.. meta::
   :description: GPSW is a tool for analysing Global Protein Stability Profiling data.
   :keywords: Snakemake, bioinformatics, protein stability

.. figure:: _static/gpsw_logo9.png
   :width: 150px
   :align: center
   :name: gpsw_logo
   :alt: GPSW logo

==================
GPSW documentation
==================

**Version**: |version|

Description
===========

:mod:`GPSW` is a Python package for analysing Global Protein Stability Profiling data as described in `Koren et al. Cell 2018 <https://pubmed.ncbi.nlm.nih.gov/29779948/>`_ and `Timms et al. Science 2019 <https://pubmed.ncbi.nlm.nih.gov/31273098/>`_. It employs the `Snakemake <https://snakemake.readthedocs.io/>`_ workflow management system to provide a reproducible and scalable analysis workflow.


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   .. grid-item-card:: Background
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      The background section provides an overview of the Global Protein Stability Profiling (GPS) method and the output of the *GPSW* workflow.

      +++

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         To the background guides

   .. grid-item-card::  User guide
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      The user guide provides in-depth information on how to install and use *GPSW*.

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         To the user guide

   .. grid-item-card::  About GPSW
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      Information about the GPSW project, its authors, and how to cite it.

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         To the about section

   .. grid-item-card::  Report issues
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      Saw a typo in the documentation? Want to improve
      existing functionalities? The contributing guidelines will guide
      you through the process of improving GPSW.

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      .. button-ref:: report_issues
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         To the issues guide


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   background
   user_guide
   about
   report_issues

.. toctree::
   :hidden:

   Changelog <https://github.com/niekwit/gps-orfeome/releases>

Quick Start
===========

To install `GPSW`, you can use `conda`:


::

   $ conda install -c bioconda gpsw

To download the workflow code:


::

   $ gpsw fetch

Configure your analysis in `config/config.yml`, place your sequencing data in `reads`, and provide ORF metadata in a csv file in `resources`. Then run the workflow with:


::

   $ gpsw run