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

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

bioconductor-artms
==================

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

   Analytical R tools for Mass Spectrometry

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/artMS.html
   :license: GPL (>= 3) + file LICENSE
   :recipe: /`bioconductor-artms <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-artms>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-artms/meta.yaml>`_

   artMS provides a set of tools for the analysis of proteomics label\-free datasets. It takes as input the MaxQuant search result output \(evidence.txt file\) and performs quality control\, relative quantification using MSstats\, downstream analysis and integration. artMS also provides a set of functions to re\-format and make it compatible with other analytical tools\, including\, SAINTq\, SAINTexpress\, Phosfate\, and PHOTON. Check \[http\:\/\/artms.org\]\(http\:\/\/artms.org\) for details.


.. conda:package:: bioconductor-artms

   |downloads_bioconductor-artms| |docker_bioconductor-artms|

   :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>1.8.2-0</code>,  <code>1.8.0-0</code>,  <code>1.6.3-0</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``,  ``1.8.2-0``,  ``1.8.0-0``,  ``1.6.3-0``,  ``1.4.0-0``,  ``1.2.6-0``,  ``1.0.10-0``,  ``1.0.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-limma: ``>=3.58.0,<3.59.0``
   :depends bioconductor-msstats: ``>=4.10.0,<4.11.0``
   :depends bioconductor-org.hs.eg.db: ``>=3.18.0,<3.19.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-bit64: 
   :depends r-circlize: 
   :depends r-cluster: 
   :depends r-corrplot: 
   :depends r-data.table: 
   :depends r-dplyr: 
   :depends r-getopt: 
   :depends r-ggdendro: 
   :depends r-ggplot2: 
   :depends r-ggrepel: 
   :depends r-gplots: 
   :depends r-openxlsx: 
   :depends r-pheatmap: 
   :depends r-plotly: 
   :depends r-plyr: 
   :depends r-rcolorbrewer: 
   :depends r-scales: 
   :depends r-seqinr: 
   :depends r-stringr: 
   :depends r-tidyr: 
   :depends r-upsetr: 
   :depends r-venndiagram: 
   :depends r-yaml: 
   :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-artms

   and update with::

      mamba update bioconductor-artms

  To create a new environment, run::

      mamba create --name myenvname bioconductor-artms

  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-artms:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-artms";
        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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