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

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

bioconductor-eventpointer
=========================

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

   An effective identification of alternative splicing events using junction arrays and RNA\-Seq data

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/EventPointer.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-eventpointer <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-eventpointer>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-eventpointer/meta.yaml>`_

   EventPointer is an R package to identify alternative splicing events that involve either simple \(case\-control experiment\) or complex experimental designs such as time course experiments and studies including paired\-samples. The algorithm can be used to analyze data from either junction arrays \(Affymetrix Arrays\) or sequencing data \(RNA\-Seq\). The software returns a data.frame with the detected alternative splicing events\: gene name\, type of event \(cassette\, alternative 3\'\,...\,etc\)\, genomic position\, statistical significance and increment of the percent spliced in \(Delta PSI\) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.


.. conda:package:: bioconductor-eventpointer

   |downloads_bioconductor-eventpointer| |docker_bioconductor-eventpointer|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>3.18.0-0</code>,  <code>3.14.0-0</code>,  <code>3.10.0-0</code>,  <code>3.8.0-0</code>,  <code>3.6.0-1</code>,  <code>3.6.0-0</code>,  <code>3.2.0-2</code>,  <code>3.2.0-1</code>,  <code>3.2.0-0</code>,  </span></summary>
      

      ``3.18.0-0``,  ``3.14.0-0``,  ``3.10.0-0``,  ``3.8.0-0``,  ``3.6.0-1``,  ``3.6.0-0``,  ``3.2.0-2``,  ``3.2.0-1``,  ``3.2.0-0``,  ``3.0.0-0``,  ``2.8.0-1``,  ``2.8.0-0``,  ``2.6.0-0``,  ``2.4.0-0``,  ``2.2.4-0``,  ``2.0.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends on bioconductor-affxparser: ``>=1.82.0,<1.83.0``
   :depends on bioconductor-affxparser: ``>=1.82.0,<1.83.0a0``
   :depends on bioconductor-biostrings: ``>=2.78.0,<2.79.0``
   :depends on bioconductor-biostrings: ``>=2.78.0,<2.79.0a0``
   :depends on bioconductor-bsgenome: ``>=1.78.0,<1.79.0``
   :depends on bioconductor-bsgenome: ``>=1.78.0,<1.79.0a0``
   :depends on bioconductor-fgsea: ``>=1.36.0,<1.37.0``
   :depends on bioconductor-fgsea: ``>=1.36.2,<1.37.0a0``
   :depends on bioconductor-genomeinfodb: ``>=1.46.0,<1.47.0``
   :depends on bioconductor-genomeinfodb: ``>=1.46.2,<1.47.0a0``
   :depends on bioconductor-genomicfeatures: ``>=1.62.0,<1.63.0``
   :depends on bioconductor-genomicfeatures: ``>=1.62.0,<1.63.0a0``
   :depends on bioconductor-genomicranges: ``>=1.62.0,<1.63.0``
   :depends on bioconductor-genomicranges: ``>=1.62.1,<1.63.0a0``
   :depends on bioconductor-graph: ``>=1.88.0,<1.89.0``
   :depends on bioconductor-graph: ``>=1.88.1,<1.89.0a0``
   :depends on bioconductor-iranges: ``>=2.44.0,<2.45.0``
   :depends on bioconductor-iranges: ``>=2.44.0,<2.45.0a0``
   :depends on bioconductor-limma: ``>=3.66.0,<3.67.0``
   :depends on bioconductor-limma: ``>=3.66.0,<3.67.0a0``
   :depends on bioconductor-qvalue: ``>=2.42.0,<2.43.0``
   :depends on bioconductor-qvalue: ``>=2.42.0,<2.43.0a0``
   :depends on bioconductor-rbgl: ``>=1.86.0,<1.87.0``
   :depends on bioconductor-rbgl: ``>=1.86.0,<1.87.0a0``
   :depends on bioconductor-rhdf5: ``>=2.54.0,<2.55.0``
   :depends on bioconductor-rhdf5: ``>=2.54.1,<2.55.0a0``
   :depends on bioconductor-s4vectors: ``>=0.48.0,<0.49.0``
   :depends on bioconductor-s4vectors: ``>=0.48.0,<0.49.0a0``
   :depends on bioconductor-sgseq: ``>=1.44.0,<1.45.0``
   :depends on bioconductor-sgseq: ``>=1.44.0,<1.45.0a0``
   :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0``
   :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0a0``
   :depends on bioconductor-tximport: ``>=1.38.0,<1.39.0``
   :depends on bioconductor-tximport: ``>=1.38.2,<1.39.0a0``
   :depends on libblas: ``>=3.9.0,<4.0a0``
   :depends on liblapack: ``>=3.9.0,<4.0a0``
   :depends on liblzma: ``>=5.8.2,<6.0a0``
   :depends on libzlib: ``>=1.3.1,<2.0a0``
   :depends on r-abind: 
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-cobs: 
   :depends on r-doparallel: 
   :depends on r-foreach: 
   :depends on r-glmnet: 
   :depends on r-igraph: 
   :depends on r-iterators: 
   :depends on r-lpsolve: 
   :depends on r-mass: 
   :depends on r-matrix: 
   :depends on r-matrixstats: 
   :depends on r-nnls: 
   :depends on r-poibin: 
   :depends on r-prodlim: 
   :depends on r-speedglm: 
   :depends on r-stringr: 

   :additional platforms:
      

Installation
------------

You need a conda-compatible package manager
(currently either `pixi <https://pixi.sh>`__, `conda <https://docs.conda.io/projects/conda>`__, or `micromamba <https://mamba.readthedocs.io>`__)
and the Bioconda channel already activated (see :ref:`bioconda_setup`).
Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi
""""

With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`),
to install globally, run::

    pixi global install bioconductor-eventpointer

to add into an existing workspace instead, run::

    pixi add bioconductor-eventpointer

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace::

    pixi workspace channel add conda-forge
    pixi workspace channel add bioconda

Conda
"""""

With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run::

    conda install bioconductor-eventpointer

Alternatively, to install into a new environment, run::

    conda create -n envname bioconductor-eventpointer

with ``envname`` being the name of the desired environment.

Container
"""""""""

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime.
For e.g. docker, run::

    docker pull quay.io/biocontainers/bioconductor-eventpointer:<tag>

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

Integrated deployment
"""""""""""""""""""""

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment.
Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency.
Check the documentation of your workflow management system to find out about the integration.

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


.. raw:: html

    <script>
        var package = "bioconductor-eventpointer";
        var versions = ["3.18.0","3.14.0","3.10.0","3.8.0","3.6.0"];
    </script>






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

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

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-eventpointer/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/bioconductor-eventpointer/README.html