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

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

bioconductor-methylaid
======================

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

   Visual and interactive quality control of large Illumina DNA Methylation array data sets

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/MethylAid.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-methylaid <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-methylaid>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-methylaid/meta.yaml>`_

   A visual and interactive web application using RStudio\'s shiny package. Bad quality samples are detected using sample\-dependent and sample\-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore\, the impact of any batch effect provided by the user can be explored.


.. conda:package:: bioconductor-methylaid

   |downloads_bioconductor-methylaid| |docker_bioconductor-methylaid|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.36.0-0</code>,  <code>1.34.0-0</code>,  <code>1.32.0-0</code>,  <code>1.28.0-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-1</code>,  <code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.0-0</code>,  </span></summary>
      

      ``1.36.0-0``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-1``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.16.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0``
   :depends bioconductor-minfi: ``>=1.48.0,<1.49.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-ggplot2: 
   :depends r-gridbase: 
   :depends r-hexbin: 
   :depends r-matrixstats: 
   :depends r-rcolorbrewer: 
   :depends r-shiny: 
   :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-methylaid

   and update with::

      mamba update bioconductor-methylaid

  To create a new environment, run::

      mamba create --name myenvname bioconductor-methylaid

  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-methylaid:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-methylaid";
        var versions = ["1.36.0","1.34.0","1.32.0","1.28.0","1.26.0"];
    </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-methylaid/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-methylaid/README.html