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

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

bioconductor-famat
==================

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

   Functional analysis of metabolic and transcriptomic data

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/famat.html
   :license: GPL-3
   :recipe: /`bioconductor-famat <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-famat>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-famat/meta.yaml>`_

   Famat is made to collect data about lists of genes and metabolites provided by user\, and to visualize it through a Shiny app. Information collected is\: \- Pathways containing some of the user\'s genes and metabolites \(obtained using a pathway enrichment analysis\). \- Direct interactions between user\'s elements inside pathways. \- Information about elements \(their identifiers and descriptions\). \- Go terms enrichment analysis performed on user\'s genes. The Shiny app is composed of\: \- information about genes\, metabolites\, and direct interactions between them inside pathways. \- an heatmap showing which elements from the list are in pathways \(pathways are structured in hierarchies\). \- hierarchies of enriched go terms using Molecular Function and Biological Process.


.. conda:package:: bioconductor-famat

   |downloads_bioconductor-famat| |docker_bioconductor-famat|

   :versions:
      
      

      ``1.16.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.1.1-0``,  ``1.0.0-1``,  ``1.0.0-0``

      

   
   :depends bioconductor-clusterprofiler: ``>=4.14.0,<4.15.0``
   :depends bioconductor-go.db: ``>=3.20.0,<3.21.0``
   :depends bioconductor-keggrest: ``>=1.46.0,<1.47.0``
   :depends bioconductor-org.hs.eg.db: ``>=3.20.0,<3.21.0``
   :depends bioconductor-reactome.db: ``>=1.89.0,<1.90.0``
   :depends bioconductor-rwikipathways: ``>=1.26.0,<1.27.0``
   :depends r-base: ``>=4.4,<4.5.0a0``
   :depends r-biasedurn: 
   :depends r-dplyr: 
   :depends r-dt: 
   :depends r-gprofiler2: 
   :depends r-magrittr: 
   :depends r-mgcv: 
   :depends r-ontologyindex: 
   :depends r-plotly: 
   :depends r-shiny: 
   :depends r-shinybs: 
   :depends r-shinydashboard: 
   :depends r-stringr: 
   :depends r-tidyr: 
   :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-famat

   and update with::

      mamba update bioconductor-famat

  To create a new environment, run::

      mamba create --name myenvname bioconductor-famat

  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-famat:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-famat";
        var versions = ["1.16.0","1.12.0","1.10.0","1.8.0","1.4.0"];
    </script>






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

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