.. GrapHiC documentation master file, created by
   sphinx-quickstart on Mon Jun  8 18:43:36 2020.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to GrapHiC's documentation!
====================================
This package provides 
    * functionality for producing graph based represenations of 3D chromatin configurations from Hi-C data
    * functionality for integrating 1D epigenetic datatracks with Hi-C graph representations

.. note::
   This is an early-stage project and a lot more documentation and functionality is planned to be included. If you are a structural biologist or machine learning researcher in computational biology, my inbox is always open (dh486@cam.ac.uk)

.. toctree::
   :glob:
   :maxdepth: 1
   :caption: Getting Started:

   getting_started/installation
   getting_started/introduction
   license

.. toctree::
   :glob:
   :maxdepth: 2
   :caption: Package Reference:
   
   modules/Datatrack_creation
   modules/Graph_creation

.. modules/GrapHiC.graph_creation
   modules/GrapHiC.datatrack_creation
   modules/GrapHiC.utils.dtrack_utils
   modules/GrapHiC.utils.Datatrack
   modules/GrapHiC.utils.parse_cooler
   modules/GrapHiC.layers.GATEConv



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

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