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

.. title:: Package Recipe 'bioconductor-exomepeak2'
.. highlight: bash

bioconductor-exomepeak2
=======================

.. conda:recipe:: bioconductor-exomepeak2
   :replaces_section_title:
   :noindex:

   Bias\-aware Peak Calling and Quantification for MeRIP\-Seq

   :homepage: https://bioconductor.org/packages/3.14/bioc/html/exomePeak2.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-exomepeak2 <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-exomepeak2>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-exomepeak2/meta.yaml>`_

   exomePeak2 provides bias\-aware quantification and peak detection for Methylated RNA immunoprecipitation sequencing data \(MeRIP\-Seq\). MeRIP\-Seq is a commonly applied sequencing technology that can measure the location and abundance of RNA modification sites under given cell line conditions. However\, quantification and peak calling in MeRIP\-Seq are sensitive to PCR amplification biases\, which generally present in next\-generation sequencing \(NGS\) technologies. In addition\, the count data generated by RNA\-Seq exhibits significant biological variations between biological replicates. exomePeak2 collectively address the challenges by introducing a series of robust data science tools tailored for MeRIP\-Seq. Using exomePeak2\, users can perform peak calling\, modification site quantification and differential analysis through a straightforward single\-step function. Alternatively\, multi\-step functions can be used to generate diagnostic plots and perform customized analyses.


.. conda:package:: bioconductor-exomepeak2

   |downloads_bioconductor-exomepeak2| |docker_bioconductor-exomepeak2|

   :versions:
      
      

      ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.2.0-0``,  ``1.0.0-0``

      

   
   :depends bioconductor-apeglm: ``>=1.16.0,<1.17.0``
   :depends bioconductor-biobase: ``>=2.54.0,<2.55.0``
   :depends bioconductor-biocgenerics: ``>=0.40.0,<0.41.0``
   :depends bioconductor-biocparallel: ``>=1.28.0,<1.29.0``
   :depends bioconductor-biostrings: ``>=2.62.0,<2.63.0``
   :depends bioconductor-bsgenome: ``>=1.62.0,<1.63.0``
   :depends bioconductor-cqn: ``>=1.40.0,<1.41.0``
   :depends bioconductor-deseq2: ``>=1.34.0,<1.35.0``
   :depends bioconductor-genefilter: ``>=1.76.0,<1.77.0``
   :depends bioconductor-genomeinfodb: ``>=1.30.0,<1.31.0``
   :depends bioconductor-genomicalignments: ``>=1.30.0,<1.31.0``
   :depends bioconductor-genomicfeatures: ``>=1.46.0,<1.47.0``
   :depends bioconductor-genomicranges: ``>=1.46.0,<1.47.0``
   :depends bioconductor-iranges: ``>=2.28.0,<2.29.0``
   :depends bioconductor-rsamtools: ``>=2.10.0,<2.11.0``
   :depends bioconductor-rtracklayer: ``>=1.54.0,<1.55.0``
   :depends bioconductor-s4vectors: ``>=0.32.0,<0.33.0``
   :depends bioconductor-summarizedexperiment: ``>=1.24.0,<1.25.0``
   :depends r-base: ``>=4.1,<4.2.0a0``
   :depends r-ggplot2: 
   :depends r-mclust: 
   :depends r-reshape2: 
   :requirements:

   .. rubric:: Installation

   With an activated Bioconda channel (see :ref:`set-up-channels`), install with::

      conda install bioconductor-exomepeak2

   and update with::

      conda update bioconductor-exomepeak2

   or use the docker container::

      docker pull quay.io/biocontainers/bioconductor-exomepeak2:<tag>

   (see `bioconductor-exomepeak2/tags`_ for valid values for ``<tag>``)


.. |downloads_bioconductor-exomepeak2| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-exomepeak2.svg?style=flat
   :target: https://anaconda.org/bioconda/bioconductor-exomepeak2
   :alt:   (downloads)
.. |docker_bioconductor-exomepeak2| image:: https://quay.io/repository/biocontainers/bioconductor-exomepeak2/status
   :target: https://quay.io/repository/biocontainers/bioconductor-exomepeak2
.. _`bioconductor-exomepeak2/tags`: https://quay.io/repository/biocontainers/bioconductor-exomepeak2?tab=tags


.. raw:: html

    <script>
        var package = "bioconductor-exomepeak2";
        var versions = ["1.6.0","1.4.0","1.2.0","1.2.0","1.0.0"];
    </script>






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

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

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
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