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

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

bioconductor-quasr
==================

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

   Quantify and Annotate Short Reads in R

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/QuasR.html
   :license: GPL-2
   :recipe: /`bioconductor-quasr <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-quasr>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-quasr/meta.yaml>`_
   :links: biotools: :biotools:`quasr`

   This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads\, over creation of alignments and quality control plots\, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie \(data from DNA\/ChIP\/ATAC\/Bis\-seq experiments\) or Rhisat2 \(data from RNA\-seq experiments that require spliced alignments\)\, or can be provided in the form of bam files.


.. conda:package:: bioconductor-quasr

   |downloads_bioconductor-quasr| |docker_bioconductor-quasr|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.46.0-0</code>,  <code>1.42.1-0</code>,  <code>1.40.1-0</code>,  <code>1.38.0-1</code>,  <code>1.38.0-0</code>,  <code>1.34.0-2</code>,  <code>1.34.0-1</code>,  <code>1.34.0-0</code>,  <code>1.32.0-0</code>,  </span></summary>
      

      ``1.46.0-0``,  ``1.42.1-0``,  ``1.40.1-0``,  ``1.38.0-1``,  ``1.38.0-0``,  ``1.34.0-2``,  ``1.34.0-1``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-2``,  ``1.30.0-1``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.2-0``,  ``1.22.1-0``,  ``1.20.0-0``,  ``1.18.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.68.0,<1.69.0``
   :depends bioconductor-annotationdbi: ``>=1.68.0,<1.69.0a0``
   :depends bioconductor-biobase: ``>=2.66.0,<2.67.0``
   :depends bioconductor-biobase: ``>=2.66.0,<2.67.0a0``
   :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0``
   :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0a0``
   :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0``
   :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0a0``
   :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0``
   :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0a0``
   :depends bioconductor-bsgenome: ``>=1.74.0,<1.75.0``
   :depends bioconductor-bsgenome: ``>=1.74.0,<1.75.0a0``
   :depends bioconductor-genomeinfodb: ``>=1.42.0,<1.43.0``
   :depends bioconductor-genomeinfodb: ``>=1.42.0,<1.43.0a0``
   :depends bioconductor-genomicfeatures: ``>=1.58.0,<1.59.0``
   :depends bioconductor-genomicfeatures: ``>=1.58.0,<1.59.0a0``
   :depends bioconductor-genomicfiles: ``>=1.42.0,<1.43.0``
   :depends bioconductor-genomicfiles: ``>=1.42.0,<1.43.0a0``
   :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0``
   :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0a0``
   :depends bioconductor-iranges: ``>=2.40.0,<2.41.0``
   :depends bioconductor-iranges: ``>=2.40.0,<2.41.0a0``
   :depends bioconductor-rbowtie: ``>=1.46.0,<1.47.0``
   :depends bioconductor-rbowtie: ``>=1.46.0,<1.47.0a0``
   :depends bioconductor-rhtslib: ``>=3.2.0,<3.3.0``
   :depends bioconductor-rhtslib: ``>=3.2.0,<3.3.0a0``
   :depends bioconductor-rsamtools: ``>=2.22.0,<2.23.0``
   :depends bioconductor-rsamtools: ``>=2.22.0,<2.23.0a0``
   :depends bioconductor-rtracklayer: ``>=1.66.0,<1.67.0``
   :depends bioconductor-rtracklayer: ``>=1.66.0,<1.67.0a0``
   :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0``
   :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0a0``
   :depends bioconductor-shortread: ``>=1.64.0,<1.65.0``
   :depends bioconductor-shortread: ``>=1.64.0,<1.65.0a0``
   :depends bioconductor-txdbmaker: ``>=1.2.0,<1.3.0``
   :depends bioconductor-txdbmaker: ``>=1.2.0,<1.3.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc: ``>=13``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends liblzma: ``>=5.6.3,<6.0a0``
   :depends libstdcxx: ``>=13``
   :depends libzlib: ``>=1.3.1,<2.0a0``
   :depends r-base: ``>=4.4,<4.5.0a0``
   :requirements:

   :additional platforms:
      

   .. 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-quasr

   and update with::

      mamba update bioconductor-quasr

  To create a new environment, run::

      mamba create --name myenvname bioconductor-quasr

  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-quasr:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-quasr";
        var versions = ["1.46.0","1.42.1","1.40.1","1.38.0","1.38.0"];
    </script>






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

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

Link to this page
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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
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