PEN-COMPARE Documentation
==========================

**PEN-COMPARE** is the capstone of the PEN-STACK framework — a hierarchical certification
system that classifies genome editors as TRUE_WRITER, PROBABLE_WRITER, EMERGING_WRITER,
or NOT_WRITER using five pre-registered gates (v3.2).

.. toctree::
   :maxdepth: 2
   :caption: Getting Started

   installation
   quickstart

.. toctree::
   :maxdepth: 2
   :caption: Framework

   framework/gates
   framework/tier_ladder
   MODEL_CARD

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   api/core
   api/triangulation
   api/rag
   api/server

.. toctree::
   :maxdepth: 1
   :caption: Results

   results/preregistration
   results/sensitivity
   results/triangulation

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

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