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

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

bioconductor-genomicalignments
==============================

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

   Representation and manipulation of short genomic alignments

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/GenomicAlignments.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-genomicalignments <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-genomicalignments>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-genomicalignments/meta.yaml>`_
   :links: biotools: :biotools:`genomicalignments`

   Provides efficient containers for storing and manipulating short genomic alignments \(typically obtained by aligning short reads to a reference genome\). This includes read counting\, computing the coverage\, junction detection\, and working with the nucleotide content of the alignments.


.. conda:package:: bioconductor-genomicalignments

   |downloads_bioconductor-genomicalignments| |docker_bioconductor-genomicalignments|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.46.0-0</code>,  <code>1.42.0-1</code>,  <code>1.42.0-0</code>,  <code>1.38.0-1</code>,  <code>1.38.0-0</code>,  <code>1.36.0-0</code>,  <code>1.34.0-1</code>,  <code>1.34.0-0</code>,  <code>1.30.0-2</code>,  </span></summary>
      

      ``1.46.0-0``,  ``1.42.0-1``,  ``1.42.0-0``,  ``1.38.0-1``,  ``1.38.0-0``,  ``1.36.0-0``,  ``1.34.0-1``,  ``1.34.0-0``,  ``1.30.0-2``,  ``1.30.0-1``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.1-0``,  ``1.20.0-0``,  ``1.18.1-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.1-0``,  ``1.14.0-0``,  ``1.12.2-0``,  ``1.10.0-0``,  ``1.8.4-0``,  ``1.6.3-1``,  ``1.6.3-0``,  ``1.6.1-0``,  ``1.6.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocgenerics: ``>=0.56.0,<0.57.0``
   :depends bioconductor-biocgenerics: ``>=0.56.0,<0.57.0a0``
   :depends bioconductor-biocparallel: ``>=1.44.0,<1.45.0``
   :depends bioconductor-biocparallel: ``>=1.44.0,<1.45.0a0``
   :depends bioconductor-biostrings: ``>=2.78.0,<2.79.0``
   :depends bioconductor-biostrings: ``>=2.78.0,<2.79.0a0``
   :depends bioconductor-cigarillo: ``>=1.0.0,<1.1.0``
   :depends bioconductor-cigarillo: ``>=1.0.0,<1.1.0a0``
   :depends bioconductor-genomicranges: ``>=1.62.0,<1.63.0``
   :depends bioconductor-genomicranges: ``>=1.62.1,<1.63.0a0``
   :depends bioconductor-iranges: ``>=2.44.0,<2.45.0``
   :depends bioconductor-iranges: ``>=2.44.0,<2.45.0a0``
   :depends bioconductor-rsamtools: ``>=2.26.0,<2.27.0``
   :depends bioconductor-rsamtools: ``>=2.26.0,<2.27.0a0``
   :depends bioconductor-s4vectors: ``>=0.48.0,<0.49.0``
   :depends bioconductor-s4vectors: ``>=0.48.0,<0.49.0a0``
   :depends bioconductor-seqinfo: ``>=1.0.0,<1.1.0``
   :depends bioconductor-seqinfo: ``>=1.0.0,<1.1.0a0``
   :depends bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc: ``>=14``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends liblzma: ``>=5.8.2,<6.0a0``
   :depends libzlib: ``>=1.3.1,<2.0a0``
   :depends r-base: ``>=4.5,<4.6.0a0``
   :requirements:

   :additional platforms:
      
      .. raw:: html

         <span class="additional-platforms"><code>linux-aarch64</code>,  <code>osx-arm64</code></span>
      

   .. 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-genomicalignments

   and update with::

      mamba update bioconductor-genomicalignments

  To create a new environment, run::

      mamba create --name myenvname bioconductor-genomicalignments

  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-genomicalignments:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-genomicalignments";
        var versions = ["1.46.0","1.42.0","1.42.0","1.38.0","1.38.0"];
    </script>






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

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