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   :caption: Contents:

   quickStart
   installation
   outputFormats
   visualisation
   examples
   troubleshooting
   releaseNotes


Overview
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ORILINX is a large language model built on DNABERT-2 to detect the location of replication origins in mammalian genomes.

ORILINX is under active development by the `Boemo Group <https://www.boemogroup.org/>`_ based in the `Department of Pathology, University of Cambridge <https://www.path.cam.ac.uk/>`_.  We aim to push regular updates and improvements and incorporating new functionality is an active area of our computational research.


Publications
------------

If you use ORILINX for your research, please cite our publication:

Pfuderer PL, Berkemeier F, Nassar J, Crisp A, Jaworski JJ, Moore J, Sale JE, Boemo MA. A genome language model for mapping DNA replication origins. bioRxiv 2026. [`Read on bioRxiv <https://doi.org/10.64898/2026.01.29.702604>`_]

Bugs, Questions, and Comments
-----------------------------

Should any bugs arise or if you have any questions about usage, please raise a `GitHub issue <https://github.com/Pfuderer/ORILINX/issues>`_. Your feedback is an important part of the development process. If you have comments or suggestions to improve the software or the documentation, please Email Michael Boemo at mb915@cam.ac.uk.