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

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

bioconductor-pigengene
======================

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

   Infers biological signatures from gene expression data

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

   Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform\, e.g.\, the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform\, and evaluate them on the other. Pigengene identifies the modules \(clusters\) of highly coexpressed genes using coexpression network analysis\, summarizes the biological information of each module in an eigengene\, learns a Bayesian network that models the probabilistic dependencies between modules\, and builds a decision tree based on the expression of eigengenes.


.. conda:package:: bioconductor-pigengene

   |downloads_bioconductor-pigengene| |docker_bioconductor-pigengene|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.28.0-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-1</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  </span></summary>
      

      ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.8.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocstyle: ``>=2.30.0,<2.31.0``
   :depends bioconductor-clusterprofiler: ``>=4.10.0,<4.11.0``
   :depends bioconductor-dose: ``>=3.28.0,<3.29.0``
   :depends bioconductor-go.db: ``>=3.18.0,<3.19.0``
   :depends bioconductor-graph: ``>=1.80.0,<1.81.0``
   :depends bioconductor-impute: ``>=1.76.0,<1.77.0``
   :depends bioconductor-preprocesscore: ``>=1.64.0,<1.65.0``
   :depends bioconductor-reactomepa: ``>=1.46.0,<1.47.0``
   :depends bioconductor-rgraphviz: ``>=2.46.0,<2.47.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-bnlearn: ``>=4.7``
   :depends r-c50: ``>=0.1.2``
   :depends r-dbi: 
   :depends r-dplyr: 
   :depends r-gdata: 
   :depends r-ggplot2: 
   :depends r-mass: 
   :depends r-matrixstats: 
   :depends r-openxlsx: 
   :depends r-partykit: 
   :depends r-pheatmap: ``>=1.0.8``
   :depends r-wgcna: 
   :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-pigengene

   and update with::

      mamba update bioconductor-pigengene

  To create a new environment, run::

      mamba create --name myenvname bioconductor-pigengene

  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-pigengene:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-pigengene";
        var versions = ["1.28.0","1.26.0","1.24.0","1.20.0","1.18.0"];
    </script>






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

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

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