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

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

bioconductor-dep
================

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

   Differential Enrichment analysis of Proteomics data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/DEP.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-dep <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-dep>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-dep/meta.yaml>`_

   This package provides an integrated analysis workflow for robust and reproducible analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment. It requires tabular input \(e.g. txt files\) as generated by quantitative analysis softwares of raw mass spectrometry data\, such as MaxQuant or IsobarQuant. Functions are provided for data preparation\, filtering\, variance normalization and imputation of missing values\, as well as statistical testing of differentially enriched \/ expressed proteins. It also includes tools to check intermediate steps in the workflow\, such as normalization and missing values imputation. Finally\, visualization tools are provided to explore the results\, including heatmap\, volcano plot and barplot representations. For scientists with limited experience in R\, the package also contains wrapper functions that entail the complete analysis workflow and generate a report. Even easier to use are the interactive Shiny apps that are provided by the package.


.. conda:package:: bioconductor-dep

   |downloads_bioconductor-dep| |docker_bioconductor-dep|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-1</code>,  <code>1.12.0-0</code>,  <code>1.10.0-0</code>,  <code>1.8.0-0</code>,  </span></summary>
      

      ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.4.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0``
   :depends bioconductor-limma: ``>=3.58.0,<3.59.0``
   :depends bioconductor-msnbase: ``>=2.28.0,<2.29.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends bioconductor-vsn: ``>=3.70.0,<3.71.0``
   :depends r-assertthat: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-circlize: 
   :depends r-cluster: 
   :depends r-dplyr: 
   :depends r-dt: 
   :depends r-fdrtool: 
   :depends r-ggplot2: 
   :depends r-ggrepel: 
   :depends r-gridextra: 
   :depends r-imputelcmd: 
   :depends r-purrr: 
   :depends r-rcolorbrewer: 
   :depends r-readr: 
   :depends r-rmarkdown: 
   :depends r-shiny: 
   :depends r-shinydashboard: 
   :depends r-tibble: 
   :depends r-tidyr: 
   :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-dep

   and update with::

      mamba update bioconductor-dep

  To create a new environment, run::

      mamba create --name myenvname bioconductor-dep

  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-dep:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-dep";
        var versions = ["1.24.0","1.22.0","1.20.0","1.16.0","1.14.0"];
    </script>






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

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

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/bioconductor-dep/README.html