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

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

bioconductor-proteomm
=====================

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

   Multi\-Dataset Model\-based Differential Expression Proteomics Analysis Platform

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/ProteoMM.html
   :license: MIT
   :recipe: /`bioconductor-proteomm <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-proteomm>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-proteomm/meta.yaml>`_

   ProteoMM is a statistical method to perform model\-based peptide\-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p\-value for each protein across multiple datasets. ProteoMM provides functionality for normalization\, missing value imputation and differential expression. Model\-based peptide\-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom\-up MS based proteomics\" \(Karpievitch et al. Bioinformatics 2009\). EigenMS normalisation is implemented as described in \"Normalization of peak intensities in bottom\-up MS\-based proteomics using singular value decomposition.\" \(Karpievitch et al. Bioinformatics 2009\).


.. conda:package:: bioconductor-proteomm

   |downloads_bioconductor-proteomm| |docker_bioconductor-proteomm|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-0</code>,  <code>1.12.0-0</code>,  <code>1.10.0-0</code>,  <code>1.8.0-1</code>,  <code>1.8.0-0</code>,  <code>1.6.0-0</code>,  <code>1.4.0-0</code>,  </span></summary>
      

      ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.0.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-gdata: 
   :depends r-ggplot2: 
   :depends r-ggrepel: 
   :depends r-gtools: 
   :depends r-matrixstats: 
   :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-proteomm

   and update with::

      mamba update bioconductor-proteomm

  To create a new environment, run::

      mamba create --name myenvname bioconductor-proteomm

  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-proteomm:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-proteomm";
        var versions = ["1.20.0","1.18.0","1.16.0","1.12.0","1.10.0"];
    </script>






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

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

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