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

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

bioconductor-msnid
==================

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

   Utilities for Exploration and Assessment of Confidence of LC\-MSn Proteomics Identifications

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/MSnID.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-msnid <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-msnid>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-msnid/meta.yaml>`_
   :links: biotools: :biotools:`msnid`, doi: :doi:`10.1038/nmeth.3252`

   Extracts MS\/MS ID data from mzIdentML \(leveraging mzID package\) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS\/MS results and assess missed and irregular enzymatic cleavages\, mass measurement accuracy\, etc.


.. conda:package:: bioconductor-msnid

   |downloads_bioconductor-msnid| |docker_bioconductor-msnid|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.36.0-0</code>,  <code>1.34.0-0</code>,  <code>1.32.0-1</code>,  <code>1.32.0-0</code>,  <code>1.28.0-2</code>,  <code>1.28.0-1</code>,  <code>1.28.0-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-1</code>,  </span></summary>
      

      ``1.36.0-0``,  ``1.34.0-0``,  ``1.32.0-1``,  ``1.32.0-0``,  ``1.28.0-2``,  ``1.28.0-1``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-1``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.1-0``,  ``1.16.1-0``,  ``1.12.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-annotationdbi: ``>=1.64.1,<1.65.0a0``
   :depends bioconductor-annotationhub: ``>=3.10.0,<3.11.0``
   :depends bioconductor-annotationhub: ``>=3.10.0,<3.11.0a0``
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0a0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0``
   :depends bioconductor-biocstyle: ``>=2.30.0,<2.31.0``
   :depends bioconductor-biocstyle: ``>=2.30.0,<2.31.0a0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0``
   :depends bioconductor-msmstests: ``>=1.40.0,<1.41.0``
   :depends bioconductor-msmstests: ``>=1.40.0,<1.41.0a0``
   :depends bioconductor-msnbase: ``>=2.28.0,<2.29.0``
   :depends bioconductor-msnbase: ``>=2.28.1,<2.29.0a0``
   :depends bioconductor-mzid: ``>=1.40.0,<1.41.0``
   :depends bioconductor-mzid: ``>=1.40.0,<1.41.0a0``
   :depends bioconductor-mzr: ``>=2.36.0,<2.37.0``
   :depends bioconductor-mzr: ``>=2.36.0,<2.37.0a0``
   :depends bioconductor-protgenerics: ``>=1.34.0,<1.35.0``
   :depends bioconductor-protgenerics: ``>=1.34.0,<1.35.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc-ng: ``>=12``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends libstdcxx-ng: ``>=12``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-doparallel: 
   :depends r-dplyr: 
   :depends r-foreach: 
   :depends r-ggplot2: 
   :depends r-iterators: 
   :depends r-purrr: 
   :depends r-r.cache: 
   :depends r-rcpp: 
   :depends r-reshape2: 
   :depends r-rlang: 
   :depends r-runit: 
   :depends r-stringr: 
   :depends r-tibble: 
   :depends r-xtable: 
   :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-msnid

   and update with::

      mamba update bioconductor-msnid

  To create a new environment, run::

      mamba create --name myenvname bioconductor-msnid

  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-msnid:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-msnid";
        var versions = ["1.36.0","1.34.0","1.32.0","1.32.0","1.28.0"];
    </script>






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

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

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