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

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

bioconductor-inpas
==================

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

   Identify Novel Alternative PolyAdenylation Sites \(PAS\) from RNA\-seq data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/InPAS.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-inpas <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-inpas>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-inpas/meta.yaml>`_

   Alternative polyadenylation \(APA\) is one of the important post\- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA\-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.


.. conda:package:: bioconductor-inpas

   |downloads_bioconductor-inpas| |docker_bioconductor-inpas|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.10.0-0</code>,  <code>2.8.0-0</code>,  <code>2.6.0-0</code>,  <code>2.2.0-0</code>,  <code>2.0.0-0</code>,  <code>1.22.0-1</code>,  <code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-0</code>,  </span></summary>
      

      ``2.10.0-0``,  ``2.8.0-0``,  ``2.6.0-0``,  ``2.2.0-0``,  ``2.0.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.3-0``,  ``1.14.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0``
   :depends bioconductor-cleanupdtseq: ``>=1.40.0,<1.41.0``
   :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-limma: ``>=3.58.0,<3.59.0``
   :depends bioconductor-plyranges: ``>=1.22.0,<1.23.0``
   :depends bioconductor-preprocesscore: ``>=1.64.0,<1.65.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-batchtools: 
   :depends r-depmixs4: 
   :depends r-dplyr: 
   :depends r-flock: 
   :depends r-future: 
   :depends r-future.apply: 
   :depends r-ggplot2: 
   :depends r-magrittr: 
   :depends r-parallelly: 
   :depends r-readr: 
   :depends r-reshape2: 
   :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-inpas

   and update with::

      mamba update bioconductor-inpas

  To create a new environment, run::

      mamba create --name myenvname bioconductor-inpas

  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-inpas:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-inpas";
        var versions = ["2.10.0","2.8.0","2.6.0","2.2.0","2.0.0"];
    </script>






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-----------------

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

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