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

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

bioconductor-methylumi
======================

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

   Handle Illumina methylation data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/methylumi.html
   :license: GPL-2
   :recipe: /`bioconductor-methylumi <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-methylumi>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-methylumi/meta.yaml>`_
   :links: biotools: :biotools:`methylumi`, doi: :doi:`10.1186/1471-2164-14-293`

   This package provides classes for holding and manipulating Illumina methylation data.  Based on eSet\, it can contain MIAME information\, sample information\, feature information\, and multiple matrices of data.  An \"intelligent\" import function\, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization\, background correction\, and quality control features for GoldenGate\, Infinium\, and Infinium HD arrays are also included.


.. conda:package:: bioconductor-methylumi

   |downloads_bioconductor-methylumi| |docker_bioconductor-methylumi|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.48.0-0</code>,  <code>2.46.0-0</code>,  <code>2.44.0-0</code>,  <code>2.40.1-0</code>,  <code>2.38.0-0</code>,  <code>2.36.0-1</code>,  <code>2.36.0-0</code>,  <code>2.34.0-0</code>,  <code>2.32.0-0</code>,  </span></summary>
      

      ``2.48.0-0``,  ``2.46.0-0``,  ``2.44.0-0``,  ``2.40.1-0``,  ``2.38.0-0``,  ``2.36.0-1``,  ``2.36.0-0``,  ``2.34.0-0``,  ``2.32.0-0``,  ``2.30.0-1``,  ``2.28.0-0``,  ``2.26.0-0``,  ``2.24.1-0``,  ``2.22.0-1``,  ``2.22.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotate: ``>=1.80.0,<1.81.0``
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-fdb.infiniummethylation.hg19: ``>=2.2.0,<2.3.0``
   :depends bioconductor-genefilter: ``>=1.84.0,<1.85.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-illuminaio: ``>=0.44.0,<0.45.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-minfi: ``>=1.48.0,<1.49.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-ggplot2: 
   :depends r-lattice: 
   :depends r-matrixstats: 
   :depends r-reshape2: 
   :depends r-scales: 
   :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-methylumi

   and update with::

      mamba update bioconductor-methylumi

  To create a new environment, run::

      mamba create --name myenvname bioconductor-methylumi

  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-methylumi:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-methylumi";
        var versions = ["2.48.0","2.46.0","2.44.0","2.40.1","2.38.0"];
    </script>






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

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

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