Welcome to genomeNLP's documentation!
=====================================

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  Copyright (c) 2022 <a href="https://orcid.org/0000-0002-9207-0385">Tyrone Chen <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-8797-3168">Navya Tyagi <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, Sarthak Chauhan, <a href="https://orcid.org/0000-0002-2296-2126">Anton Y. Peleg <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, and <a href="https://orcid.org/0000-0003-0181-6258">Sonika Tyagi <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>.

Code in this repository is provided under a `MIT license`_. This documentation is provided under a `CC-BY-3.0 AU license`_.

.. _MIT license: https://opensource.org/licenses/MIT

.. _CC-BY-3.0 AU license: https://creativecommons.org/licenses/by/3.0/au/

`Visit our lab website here.`_ Contact Sonika Tyagi at `sonika.tyagi@monash.edu`_.

.. _Visit our lab website here.: https://bioinformaticslab.erc.monash.edu/

.. _sonika.tyagi@monash.edu: mailto:sonika.tyagi@monash.edu

.. NOTE::

  `The main repository is on github`_ but also mirrored on gitlab. Please submit any issues to the main github repository only.

.. _The main repository is on github: https://github.com/tyronechen/genomenlp

.. toctree::
  :maxdepth: 3
  :caption: Contents:

  intro
  case_study_intro
  case_study_dna
  case_study_protein
  tokenise
  create_dataset_bio
  create_embedding
  sweep
  train_model
  cross_validate
  fit_powerlaw
  generate_synthetic
  interpret


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

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