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

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

bioconductor-methped
====================

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

   A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/MethPed.html
   :license: GPL-2
   :recipe: /`bioconductor-methped <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-methped>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-methped/meta.yaml>`_
   :links: biotools: :biotools:`methped`, doi: :doi:`10.1186/s13148-015-0103-3`

   Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim\, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy\-to\-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors.  The current version of MethPed can classify the following tumor diagnoses\/subgroups\: Diffuse Intrinsic Pontine Glioma \(DIPG\)\, Ependymoma\, Embryonal tumors with multilayered rosettes \(ETMR\)\, Glioblastoma \(GBM\)\, Medulloblastoma \(MB\) \- Group 3 \(MB\_Gr3\)\, Group 4 \(MB\_Gr3\)\, Group WNT \(MB\_WNT\)\, Group SHH \(MB\_SHH\) and Pilocytic Astrocytoma \(PiloAstro\).


.. conda:package:: bioconductor-methped

   |downloads_bioconductor-methped| |docker_bioconductor-methped|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.30.0-0</code>,  <code>1.28.0-0</code>,  <code>1.26.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-1</code>,  <code>1.18.0-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  </span></summary>
      

      ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.10.1-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-randomforest: 
   :requirements:

   .. 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-methped

   and update with::

      mamba update bioconductor-methped

  To create a new environment, run::

      mamba create --name myenvname bioconductor-methped

  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-methped:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-methped";
        var versions = ["1.30.0","1.28.0","1.26.0","1.22.0","1.20.0"];
    </script>






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

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

Link to this page
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