.. PyProphet documentation master file

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PyProphet
=========

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PyProphet is a Python package designed for scoring and post-processing of DIA-MS data, particularly in the context of OpenSWATH and related workflows. It provides tools for scoring, inference of levels context, and exporting results in various formats. For more information on the general usage of pyprophet, consult the `OpenSWATH website <http://openswath.org/en/latest/>`_.

.. toctree::
   :maxdepth: 2

   user_guide/index.rst
   file_formats
   cli
   api/index.rst