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

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

bioconductor-circseqaligntk
===========================

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

   A toolkit for end\-to\-end analysis of RNA\-seq data for circular genomes

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/CircSeqAlignTk.html
   :license: MIT + file LICENSE
   :recipe: /`bioconductor-circseqaligntk <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-circseqaligntk>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-circseqaligntk/meta.yaml>`_

   CircSeqAlignTk is designed for end\-to\-end RNA\-Seq data analysis of circular genome sequences\, from alignment to visualization. It mainly targets viroids which are composed of 246\-401 nt circular RNAs. In addition\, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA\-Seq data\, allowing developers to evaluate the performance of alignment tools and workflows.


.. conda:package:: bioconductor-circseqaligntk

   |downloads_bioconductor-circseqaligntk| |docker_bioconductor-circseqaligntk|

   :versions:
      
      

      ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0``

      

   
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-rbowtie2: ``>=2.8.0,<2.9.0``
   :depends bioconductor-rhisat2: ``>=1.18.0,<1.19.0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-shortread: ``>=1.60.0,<1.61.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-magrittr: 
   :depends r-rlang: 
   :depends r-tidyr: 
   :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-circseqaligntk

   and update with::

      mamba update bioconductor-circseqaligntk

  To create a new environment, run::

      mamba create --name myenvname bioconductor-circseqaligntk

  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-circseqaligntk:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-circseqaligntk";
        var versions = ["1.4.0","1.2.0","1.0.0"];
    </script>






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