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

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

bioconductor-topdownr
=====================

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

   Investigation of Fragmentation Conditions in Top\-Down Proteomics

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

   The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.


.. conda:package:: bioconductor-topdownr

   |downloads_bioconductor-topdownr| |docker_bioconductor-topdownr|

   :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``,  ``1.4.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-msnbase: ``>=2.28.0,<2.29.0``
   :depends bioconductor-mzr: ``>=2.36.0,<2.37.0``
   :depends bioconductor-protgenerics: ``>=1.34.0,<1.35.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-ggplot2: ``>=2.2.1``
   :depends r-matrix: ``>=1.4-2``
   :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-topdownr

   and update with::

      mamba update bioconductor-topdownr

  To create a new environment, run::

      mamba create --name myenvname bioconductor-topdownr

  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-topdownr:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-topdownr";
        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::

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-topdownr/README.html)

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