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

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

bioconductor-safe
=================

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

   Significance Analysis of Function and Expression

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/safe.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-safe <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-safe>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-safe/meta.yaml>`_
   :links: biotools: :biotools:`safe`, doi: :doi:`10.1093/bioinformatics/bti260`

   SAFE is a resampling\-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2\-sample and multi\-class comparisons\, or simple linear regressions. Other experimental designs can also be accommodated through user\-defined functions.


.. conda:package:: bioconductor-safe

   |downloads_bioconductor-safe| |docker_bioconductor-safe|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>3.46.0-0</code>,  <code>3.42.0-0</code>,  <code>3.40.0-0</code>,  <code>3.38.0-0</code>,  <code>3.34.0-0</code>,  <code>3.32.0-0</code>,  <code>3.30.0-1</code>,  <code>3.30.0-0</code>,  <code>3.27.0-0</code>,  </span></summary>
      

      ``3.46.0-0``,  ``3.42.0-0``,  ``3.40.0-0``,  ``3.38.0-0``,  ``3.34.0-0``,  ``3.32.0-0``,  ``3.30.0-1``,  ``3.30.0-0``,  ``3.27.0-0``,  ``3.26.0-0``,  ``3.24.0-1``,  ``3.22.0-0``,  ``3.20.0-0``,  ``3.18.0-0``,  ``3.16.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.68.0,<1.69.0``
   :depends bioconductor-biobase: ``>=2.66.0,<2.67.0``
   :depends r-base: ``>=4.4,<4.5.0a0``
   :depends r-sparsem: 
   :requirements:

   :additional platforms:
      

   .. 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-safe

   and update with::

      mamba update bioconductor-safe

  To create a new environment, run::

      mamba create --name myenvname bioconductor-safe

  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-safe:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-safe";
        var versions = ["3.46.0","3.42.0","3.40.0","3.38.0","3.34.0"];
    </script>






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

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

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-safe/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/bioconductor-safe/README.html