:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'pyprophet'
.. highlight: bash

pyprophet
=========

.. conda:recipe:: pyprophet
   :replaces_section_title:
   :noindex:

   PyProphet\: Semi\-supervised learning and scoring of OpenSWATH results.

   :homepage: https://github.com/PyProphet/pyprophet
   :documentation: https://openswath.org/en/latest
   
   :license: BSD / BSD-3-Clause
   :recipe: /`pyprophet <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pyprophet>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pyprophet/meta.yaml>`_
   :links: doi: :doi:`10.1038/nmeth.1584`

   


.. conda:package:: pyprophet

   |downloads_pyprophet| |docker_pyprophet|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>3.0.5-0</code>,  <code>3.0.4-0</code>,  <code>3.0.3-0</code>,  <code>3.0.2-0</code>,  <code>3.0.1-0</code>,  <code>2.2.5-4</code>,  <code>2.2.5-3</code>,  <code>2.2.5-1</code>,  <code>2.2.5-0</code>,  </span></summary>
      

      ``3.0.5-0``,  ``3.0.4-0``,  ``3.0.3-0``,  ``3.0.2-0``,  ``3.0.1-0``,  ``2.2.5-4``,  ``2.2.5-3``,  ``2.2.5-1``,  ``2.2.5-0``,  ``2.2.4-0``,  ``2.2.3-0``,  ``2.1.12-0``,  ``2.1.11-0``,  ``2.1.10-2``,  ``2.1.10-1``,  ``2.1.10-0``,  ``2.1.6-0``,  ``2.1.5-1``,  ``2.1.5-0``,  ``2.1.4-0``,  ``2.1.3-0``,  ``0.24.1-1``,  ``0.24.1-0``,  ``0.22.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends _openmp_mutex: ``>=4.5``
   :depends click: 
   :depends libgcc: ``>=13``
   :depends libgomp: 
   :depends loguru: 
   :depends lxml: 
   :depends numexpr: ``2.10.2``
   :depends numpy: ``2.0.2``
   :depends numpy: ``>=1.19,<3``
   :depends pandas: ``>=2.0``
   :depends polars: 
   :depends psutil: 
   :depends pyarrow: 
   :depends pyopenms: 
   :depends pypdf: 
   :depends python: ``>=3.10,<3.11.0a0``
   :depends python-duckdb: 
   :depends python_abi: ``3.10.* *_cp310``
   :depends scikit-learn: ``>=1.5``
   :depends scipy: 
   :depends seaborn-base: 
   :depends statsmodels: ``>=0.8.0``
   :depends tabulate: 
   :depends typing-extensions: 
   :depends xgboost: 
   :requirements:

   :additional platforms:
      
      .. raw:: html

         <span class="additional-platforms"><code>linux-aarch64</code>,  <code>osx-arm64</code></span>
      

   .. rubric:: Installation

  You need a conda-compatible package manager
  (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
  and the Bioconda channel already activated (see :ref:`set-up-channels`).

  While any of above package managers is fine, it is currently recommended to use either
  micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ for installation instructions).
  We will show all commands using mamba below, but the arguments are the same for the two
  others.

  Given that you already have a conda environment in which you want to have this package, install with::

      mamba install pyprophet

   and update with::

      mamba update pyprophet

  To create a new environment, run::

      mamba create --name myenvname pyprophet

  with ``myenvname`` being a reasonable name for the environment
  (see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).

  Alternatively, use the docker container::

      docker pull quay.io/biocontainers/pyprophet:<tag>

   (see `pyprophet/tags`_ for valid values for ``<tag>``)


.. |downloads_pyprophet| image:: https://img.shields.io/conda/dn/bioconda/pyprophet.svg?style=flat
   :target: https://anaconda.org/bioconda/pyprophet
   :alt:   (downloads)
.. |docker_pyprophet| image:: https://quay.io/repository/biocontainers/pyprophet/status
   :target: https://quay.io/repository/biocontainers/pyprophet
.. _`pyprophet/tags`: https://quay.io/repository/biocontainers/pyprophet?tab=tags


.. raw:: html

    <script>
        var package = "pyprophet";
        var versions = ["3.0.5","3.0.4","3.0.3","3.0.2","3.0.1"];
    </script>






Download stats
-----------------

.. raw:: html
    :file: ../../templates/package_dashboard.html

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pyprophet/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/pyprophet/README.html