INDRA modules referenceΒΆ
- INDRA Statements (
indra.statements) - Processors for model input (
indra.sources) - Database clients (
indra.databases)- HGNC client (
indra.hgnc_client) - Uniprot client (
indra.databases.uniprot_client) - ChEBI client (
indra.databases.chebi_client) - BioGRID client (
indra.databases.biogrid_client) - Cell type context client (
indra.databases.context_client) - Network relevance client (
indra.databases.relevance_client) - NDEx client (
indra.databases.ndex_client) - cBio portal client (
indra.databases.cbio_client)
- HGNC client (
- Literature clients (
indra.literature) - Preassembly (
indra.preassembler) - Belief Engine (
indra.belief) - Mechanism Linker (
indra.mechlinker) - Assemblers of model output (
indra.assemblers)- Executable PySB models (
indra.assemblers.pysb_assembler) - Cytoscape networks (
indra.assemblers.cx_assembler) - Natural language (
indra.assemblers.english_assembler) - Node-edge graphs (
indra.assemblers.graph_assembler) - SIF / Boolean networks (
indra.assemblers.sif_assembler) - MITRE “index cards” (
indra.assemblers.index_card_assembler) - SBGN output (
indra.assemblers.sbgn_assembler)
- Executable PySB models (
- Explanation (
indra.explanation) - Tools (
indra.tools)- Run assembly components in a pipeline (
indra.tools.assemble_corpus) - Build a network from a gene list (
indra.tools.gene_network) - Build an executable model from a fragment of a large network (
indra.tools.executable_subnetwork) - Build a model incrementally over time (
indra.tools.incremental_model) - High-throughput reading tools (
indra.tools.reading) - Scoring INDRA Statements manually (
indra.tools.stmt_scoring) - Generate English language questions on linked mechanisms (
indra.tools.mechlinker_queries)
- Run assembly components in a pipeline (