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 (