Welcome to the LENS documentation!
===================================

**LENS** (Landscape of Effective Neoantigen Software) is a tumor antigen
discovery workflow capable of identifying potential therapeutic cancer
immunotherapy targets from seven antigen sources.

.. image::
   title_figure.png
   :width: 100%

The LENS manuscript is available `here <https://academic.oup.com/bioinformatics/article/39/6/btad322/7162685>`_. LENS can be cited as:

.. code-block:: text

   Vensko II SP, et al. LENS: Landscape of Effective Neoantigens Software. Bioinformatics. 2023;39(6):btad322. doi:10.1093/bioinformatics/btad322

.. note::

   **New to LENS?** Head to :doc:`quick_start` to install RAFT and run a
   demonstration in minutes.

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

   introduction
   quick_start

.. toctree::
   :caption: User Guide
   :maxdepth: 1

   running_lens
   accessing_and_reviewing_outputs
   interpreting_report
   faq

.. toctree::
   :caption: Reference
   :maxdepth: 1
   :hidden:

   manifest_specifications
   report_column_reference
   technical_details
   netmhc_setup
   troubleshooting
   lenstools
   module_test_status
   changelog

Contact
-------

The development team can be reached using:

  - Slack: https://join.slack.com/t/pirl-raft/shared_invite/zt-1y6mngjxf-VYLGMNiCFlXt9FabKcxw
  - E-mail: steven_vensko@med.unc.edu