.. egrin2-tools documentation master file, created by
   sphinx-quickstart on Fri Oct 13 13:01:56 2017.
   You can adapt this file completely to your liking, but it should at least
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Welcome to egrin2-tools's documentation!
========================================

Utilities and scripts for generating, assembling, and querying EGRIN2.0 ensembles generated by cMonkey2 biclustering algorithm.



including running multiple cMonkey2 runs and postprocessing the cMonkey2 results is as follows:

  - Run ensemble of cMonkey2 runs
  - FIMO
  - Coding fractions
  - TOMTOM
  - Motif clustering
  - Corem discovery
  - Inferelator (TODO)

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   Introduction <introduction>
   Build <build>
   Build Tutorial <build_tutorial>
   Postprocessing <postprocessing>
   Assemble <assemble>
   Assemble Tutorial <assemble_tutorial>
   Query <query>
   Basic Mining Using agglom <basic_mining_agglom>
   Basic Mining Using coremFinder <basic_mining_coremfinder>
   Advanced Mining <advanced_mining>
   Plot Expression Tutorial <plot_expression_tutorial>


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`