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

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

peptdeep
========

.. conda:recipe:: peptdeep
   :replaces_section_title:
   :noindex:

   The AlphaX deep learning framework for Proteomics

   :homepage: https://github.com/MannLabs/alphapeptdeep
   :documentation: https://alphapeptdeep.readthedocs.io/en/latest/
   
   :license: APACHE / Apache-2.0
   :recipe: /`peptdeep <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/peptdeep>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/peptdeep/meta.yaml>`_

   PeptDeep provides deep learning models for mass spectrometry\-based
   proteomics. It includes built\-in models for predicting retention time\,
   collision cross section\, and tandem mass spectra for peptides\, enabling
   users to generate predicted spectral libraries from protein sequences.



.. conda:package:: peptdeep

   |downloads_peptdeep| |docker_peptdeep|

   :versions:
      
      

      ``1.4.1-1``,  ``1.4.1-0``

      

   
   :depends alphabase: ``>=1.5.0``
   :depends alpharaw: ``>=0.2.0``
   :depends click: 
   :depends lxml: 
   :depends numba: 
   :depends numpy: ``<2``
   :depends pandas: ``<3.0``
   :depends psutil: 
   :depends pyteomics: 
   :depends python: ``>=3.8``
   :depends pytorch: 
   :depends scikit-learn: 
   :depends tqdm: 
   :depends transformers: 
   :requirements:

   :additional platforms:
      

   .. 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 peptdeep

   and update with::

      mamba update peptdeep

  To create a new environment, run::

      mamba create --name myenvname peptdeep

  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/peptdeep:<tag>

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


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


.. raw:: html

    <script>
        var package = "peptdeep";
        var versions = ["1.4.1","1.4.1"];
    </script>






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

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

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