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

.. title:: Package Recipe 'bioconductor-mofa2'
.. highlight: bash

bioconductor-mofa2
==================

.. conda:recipe:: bioconductor-mofa2
   :replaces_section_title:
   :noindex:

   Multi\-Omics Factor Analysis v2

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/MOFA2.html
   :license: file LICENSE
   :recipe: /`bioconductor-mofa2 <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-mofa2>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-mofa2/meta.yaml>`_

   The MOFA2 package contains a collection of tools for training and analysing multi\-omic factor analysis \(MOFA\). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and\/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework\, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor\, vizualisation\, imputation etc are available.


.. conda:package:: bioconductor-mofa2

   |downloads_bioconductor-mofa2| |docker_bioconductor-mofa2|

   :versions:
      
      

      ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.1-0``,  ``1.0.0-1``

      

   
   :depends bioconductor-basilisk: ``>=1.14.0,<1.15.0``
   :depends bioconductor-basilisk: ``>=1.14.1,<1.15.0a0``
   :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0``
   :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0a0``
   :depends bioconductor-hdf5array: ``>=1.30.0,<1.31.0``
   :depends bioconductor-hdf5array: ``>=1.30.0,<1.31.0a0``
   :depends bioconductor-rhdf5: ``>=2.46.0,<2.47.0``
   :depends bioconductor-rhdf5: ``>=2.46.1,<2.47.0a0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-corrplot: 
   :depends r-cowplot: 
   :depends r-dplyr: 
   :depends r-forcats: 
   :depends r-ggplot2: 
   :depends r-ggrepel: 
   :depends r-magrittr: 
   :depends r-pheatmap: 
   :depends r-rcolorbrewer: 
   :depends r-reshape2: 
   :depends r-reticulate: 
   :depends r-rtsne: 
   :depends r-stringi: 
   :depends r-tidyr: 
   :depends r-uwot: 
   :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-mofa2

   and update with::

      mamba update bioconductor-mofa2

  To create a new environment, run::

      mamba create --name myenvname bioconductor-mofa2

  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-mofa2:<tag>

   (see `bioconductor-mofa2/tags`_ for valid values for ``<tag>``)


.. |downloads_bioconductor-mofa2| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-mofa2.svg?style=flat
   :target: https://anaconda.org/bioconda/bioconductor-mofa2
   :alt:   (downloads)
.. |docker_bioconductor-mofa2| image:: https://quay.io/repository/biocontainers/bioconductor-mofa2/status
   :target: https://quay.io/repository/biocontainers/bioconductor-mofa2
.. _`bioconductor-mofa2/tags`: https://quay.io/repository/biocontainers/bioconductor-mofa2?tab=tags


.. raw:: html

    <script>
        var package = "bioconductor-mofa2";
        var versions = ["1.12.0","1.10.0","1.8.0","1.4.0","1.2.0"];
    </script>






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