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Welcome to the MacCoss Lab Proteomics Analysis Documentation!
=============================================================

These pages provide instructions for processing different kinds of proteomics data using fully-automated workflows on the Genome Sciences (GS) cluster. These workflows, written in Nextflow, automate the entire process--starting with the raw mass spectrometer data and ending with data visualization in tools like Limelight or Skyline.

.. toctree::
   :maxdepth: 2
   :caption: Analysis Workflows

   dda_comet
   dda_magnum
   dda_casanovo
   dia_analysis
   carafe

.. toctree::
   :maxdepth: 2
   :caption: Helper Guides

   credentials_limelight
   credentials_panorama
   ssh_access
   getting_help



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

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