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

.. title:: Package Recipe 'bioconductor-proteingymr'
.. highlight: bash

bioconductor-proteingymr
========================

.. conda:recipe:: bioconductor-proteingymr
   :replaces_section_title:
   :noindex:

   Programmatic access to ProteinGym datasets in R\/Bioconductor

   :homepage: https://bioconductor.org/packages/3.20/data/experiment/html/ProteinGymR.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-proteingymr <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-proteingymr>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-proteingymr/meta.yaml>`_

   The ProteinGymR package provides analysis\-ready data resources from ProteinGym\, generated by Notin et al.\, 2023. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. Deep mutational scanning \(DMS\) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins\, 2. AlphaMissense pathogenicity scores for \~1.6 M substitutions in the ProteinGym DMS data\, and 3. five performance metrics for 62 variant prediction models in a zero\-shot setting.


.. conda:package:: bioconductor-proteingymr

   |downloads_bioconductor-proteingymr| |docker_bioconductor-proteingymr|

   :versions:
      
      

      

      

   
   :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 bioconductor-proteingymr

   and update with::

      mamba update bioconductor-proteingymr

  To create a new environment, run::

      mamba create --name myenvname bioconductor-proteingymr

  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/bioconductor-proteingymr:<tag>

   (see `bioconductor-proteingymr/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "bioconductor-proteingymr";
        var versions = [];
    </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/bioconductor-proteingymr/README.html)

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