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

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

bioconductor-vegamc
===================

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

   VegaMC\: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/VegaMC.html
   :license: GPL-2
   :recipe: /`bioconductor-vegamc <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-vegamc>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-vegamc/meta.yaml>`_
   :links: biotools: :biotools:`vegamc`, doi: :doi:`10.1093/bioinformatics/bts453`

   This package enables the detection of driver chromosomal imbalances including loss of heterozygosity \(LOH\) from array comparative genomic hybridization \(aCGH\) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition\, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes\, the link to the respective Ensembl gene web page is reported.


.. conda:package:: bioconductor-vegamc

   |downloads_bioconductor-vegamc| |docker_bioconductor-vegamc|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>3.40.0-0</code>,  <code>3.38.0-0</code>,  <code>3.36.0-1</code>,  <code>3.36.0-0</code>,  <code>3.32.0-2</code>,  <code>3.32.0-1</code>,  <code>3.32.0-0</code>,  <code>3.30.0-0</code>,  <code>3.28.0-1</code>,  </span></summary>
      

      ``3.40.0-0``,  ``3.38.0-0``,  ``3.36.0-1``,  ``3.36.0-0``,  ``3.32.0-2``,  ``3.32.0-1``,  ``3.32.0-0``,  ``3.30.0-0``,  ``3.28.0-1``,  ``3.28.0-0``,  ``3.26.0-0``,  ``3.24.0-0``,  ``3.22.0-1``,  ``3.20.0-0``,  ``3.18.0-0``,  ``3.16.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0a0``
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0``
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc-ng: ``>=12``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :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-vegamc

   and update with::

      mamba update bioconductor-vegamc

  To create a new environment, run::

      mamba create --name myenvname bioconductor-vegamc

  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-vegamc:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-vegamc";
        var versions = ["3.40.0","3.38.0","3.36.0","3.36.0","3.32.0"];
    </script>






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

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

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