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.tools.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:

The RAS Machine (:py:mod:`indra.tools.machine`)
-----------------------------------------------

.. automodule:: indra.tools.machine
    :members:

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

.. toctree::
   :maxdepth: 2

   reading/index


.. 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.tools.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:

The RAS Machine (:py:mod:`indra.tools.machine`)
-----------------------------------------------

.. automodule:: indra.tools.machine
    :members:

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

.. toctree::
   :maxdepth: 2

   reading/index


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

Remove old and removed sections from tools.
Remove old and removed sections from tools.
