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

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

bioconductor-npgsea
===================

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

   Permutation approximation methods for gene set enrichment analysis \(non\-permutation GSEA\)

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

   Current gene set enrichment methods rely upon permutations for inference.  These approaches are computationally expensive and have minimum achievable p\-values based on the number of permutations\, not on the actual observed statistics.  We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics.  We are able to reduce the computational burden and granularity issues of permutation testing with our method\, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p\-values without the computational cost of permutations.  It is applicable in settings where one or many gene sets are of interest.  There are also built\-in plotting functions to help users visualize results.


.. conda:package:: bioconductor-npgsea

   |downloads_bioconductor-npgsea| |docker_bioconductor-npgsea|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.38.0-0</code>,  <code>1.36.0-0</code>,  <code>1.34.0-0</code>,  <code>1.30.0-0</code>,  <code>1.28.0-0</code>,  <code>1.26.0-1</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-0</code>,  </span></summary>
      

      ``1.38.0-0``,  ``1.36.0-0``,  ``1.34.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-gseabase: ``>=1.64.0,<1.65.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :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-npgsea

   and update with::

      mamba update bioconductor-npgsea

  To create a new environment, run::

      mamba create --name myenvname bioconductor-npgsea

  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-npgsea:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-npgsea";
        var versions = ["1.38.0","1.36.0","1.34.0","1.30.0","1.28.0"];
    </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-npgsea/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-npgsea/README.html