OICR Genome Sequence Informatics documentation
==============================================

GSI is a team of bioinformaticians and software developers at `Ontario Institute for Cancer Research`_ that develop, maintain, and operate the core analysis infrastructure, analyze genomic data produced at the institute, and support collaborators and researchers with their bioinformatics analysis. To support these activities, we have developed a large suite of open-source software that can be found under our Github organizations: `oicr-gsi`_ and `miso-lims`_.


.. _Ontario Institute for Cancer Research: https://oicr.on.ca

.. _oicr-gsi : https://github.com/oicr-gsi

.. _miso-lims : https://github.com/miso-lims


Contact us
-----------

Contact us through the Github issue tracker on any project.



.. toctree::
   :maxdepth: 1
   :caption: Accredited Pipelines

   informatics-pipelines/informatics-pipelines
   informatics-pipelines/assays
   
.. toctree::
   :maxdepth: 1
   :caption: Data Review and Reporting

   data-review-reporting/data-review-and-reporting
   data-review-reporting/report-tips


.. In most cases, we can use Intersphinx to link between the main project and the subproject
.. But not in toctree. For some reason.

.. toctree::
   :maxdepth: 1
   :caption: Research Use Only Pipelines

   ruo-pipelines/ruo-assays

.. toctree::
   :maxdepth: 1
   :caption: Software

   Requisition System <https://oicr-gsi.readthedocs.io/projects/requisition-system/stable>
   infrastructure

+----------------+----------------------+
| **Change Log** | `Github commit log`_ |
+----------------+----------------------+

.. _Github commit log : https://github.com/oicr-gsi/oicr-gsi/commits/main/source/index.rst