.. msproteomicstools documentation master file, created by
   sphinx-quickstart on Wed Aug 27 17:12:45 2014.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to msproteomicstools's documentation!
=============================================

`msproteomicstools` is a Python library that can be used in LC-MS/MS based
proteomics. It features a core library called `msproteomicstoolslib` and several
associated executable scripts that use the library as well as a GUI for
visualizing chromatograms, specifically output from `OpenSWATH
<http://openswath.org/>`_.

For questions, bug reports and contributions, please visit the official `GitHub page
<https://github.com/msproteomicstools/msproteomicstools>`_.

Contents of the library:

.. toctree::
    :maxdepth: 2

    msproteomicstoolslib.algorithms
    msproteomicstoolslib.math
    msproteomicstoolslib.data_structures
    msproteomicstoolslib.format
    msproteomicstoolslib.cython

Contents of the GUI code:

.. toctree::
    :maxdepth: 3

    tapir

Contents of the executables:

.. toctree::
    :maxdepth: 2

    analysis.alignment

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

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