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

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

bioconductor-cleanuprnaseq
==========================

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

   Detect and Correct Genomic DNA Contamination in RNA\-seq Data

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/CleanUpRNAseq.html
   :license: GPL-3
   :recipe: /`bioconductor-cleanuprnaseq <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-cleanuprnaseq>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-cleanuprnaseq/meta.yaml>`_

   RNA\-seq data generated by some library preparation methods\, such as rRNA\-depletion\-based method and the SMART\-seq method\, might be contaminated by genomic DNA \(gDNA\)\, if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA\-seq data is suffered from gDNA contamination. If so\, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.


.. conda:package:: bioconductor-cleanuprnaseq

   |downloads_bioconductor-cleanuprnaseq| |docker_bioconductor-cleanuprnaseq|

   :versions:
      
      

      ``1.0.0-0``

      

   
   :depends bioconductor-annotationfilter: ``>=1.30.0,<1.31.0``
   :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0``
   :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0``
   :depends bioconductor-bsgenome: ``>=1.74.0,<1.75.0``
   :depends bioconductor-deseq2: ``>=1.46.0,<1.47.0``
   :depends bioconductor-edger: ``>=4.4.0,<4.5.0``
   :depends bioconductor-ensembldb: ``>=2.30.0,<2.31.0``
   :depends bioconductor-genomeinfodb: ``>=1.42.0,<1.43.0``
   :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0``
   :depends bioconductor-limma: ``>=3.62.0,<3.63.0``
   :depends bioconductor-qsmooth: ``>=1.22.0,<1.23.0``
   :depends bioconductor-rsamtools: ``>=2.22.0,<2.23.0``
   :depends bioconductor-rsubread: ``>=2.20.0,<2.21.0``
   :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0``
   :depends bioconductor-tximport: ``>=1.34.0,<1.35.0``
   :depends r-base: ``>=4.4,<4.5.0a0``
   :depends r-ggplot2: 
   :depends r-ggrepel: 
   :depends r-kernsmooth: 
   :depends r-pheatmap: 
   :depends r-r6: 
   :depends r-rcolorbrewer: 
   :depends r-reshape2: 
   :requirements:

   :additional platforms:
      

   .. 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-cleanuprnaseq

   and update with::

      mamba update bioconductor-cleanuprnaseq

  To create a new environment, run::

      mamba create --name myenvname bioconductor-cleanuprnaseq

  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-cleanuprnaseq:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-cleanuprnaseq";
        var versions = ["1.0.0"];
    </script>






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

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

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