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

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

bioconductor-rcas
=================

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

   RNA Centric Annotation System

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

   RCAS is an R\/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome\-wide regions of interest detected by high\-throughput experiments. Such transcriptomic regions could be\, for instance\, signal peaks detected by CLIP\-Seq analysis for protein\-RNA interaction sites\, RNA modification sites \(alias the epitranscriptome\)\, CAGE\-tag locations\, or any other collection of query regions at the level of the transcriptome. RCAS produces in\-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features \(exons\, introns\, 5\'\/3\' UTR regions\, exon\-intron boundaries\, promoter regions\). Moreover\, RCAS can carry out functional enrichment analyses and discriminative motif discovery.


.. conda:package:: bioconductor-rcas

   |downloads_bioconductor-rcas| |docker_bioconductor-rcas|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.28.2-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-1</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  </span></summary>
      

      ``1.28.2-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.1-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.5.4-2``,  ``1.5.4-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.1.1-0``,  ``1.0.0-0``,  ``1.0.0.dev75225b9-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0``
   :depends bioconductor-bsgenome.hsapiens.ucsc.hg19: ``>=1.4.0,<1.5.0``
   :depends bioconductor-genomation: ``>=1.34.0,<1.35.0``
   :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-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends pandoc: ``>=1.12.3``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-cowplot: 
   :depends r-data.table: 
   :depends r-dt: ``>=0.2``
   :depends r-ggplot2: 
   :depends r-ggseqlogo: 
   :depends r-gprofiler2: 
   :depends r-knitr: ``>=1.12.3``
   :depends r-pbapply: 
   :depends r-pheatmap: 
   :depends r-plotly: ``>=4.5.2``
   :depends r-plotrix: 
   :depends r-proxy: 
   :depends r-ranger: 
   :depends r-rmarkdown: ``>=0.9.5``
   :depends r-rsqlite: 
   :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-rcas

   and update with::

      mamba update bioconductor-rcas

  To create a new environment, run::

      mamba create --name myenvname bioconductor-rcas

  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-rcas:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-rcas";
        var versions = ["1.28.2","1.26.0","1.24.0","1.20.0","1.18.0"];
    </script>






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

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