Tools (:py:mod:`indra.tools`)
=============================

Run all assembly components in a pipeline (:py:mod:`indra.preassembler.assemble_corpus`)
----------------------------------------------------------------------------------------

.. automodule:: indra.tools.assemble_corpus
    :members:

Build a network from a gene list (:py:mod:`indra.tools.gene_network`)
---------------------------------------------------------------------

.. automodule:: indra.tools.gene_network
    :members:

Build an executable model from a fragment of a large network (:py:mod:`indra.executable_subnetwork`)
----------------------------------------------------------------------------------------------------

.. automodule:: indra.tools.executable_subnetwork
    :members:

Build a model incrementally over time (:py:mod:`indra.tools.incremental_model`)
-------------------------------------------------------------------------------

.. automodule:: indra.tools.incremental_model
    :members:

High-throughput reading tools (:py:mod:`indra.tools.reading`)
-------------------------------------------------------------

.. automodule:: indra.tools.reading
    :members:

Scoring INDRA Statements manually (:py:mod:`indra.tools.stmt_scoring`)
----------------------------------------------------------------------

.. automodule:: indra.tools.stmt_scoring
    :members:

Generate English language questions on linked mechanisms (:py:mod:`indra.tools.mechlinker_queries`)
---------------------------------------------------------------------------------------------------

.. automodule:: indra.tools.mechlinker_queries
    :members:

Tools (:py:mod:`indra.tools`)
=============================

Run assembly components in a pipeline (:py:mod:`indra.tools.assemble_corpus`)
----------------------------------------------------------------------------------------

.. automodule:: indra.tools.assemble_corpus
    :members:

Build a network from a gene list (:py:mod:`indra.tools.gene_network`)
---------------------------------------------------------------------

.. automodule:: indra.tools.gene_network
    :members:

Build an executable model from a fragment of a large network (:py:mod:`indra.executable_subnetwork`)
----------------------------------------------------------------------------------------------------

.. automodule:: indra.tools.executable_subnetwork
    :members:

Build a model incrementally over time (:py:mod:`indra.tools.incremental_model`)
-------------------------------------------------------------------------------

.. automodule:: indra.tools.incremental_model
    :members:

High-throughput reading tools (:py:mod:`indra.tools.reading`)
-------------------------------------------------------------

.. automodule:: indra.tools.reading
    :members:

Scoring INDRA Statements manually (:py:mod:`indra.tools.stmt_scoring`)
----------------------------------------------------------------------

.. automodule:: indra.tools.stmt_scoring
    :members:

Generate English language questions on linked mechanisms (:py:mod:`indra.tools.mechlinker_queries`)
---------------------------------------------------------------------------------------------------

.. automodule:: indra.tools.mechlinker_queries
    :members:

Fix documentation link for assemble corpus
Fix documentation link for assemble corpus
