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

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

bioconductor-dmrseq
===================

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

   Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/dmrseq.html
   :license: MIT + file LICENSE
   :recipe: /`bioconductor-dmrseq <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-dmrseq>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-dmrseq/meta.yaml>`_

   This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution\, that can be implemented even when as few as two samples per population are available. Region\-level statistics are obtained by fitting a generalized least squares \(GLS\) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.


.. conda:package:: bioconductor-dmrseq

   |downloads_bioconductor-dmrseq| |docker_bioconductor-dmrseq|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  <code>1.10.0-1</code>,  <code>1.10.0-0</code>,  <code>1.8.0-0</code>,  <code>1.6.0-0</code>,  </span></summary>
      

      ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.9-0``,  ``1.2.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationhub: ``>=3.10.0,<3.11.0``
   :depends bioconductor-annotatr: ``>=1.28.0,<1.29.0``
   :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0``
   :depends bioconductor-bsseq: ``>=1.38.0,<1.39.0``
   :depends bioconductor-bumphunter: ``>=1.44.0,<1.45.0``
   :depends bioconductor-delayedmatrixstats: ``>=1.24.0,<1.25.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-ggplot2: 
   :depends r-locfit: 
   :depends r-matrixstats: 
   :depends r-nlme: 
   :depends r-outliers: 
   :depends r-rcolorbrewer: 
   :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-dmrseq

   and update with::

      mamba update bioconductor-dmrseq

  To create a new environment, run::

      mamba create --name myenvname bioconductor-dmrseq

  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-dmrseq:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-dmrseq";
        var versions = ["1.22.0","1.20.0","1.18.0","1.14.0","1.12.0"];
    </script>






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

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

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