEx Client.

• Enrichment Analysis (indra_cogex.client.enrichment)
  • Continuous Gene Enrichment Analysis (indra_cogex.client.enrichment.continuous)
  • Discrete Gene Enrichment Analysis (indra_cogex.client.enrichment.discrete)
    • go_ora()
    • indra_downstream_ora()
    • indra_upstream_ora()
    • phenotype_ora()
    • reactome_ora()
    • wikipathways_ora()
  • Signed Gene Enrichment Analysis (indra_cogex.client.enrichment.signed)
    • main()
    • reverse_causal_reasoning()
  • Gene Enrichment Analysis Utilities (indra_cogex.client.enrichment.utils)
    • collect_gene_sets()
    • get_entity_to_regulators()
    • get_entity_to_targets()
    • get_go()
    • get_phenotype_gene_sets()
    • get_reactome()
    • get_wikipathways()
• Neo4j Client (indra_cogex.client.neo4j_client)
  • Neo4jClient
    • Neo4jClient.add_node()
    • Neo4jClient.add_nodes()
    • Neo4jClient.add_relations()
    • Neo4jClient.close_session()
    • Neo4jClient.create_nodes()
    • Neo4jClient.create_single_property_node_index()
    • Neo4jClient.create_single_property_relationship_index()
    • Neo4jClient.create_tx()
    • Neo4jClient.delete_all()
    • Neo4jClient.get_all_relations()
    • Neo4jClient.get_common_sources()
    • Neo4jClient.get_common_targets()
    • Neo4jClient.get_predecessors()
    • Neo4jClient.get_property_from_relations()
    • Neo4jClient.get_relations()
    • Neo4jClient.get_session()
    • Neo4jClient.get_source_agents()
    • Neo4jClient.get_source_relations()
    • Neo4jClient.get_sources()
    • Neo4jClient.get_successors()
    • Neo4jClient.get_target_agents()
    • Neo4jClient.get_target_relations()
    • Neo4jClient.get_targets()
    • Neo4jClient.has_relation()
    • Neo4jClient.neo4j_to_node()
    • Neo4jClient.neo4j_to_relation()
    • Neo4jClient.neo4j_to_relations()
    • Neo4jClient.node_to_agent()
    • Neo4jClient.ping()
    • Neo4jClient.query_dict()
    • Neo4jClient.query_dict_value_json()
    • Neo4jClient.query_nodes()
    • Neo4jClient.query_relations()
    • Neo4jClient.query_tx()
    • Neo4jClient.session
  • autoclient()
  • process_identifier()
• The INDRA CoGEx Neo4j Client (indra_cogex.client.queries)
  • get_diseases_for_trial()
  • get_drugs_for_side_effect()
  • get_drugs_for_target()
  • get_drugs_for_targets()
  • get_drugs_for_trial()
  • get_edge_counter()
  • get_evidences_for_mesh()
  • get_evidences_for_stmt_hash()
  • get_evidences_for_stmt_hashes()
  • get_genes_for_go_term()
  • get_genes_for_pathway()
  • get_genes_in_tissue()
  • get_go_terms_for_gene()
  • get_mesh_ids_for_pmid()
  • get_mesh_ids_for_pmids()
  • get_mutated_genes()
  • get_node_counter()
  • get_ontology_child_terms()
  • get_ontology_parent_terms()
  • get_pathways_for_gene()
  • get_pmids_for_mesh()
  • get_schema_graph()
  • get_shared_pathways_for_genes()
  • get_side_effects_for_drug()
  • get_stmts_for_mesh()
  • get_stmts_for_paper()
  • get_stmts_for_pmids()
  • get_stmts_for_stmt_hashes()
  • get_stmts_meta_for_stmt_hashes()
  • get_targets_for_drug()
  • get_targets_for_drugs()
  • get_tissues_for_gene()
  • get_trials_for_disease()
  • get_trials_for_drug()
  • is_drug_target()
  • is_gene_in_pathway()
  • is_gene_in_tissue()
  • is_gene_mutated()
  • is_go_term_for_gene()
  • is_side_effect_for_drug()
  • isa_or_partof()
• Subnetwork Client (indra_cogex.client.subnetwork)
  • indra_mediated_subnetwork()
  • indra_subnetwork()
  • indra_subnetwork_go()
  • indra_subnetwork_relations()
  • indra_subnetwork_tissue()