INDRA CoGEx modules reference
- INDRA CoGEx Apps
- INDRA CoGEx Knowledge Assembly (
indra_cogex.assembly
) - INDRA CoGEx Client
- Enrichment Analysis (
indra_cogex.client.enrichment
) - 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.query_dict()
Neo4jClient.query_dict_value_json()
Neo4jClient.query_nodes()
Neo4jClient.query_relations()
Neo4jClient.query_tx()
Neo4jClient.session
autoclient()
- 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_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_pubmeds()
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
)
- Enrichment Analysis (
- Indexing of The Database
- INDRA CoGEx Sources
- Source CLI (
indra_cogex.sources.cli
) - INDRA CoGEx Sources Processor (
indra_cogex.sources.processor
) - Bgee Processor (
indra_cogex.sources.bgee
) - cBioPortal Processor (
indra_cogex.sources.cbioportal
) - CellMarker Processor (
indra_cogex.sources.cellmarker
) - chembl Processor (
indra_cogex.sources.chembl
) - clinicaltrials Processor (
indra_cogex.sources.clinicaltrials
) - goa Processor (
indra_cogex.sources.goa
) - INDRA DB Processor (
indra_cogex.sources.indra_db
) - INDRA Ontology Processor (
indra_cogex.sources.indra_ontology
) - InterPro Processor (
indra_cogex.sources.interpro
) - Odinson Processor (
indra_cogex.sources.odinson
) - Pathways Processor (
indra_cogex.sources.pathways
) - PubMed Processor (
indra_cogex.sources.pubmed
) - Sider Processor (
indra_cogex.sources.sider
)
- Source CLI (
- INDRA CoGEx Representation (
indra_cogex.representation
)