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

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

bioconductor-gofuncr
====================

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

   Gene ontology enrichment using FUNC

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/GOfuncR.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-gofuncr <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-gofuncr>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-gofuncr/meta.yaml>`_

   GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO\-annotations are obtained from OrganismDb or OrgDb packages \(\'Homo.sapiens\' by default\)\; the GO\-graph is included in the package and updated regularly \(01\-May\-2021\). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test\, as well as three additional tests\: \(i\) the Wilcoxon rank\-sum test that is used when genes are ranked\, \(ii\) a binomial test that is used when genes are associated with two counts and \(iii\) a Chi\-square or Fisher\'s exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests\, family\-wise error rates are computed based on random permutations of the gene\-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations\, and options to take gene\-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates\, annotations and ontologies.


.. conda:package:: bioconductor-gofuncr

   |downloads_bioconductor-gofuncr| |docker_bioconductor-gofuncr|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-1</code>,  <code>1.18.0-0</code>,  <code>1.14.0-2</code>,  <code>1.14.0-1</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  <code>1.10.0-1</code>,  </span></summary>
      

      ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.14.0-2``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.2.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-annotationdbi: ``>=1.64.1,<1.65.0a0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc-ng: ``>=12``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends libstdcxx-ng: ``>=12``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-gtools: ``>=3.5.0``
   :depends r-mapplots: ``>=1.5``
   :depends r-rcpp: ``>=0.11.5``
   :depends r-vioplot: ``>=0.2``
   :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-gofuncr

   and update with::

      mamba update bioconductor-gofuncr

  To create a new environment, run::

      mamba create --name myenvname bioconductor-gofuncr

  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-gofuncr:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-gofuncr";
        var versions = ["1.22.0","1.20.0","1.18.0","1.18.0","1.14.0"];
    </script>






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

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