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

.. title:: Package Recipe 'r-sigminer'
.. highlight: bash

r-sigminer
==========

.. conda:recipe:: r-sigminer
   :replaces_section_title:
   :noindex:

   Genomic alterations including single nucleotide substitution\, copy number alteration\, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations\, we can generate characteristic alteration spectra\, called \'signature\' \(Wang\, Shixiang\, et al.  \(2020\) \<DOI\:10.1101\/2020.04.27.20082404\> \& Alexandrov\, Ludmil B.\, et al. \(2020\) \<DOI\:10.1038\/s41586\-020\-1943\-3\> \& Macintyre\, Geoff\, et al. \(2018\) \<DOI\:10.1038\/s41588\-018\-0179\-8\>\).  This package helps users to extract\, analyze and visualize signatures from genomic alteration records\, thus providing new insight into cancer study.

   :homepage: https://github.com/ShixiangWang/sigminer
   :license: MIT / MIT
   :recipe: /`r-sigminer <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-sigminer>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-sigminer/meta.yaml>`_

   


.. conda:package:: r-sigminer

   |downloads_r-sigminer| |docker_r-sigminer|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.3.0-0</code>,  <code>2.2.2-0</code>,  <code>2.2.0-2</code>,  <code>2.2.0-1</code>,  <code>2.2.0-0</code>,  <code>2.1.9-2</code>,  <code>2.1.9-1</code>,  <code>2.1.9-0</code>,  <code>2.1.8-1</code>,  </span></summary>
      

      ``2.3.0-0``,  ``2.2.2-0``,  ``2.2.0-2``,  ``2.2.0-1``,  ``2.2.0-0``,  ``2.1.9-2``,  ``2.1.9-1``,  ``2.1.9-0``,  ``2.1.8-1``,  ``2.1.8-0``,  ``2.1.7-1``,  ``2.1.7-0``,  ``2.1.6-1``,  ``2.1.6-0``,  ``2.1.5-1``,  ``2.1.5-0``,  ``2.1.4-0``,  ``2.1.3-1``,  ``2.1.3-0``,  ``2.1.2-1``,  ``2.1.2-0``,  ``2.1.1-0``,  ``2.1.0-0``,  ``2.0.5-0``,  ``2.0.4-0``,  ``2.0.3-0``,  ``2.0.2-0``,  ``2.0.1-1``,  ``2.0.1-0``,  ``2.0.0-1``,  ``2.0.0-0``,  ``1.2.5-1``,  ``1.2.5-0``,  ``1.2.4-0``,  ``1.2.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-maftools: ``>=2.18.0,<2.19.0a0``
   :depends libgcc-ng: ``>=12``
   :depends libstdcxx-ng: ``>=12``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-cli: ``>=2.0.0``
   :depends r-cowplot: 
   :depends r-data.table: 
   :depends r-dplyr: 
   :depends r-furrr: ``>=0.2.0``
   :depends r-future: 
   :depends r-ggplot2: ``>=3.3.0``
   :depends r-ggpubr: 
   :depends r-magrittr: 
   :depends r-nmf: 
   :depends r-purrr: 
   :depends r-rcpp: 
   :depends r-rlang: ``>=0.1.2``
   :depends r-tidyr: 
   :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 r-sigminer

   and update with::

      mamba update r-sigminer

  To create a new environment, run::

      mamba create --name myenvname r-sigminer

  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/r-sigminer:<tag>

   (see `r-sigminer/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "r-sigminer";
        var versions = ["2.3.0","2.2.2","2.2.0","2.2.0","2.2.0"];
    </script>






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

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