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

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

bioconductor-rtn
================

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

   RTN\: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/RTN.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-rtn <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-rtn>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-rtn/meta.yaml>`_

   A transcriptional regulatory network \(TRN\) consists of a collection of transcription factors \(TFs\) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome\, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.


.. conda:package:: bioconductor-rtn

   |downloads_bioconductor-rtn| |docker_bioconductor-rtn|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.26.0-0</code>,  <code>2.24.0-0</code>,  <code>2.22.0-0</code>,  <code>2.18.0-0</code>,  <code>2.16.0-0</code>,  <code>2.14.1-0</code>,  <code>2.14.0-0</code>,  <code>2.12.0-0</code>,  <code>2.10.0-0</code>,  </span></summary>
      

      ``2.26.0-0``,  ``2.24.0-0``,  ``2.22.0-0``,  ``2.18.0-0``,  ``2.16.0-0``,  ``2.14.1-0``,  ``2.14.0-0``,  ``2.12.0-0``,  ``2.10.0-0``,  ``2.8.1-0``,  ``2.6.3-0``,  ``2.6.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-limma: ``>=3.58.0,<3.59.0``
   :depends bioconductor-minet: ``>=3.60.0,<3.61.0``
   :depends bioconductor-reder: ``>=2.6.0,<2.7.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends bioconductor-viper: ``>=1.36.0,<1.37.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-car: 
   :depends r-data.table: 
   :depends r-igraph: 
   :depends r-mixtools: 
   :depends r-pheatmap: 
   :depends r-pwr: 
   :depends r-snow: 
   :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-rtn

   and update with::

      mamba update bioconductor-rtn

  To create a new environment, run::

      mamba create --name myenvname bioconductor-rtn

  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-rtn:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-rtn";
        var versions = ["2.26.0","2.24.0","2.22.0","2.18.0","2.16.0"];
    </script>






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

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

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