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

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

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

Fix common invalidities in Statements (:py:mod:`indra.tools.fix_invalidities`)
------------------------------------------------------------------------------

.. automodule:: indra.tools.fix_invalidities
    :members:

Annotate websites with INDRA through hypothes.is (:py:mod:`indra.tools.hypothesis_annotator`)
---------------------------------------------------------------------------------------------

.. automodule:: indra.tools.hypothesis_annotator
    :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:


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

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

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

Fix common invalidities in Statements (:py:mod:`indra.tools.fix_invalidities`)
------------------------------------------------------------------------------

.. automodule:: indra.tools.fix_invalidities
    :members:

Analyze ontology graph for issues (:py:mod:`indra.tools.analyze_ontology`)
--------------------------------------------------------------------------

.. automodule:: indra.tools.analyze_ontology
    :members:

Annotate websites with INDRA through hypothes.is (:py:mod:`indra.tools.hypothesis_annotator`)
---------------------------------------------------------------------------------------------

.. automodule:: indra.tools.hypothesis_annotator
    :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:


Add ontology analysis to docs
Add ontology analysis to docs
