indra_cogex
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INDRA CoGEx modules reference
indra_cogex
Index
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Index
Symbols
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A
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B
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C
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D
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E
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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W
Symbols
--all
indra_cogex-indexing command line option
--exist-ok
indra_cogex-indexing command line option
--index-evidence-nodes
indra_cogex-indexing command line option
--index-indra-relations
indra_cogex-indexing command line option
--index-nodes
indra_cogex-indexing command line option
A
add_node() (Neo4jClient method)
add_nodes() (Neo4jClient method)
(NodeAssembler method)
add_relations() (Neo4jClient method)
assemble_nodes() (NodeAssembler method)
autoclient() (in module indra_cogex.client.neo4j_client)
B
BgeeProcessor (class in indra_cogex.sources.bgee)
C
CcleCnaProcessor (class in indra_cogex.sources.cbioportal)
CcleDrugResponseProcessor (class in indra_cogex.sources.cbioportal)
CcleMutationsProcessor (class in indra_cogex.sources.cbioportal)
CellMarkerProcessor (class in indra_cogex.sources.cellmarker)
ChemblIndicationsProcessor (class in indra_cogex.sources.chembl)
cli() (Processor class method)
ClinicaltrialsProcessor (class in indra_cogex.sources.clinicaltrials)
close_session() (Neo4jClient method)
collect_gene_sets() (in module indra_cogex.client.enrichment.utils)
create_nodes() (Neo4jClient method)
create_single_property_node_index() (Neo4jClient method)
create_single_property_relationship_index() (Neo4jClient method)
create_tx() (Neo4jClient method)
D
DbProcessor (class in indra_cogex.sources.indra_db)
delete_all() (Neo4jClient method)
dump() (Processor method)
E
EvidenceProcessor (class in indra_cogex.sources.indra_db)
G
get_ag_ns_id() (in module indra_cogex.sources.indra_db)
get_aggregate_node() (NodeAssembler method)
get_all_relations() (Neo4jClient method)
get_cli() (Processor class method)
get_common_sources() (Neo4jClient method)
get_common_targets() (Neo4jClient method)
get_diseases_for_trial() (in module indra_cogex.client.queries)
get_drugs_for_side_effect() (in module indra_cogex.client.queries)
get_drugs_for_target() (in module indra_cogex.client.queries)
get_drugs_for_targets() (in module indra_cogex.client.queries)
get_drugs_for_trial() (in module indra_cogex.client.queries)
get_edge_counter() (in module indra_cogex.client.queries)
get_entity_to_regulators() (in module indra_cogex.client.enrichment.utils)
get_entity_to_targets() (in module indra_cogex.client.enrichment.utils)
get_evidences_for_mesh() (in module indra_cogex.client.queries)
get_evidences_for_stmt_hash() (in module indra_cogex.client.queries)
get_evidences_for_stmt_hashes() (in module indra_cogex.client.queries)
get_genes_for_go_term() (in module indra_cogex.client.queries)
get_genes_for_pathway() (in module indra_cogex.client.queries)
get_genes_in_tissue() (in module indra_cogex.client.queries)
get_go() (in module indra_cogex.client.enrichment.utils)
get_go_terms_for_gene() (in module indra_cogex.client.queries)
get_mesh_ids_for_pmid() (in module indra_cogex.client.queries)
get_mutated_genes() (in module indra_cogex.client.queries)
get_node_counter() (in module indra_cogex.client.queries)
get_nodes() (BgeeProcessor method)
(CcleCnaProcessor method)
(CcleDrugResponseProcessor method)
(CcleMutationsProcessor method)
(CellMarkerProcessor method)
(ChemblIndicationsProcessor method)
(ClinicaltrialsProcessor method)
(DbProcessor method)
(EvidenceProcessor method)
(GoaProcessor method)
(InterproProcessor method)
(OntologyProcessor method)
(Processor method)
get_ontology_child_terms() (in module indra_cogex.client.queries)
get_ontology_parent_terms() (in module indra_cogex.client.queries)
get_pathways_for_gene() (in module indra_cogex.client.queries)
get_phenotype_gene_sets() (in module indra_cogex.client.enrichment.utils)
get_pmids_for_mesh() (in module indra_cogex.client.queries)
get_predecessors() (Neo4jClient method)
get_property_from_relations() (Neo4jClient static method)
get_reactome() (in module indra_cogex.client.enrichment.utils)
get_relations() (BgeeProcessor method)
(CcleCnaProcessor method)
(CcleDrugResponseProcessor method)
(CcleMutationsProcessor method)
(CellMarkerProcessor method)
(ChemblIndicationsProcessor method)
(ClinicaltrialsProcessor method)
(DbProcessor method)
(EvidenceProcessor method)
(GoaProcessor method)
(InterproProcessor method)
(Neo4jClient method)
(OntologyProcessor method)
(Processor method)
get_schema_graph() (in module indra_cogex.client.queries)
get_session() (Neo4jClient method)
get_shared_pathways_for_genes() (in module indra_cogex.client.queries)
get_side_effects_for_drug() (in module indra_cogex.client.queries)
get_source_agents() (Neo4jClient method)
get_source_relations() (Neo4jClient method)
get_sources() (Neo4jClient method)
