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

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

bioconductor-viseago
====================

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

   ViSEAGO\: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/ViSEAGO.html
   :license: GPL-3
   :recipe: /`bioconductor-viseago <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-viseago>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-viseago/meta.yaml>`_

   The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology \(GO\) analysis of complex experimental design with multiple comparisons of interest. It allows to study large\-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis\: Visualization\, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations\, which are retrieved from one of NCBI EntrezGene\, Ensembl or Uniprot databases for several species. Using available R packages and novel developments\, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists\, enhancing reporting capabilities while maintaining reproducibility.


.. conda:package:: bioconductor-viseago

   |downloads_bioconductor-viseago| |docker_bioconductor-viseago|

   :versions:
      
      

      ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0``

      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-annotationforge: ``>=1.44.0,<1.45.0``
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0``
   :depends bioconductor-fgsea: ``>=1.28.0,<1.29.0``
   :depends bioconductor-go.db: ``>=3.18.0,<3.19.0``
   :depends bioconductor-gosemsim: ``>=2.28.0,<2.29.0``
   :depends bioconductor-topgo: ``>=2.54.0,<2.55.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-dendextend: 
   :depends r-diagrammer: 
   :depends r-dt: 
   :depends r-dynamictreecut: 
   :depends r-ggplot2: 
   :depends r-heatmaply: 
   :depends r-htmlwidgets: 
   :depends r-igraph: 
   :depends r-plotly: 
   :depends r-processx: 
   :depends r-r.utils: 
   :depends r-rcolorbrewer: 
   :depends r-scales: 
   :depends r-upsetr: 
   :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-viseago

   and update with::

      mamba update bioconductor-viseago

  To create a new environment, run::

      mamba create --name myenvname bioconductor-viseago

  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-viseago:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-viseago";
        var versions = ["1.16.0","1.14.0","1.12.0","1.8.0","1.6.0"];
    </script>






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

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

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