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

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

bioconductor-madseq
===================

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

   Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/MADSEQ.html
   :license: GPL(>=2)
   :recipe: /`bioconductor-madseq <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-madseq>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-madseq/meta.yaml>`_
   :links: biotools: :biotools:`madseq`, doi: :doi:`10.1101/142299`

   The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy\, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.


.. conda:package:: bioconductor-madseq

   |downloads_bioconductor-madseq| |docker_bioconductor-madseq|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.28.0-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-1</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  </span></summary>
      

      ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.6.1-0``,  ``1.4.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0``
   :depends bioconductor-bsgenome.hsapiens.ucsc.hg19: ``>=1.4.0,<1.5.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicalignments: ``>=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-preprocesscore: ``>=1.64.0,<1.65.0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends bioconductor-variantannotation: ``>=1.48.0,<1.49.0``
   :depends bioconductor-zlibbioc: ``>=1.48.0,<1.49.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-coda: 
   :depends r-rjags: ``>=4.6``
   :depends r-vcfr: 
   :depends r-vgam: 
   :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-madseq

   and update with::

      mamba update bioconductor-madseq

  To create a new environment, run::

      mamba create --name myenvname bioconductor-madseq

  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-madseq:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-madseq";
        var versions = ["1.28.0","1.26.0","1.24.0","1.20.0","1.18.0"];
    </script>






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

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

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