get_stmts_for_mesh() (in module indra_cogex.client.queries)
get_stmts_for_paper() (in module indra_cogex.client.queries)
get_stmts_for_pubmeds() (in module indra_cogex.client.queries)
get_stmts_for_stmt_hashes() (in module indra_cogex.client.queries)
get_stmts_meta_for_stmt_hashes() (in module indra_cogex.client.queries)
get_successors() (Neo4jClient method)
get_target_agents() (Neo4jClient method)
get_target_relations() (Neo4jClient method)
get_targets() (Neo4jClient method)
get_targets_for_drug() (in module indra_cogex.client.queries)
get_targets_for_drugs() (in module indra_cogex.client.queries)
get_tissues_for_gene() (in module indra_cogex.client.queries)
get_trials_for_disease() (in module indra_cogex.client.queries)
get_trials_for_drug() (in module indra_cogex.client.queries)
get_wikipathways() (in module indra_cogex.client.enrichment.utils)
go_ora() (in module indra_cogex.client.enrichment.discrete)
GoaProcessor (class in indra_cogex.sources.goa)
grounding() (Node method)
H
has_relation() (Neo4jClient method)
I
index_evidence_on_stmt_hash() (in module indra_cogex.indexing)
index_indra_rel_on_stmt_hash() (in module indra_cogex.indexing)
index_nodes_on_id() (in module indra_cogex.indexing)
indra_cogex-indexing command line option
--all
--exist-ok
--index-evidence-nodes
--index-indra-relations
--index-nodes
indra_cogex.apps.gla
module
indra_cogex.assembly
module
indra_cogex.client.enrichment.discrete
module
indra_cogex.client.enrichment.signed
module
indra_cogex.client.enrichment.utils
module
indra_cogex.client.neo4j_client
module
indra_cogex.client.queries
module
indra_cogex.client.subnetwork
module
indra_cogex.indexing
module
indra_cogex.representation
module
indra_cogex.sources.bgee
module
indra_cogex.sources.cbioportal
module
indra_cogex.sources.cellmarker
module
indra_cogex.sources.chembl
module
indra_cogex.sources.clinicaltrials
module
indra_cogex.sources.goa
module
indra_cogex.sources.indra_db
module
indra_cogex.sources.indra_ontology
module
indra_cogex.sources.interpro
module
indra_cogex.sources.processor
module
indra_downstream_ora() (in module indra_cogex.client.enrichment.discrete)
indra_mediated_subnetwork() (in module indra_cogex.client.subnetwork)
indra_stmts_from_relations() (in module indra_cogex.representation)
indra_subnetwork() (in module indra_cogex.client.subnetwork)
indra_subnetwork_go() (in module indra_cogex.client.subnetwork)
indra_subnetwork_relations() (in module indra_cogex.client.subnetwork)
indra_subnetwork_tissue() (in module indra_cogex.client.subnetwork)
indra_upstream_ora() (in module indra_cogex.client.enrichment.discrete)
InterproProcessor (class in indra_cogex.sources.interpro)
is_drug_target() (in module indra_cogex.client.queries)
is_gene_in_pathway() (in module indra_cogex.client.queries)
is_gene_in_tissue() (in module indra_cogex.client.queries)
is_gene_mutated() (in module indra_cogex.client.queries)
is_go_term_for_gene() (in module indra_cogex.client.queries)
is_side_effect_for_drug() (in module indra_cogex.client.queries)
isa_or_partof() (in module indra_cogex.client.queries)
L
load_goa() (in module indra_cogex.sources.goa)
M
main() (in module indra_cogex.client.enrichment.signed)
module
indra_cogex.apps.gla
indra_cogex.assembly
indra_cogex.client.enrichment.discrete
indra_cogex.client.enrichment.signed
indra_cogex.client.enrichment.utils
indra_cogex.client.neo4j_client
indra_cogex.client.queries
indra_cogex.client.subnetwork
indra_cogex.indexing
indra_cogex.representation
indra_cogex.sources.bgee
indra_cogex.sources.cbioportal
indra_cogex.sources.cellmarker
indra_cogex.sources.chembl
indra_cogex.sources.clinicaltrials
indra_cogex.sources.goa
indra_cogex.sources.indra_db
indra_cogex.sources.indra_ontology
indra_cogex.sources.interpro
indra_cogex.sources.processor
MOLECULE_SQL (in module indra_cogex.sources.chembl)
N
neo4j_to_node() (Neo4jClient static method)
neo4j_to_relation() (Neo4jClient class method)
neo4j_to_relations() (Neo4jClient static method)
Neo4jClient (class in indra_cogex.client.neo4j_client)
Node (class in indra_cogex.representation)
node_to_agent() (Neo4jClient static method)
NodeAssembler (class in indra_cogex.assembly)
norm_id() (in module indra_cogex.representation)
O
OntologyProcessor (class in indra_cogex.sources.indra_ontology)
P
phenotype_ora() (in module indra_cogex.client.enrichment.discrete)
Processor (class in indra_cogex.sources.processor)
Q
query_dict() (Neo4jClient method)
query_dict_value_json() (Neo4jClient method)
query_nodes() (Neo4jClient method)
query_relations() (Neo4jClient method)
query_tx() (Neo4jClient method)
R
reactome_ora() (in module indra_cogex.client.enrichment.discrete)
Relation (class in indra_cogex.representation)
reverse_causal_reasoning() (in module indra_cogex.client.enrichment.signed)
S
session (Neo4jClient attribute)
SQL (in module indra_cogex.sources.chembl)
standardized() (Node class method)
StatementJSONDecodeError
T
to_json() (Node method)
(Relation method)
W
wikipathways_ora() (in module indra_cogex.client.enrichment.discrete)
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