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

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

bioconductor-massarray
======================

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

   Analytical Tools for MassArray Data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/MassArray.html
   :license: GPL (>=2)
   :recipe: /`bioconductor-massarray <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-massarray>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-massarray/meta.yaml>`_
   :links: biotools: :biotools:`massarray`, doi: :doi:`10.1093/bioinformatics/btp382`

   This package is designed for the import\, quality control\, analysis\, and visualization of methylation data generated using Sequenom\'s MassArray platform.  The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data\, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package.  Additionally\, automatic SNP\-detection can be used to flag potentially confounded data from specific CG sites.  Visualization includes barplots of methylation data as well as UCSC Genome Browser\-compatible BED tracks.  Multiple assays can be positionally combined for integrated analysis.


.. conda:package:: bioconductor-massarray

   |downloads_bioconductor-massarray| |docker_bioconductor-massarray|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.54.0-1</code>,  <code>1.54.0-0</code>,  <code>1.52.0-0</code>,  <code>1.50.0-0</code>,  <code>1.46.0-0</code>,  <code>1.44.0-0</code>,  <code>1.42.0-1</code>,  <code>1.42.0-0</code>,  <code>1.40.0-0</code>,  </span></summary>
      

      ``1.54.0-1``,  ``1.54.0-0``,  ``1.52.0-0``,  ``1.50.0-0``,  ``1.46.0-0``,  ``1.44.0-0``,  ``1.42.0-1``,  ``1.42.0-0``,  ``1.40.0-0``,  ``1.38.0-0``,  ``1.36.0-1``,  ``1.36.0-0``,  ``1.34.1-0``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends r-base: ``>=4.3,<4.4.0a0``
   :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-massarray

   and update with::

      mamba update bioconductor-massarray

  To create a new environment, run::

      mamba create --name myenvname bioconductor-massarray

  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-massarray:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-massarray";
        var versions = ["1.54.0","1.54.0","1.52.0","1.50.0","1.46.0"];
    </script>






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

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

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