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

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

bioconductor-dmrcaller
======================

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

   Differentially Methylated Regions caller

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/DMRcaller.html
   :license: GPL-3
   :recipe: /`bioconductor-dmrcaller <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-dmrcaller>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-dmrcaller/meta.yaml>`_

   Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non\-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.


.. conda:package:: bioconductor-dmrcaller

   |downloads_bioconductor-dmrcaller| |docker_bioconductor-dmrcaller|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.34.0-0</code>,  <code>1.32.0-0</code>,  <code>1.30.0-1</code>,  <code>1.30.0-0</code>,  <code>1.26.0-2</code>,  <code>1.26.0-1</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-1</code>,  </span></summary>
      

      ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-1``,  ``1.30.0-0``,  ``1.26.0-2``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.14.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc-ng: ``>=12``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends libstdcxx-ng: ``>=12``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-betareg: 
   :depends r-rcpp: 
   :depends r-rcpproll: 
   :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-dmrcaller

   and update with::

      mamba update bioconductor-dmrcaller

  To create a new environment, run::

      mamba create --name myenvname bioconductor-dmrcaller

  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-dmrcaller:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-dmrcaller";
        var versions = ["1.34.0","1.32.0","1.30.0","1.30.0","1.26.0"];
    </script>






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

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

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