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

**LENS** (Landscape of Effective Neoantigens Software) is a tumor antigen discovery workflow.

.. image::
   title_figure.png
   :width: 600

Instructions for installing **RAFT**, the Nextflow-based workflow manager that runs LENS, are available at :doc:`installing_raft`.

A **demonstration** of LENS can be run using the instructions at :doc:`demonstration`.

A **tutoral** for running LENS is available at :doc:`usage`.

An overview of **LENS outputs** is available at :doc:`outputs`.

A description of the **LENS report** can be found at :doc:`lens_report`.

**Frequently Asked Questions** and their answers can be found at :doc:`faq`.

Information regarding **technical details** of the workflow can be found at :doc:`technical`.

The **change log** is available at :doc:`changelog`.

The authors of RAFT can be **contacted** using:

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

Contents
--------

.. toctree::

   introduction
   installing_raft
   demonstration
   manifest
   usage
   outputs
   lens_report
   lenstools
   faq
   technical
   changelog