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

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

bioconductor-cocoa
==================

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

   Coordinate Covariation Analysis

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

   COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal\, such as DNA methylation and chromatin accessibility data. To describe the method on a high level\, COCOA quantifies inter\-sample variation with either a supervised or unsupervised technique then uses a database of \"region sets\" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation\, for instance transcription factor \(TF\) binding regions\, histone modification regions\, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.


.. conda:package:: bioconductor-cocoa

   |downloads_bioconductor-cocoa| |docker_bioconductor-cocoa|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.16.0-0</code>,  <code>2.14.0-0</code>,  <code>2.12.0-0</code>,  <code>2.8.0-0</code>,  <code>2.6.0-0</code>,  <code>2.4.0-1</code>,  <code>2.4.0-0</code>,  <code>2.2.0-0</code>,  <code>2.0.0-0</code>,  </span></summary>
      

      ``2.16.0-0``,  ``2.14.0-0``,  ``2.12.0-0``,  ``2.8.0-0``,  ``2.6.0-0``,  ``2.4.0-1``,  ``2.4.0-0``,  ``2.2.0-0``,  ``2.0.0-0``,  ``1.2.0-1``,  ``1.0.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-mira: ``>=1.24.0,<1.25.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-fitdistrplus: 
   :depends r-ggplot2: 
   :depends r-simplecache: 
   :depends r-tidyr: 
   :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-cocoa

   and update with::

      mamba update bioconductor-cocoa

  To create a new environment, run::

      mamba create --name myenvname bioconductor-cocoa

  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-cocoa:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-cocoa";
        var versions = ["2.16.0","2.14.0","2.12.0","2.8.0","2.6.0"];
    </script>






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-----------------

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

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