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

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

bioconductor-rtnsurvival
========================

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

   Survival analysis using transcriptional networks inferred by the RTN package

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

   RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon\, the 2\-tailed GSEA approach computes a differential Enrichment Score \(dES\) for each individual sample\, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows\: a Cox Proportional Hazards approach used to model regulons as predictors of survival time\, and a Kaplan\-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine\-tuned to the user\'s specifications.


.. conda:package:: bioconductor-rtnsurvival

   |downloads_bioconductor-rtnsurvival| |docker_bioconductor-rtnsurvival|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-0</code>,  <code>1.14.1-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  <code>1.10.0-0</code>,  </span></summary>
      

      ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.1-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.1-0``,  ``1.6.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-rtn: ``>=2.26.0,<2.27.0``
   :depends bioconductor-rtnduals: ``>=1.26.0,<1.27.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-dunn.test: 
   :depends r-egg: 
   :depends r-ggplot2: 
   :depends r-pheatmap: 
   :depends r-rcolorbrewer: 
   :depends r-scales: 
   :depends r-survival: 
   :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-rtnsurvival

   and update with::

      mamba update bioconductor-rtnsurvival

  To create a new environment, run::

      mamba create --name myenvname bioconductor-rtnsurvival

  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-rtnsurvival:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-rtnsurvival";
        var versions = ["1.26.0","1.24.0","1.22.0","1.18.0","1.16.0"];
    </script>






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

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

Link to this page
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Render an |install-with-bioconda| badge with the following MarkDown::

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
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