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

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

bioconductor-rgntx
==================

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

   Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/RgnTX.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-rgntx <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-rgntx>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-rgntx/meta.yaml>`_

   RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association\, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions.


.. conda:package:: bioconductor-rgntx

   |downloads_bioconductor-rgntx| |docker_bioconductor-rgntx|

   :versions:
      
      

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

      

   
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-regioner: ``>=1.34.0,<1.35.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.0,<3.3.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-ggplot2: 
   :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-rgntx

   and update with::

      mamba update bioconductor-rgntx

  To create a new environment, run::

      mamba create --name myenvname bioconductor-rgntx

  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-rgntx:<tag>

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


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


.. raw:: html

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






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

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