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:

Tool Sets
---------

.. toctree::
   :maxdepth: 2

   reading/index
   machine/index

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:

Tool Sets
---------

.. toctree::
   :maxdepth: 2

   reading/index
   reading/CLIs
   machine/index

Add CLIs to tools docs tree.
Add CLIs to tools docs tree.
