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

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

bioconductor-profileplyr
========================

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

   Visualization and annotation of read signal over genomic ranges with profileplyr

   :homepage: https://bioconductor.org/packages/3.14/bioc/html/profileplyr.html
   :license: GPL (>= 3)
   :recipe: /`bioconductor-profileplyr <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-profileplyr>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-profileplyr/meta.yaml>`_

   Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets \(e.g. ChIP\-seq\, ATAC\-seq\, bisulfite\/methyl\-seq\). Many tools both inside and outside of R and Bioconductor are available to explore these types of data\, and they typically start with a bigWig or BAM file and end with some representation of the signal \(e.g. heatmap\). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.


.. conda:package:: bioconductor-profileplyr

   |downloads_bioconductor-profileplyr| |docker_bioconductor-profileplyr|

   :versions:
      
      

      ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.6.0-0``,  ``1.4.3-0``,  ``1.2.0-0``,  ``1.0.1-0``

      

   
   :depends bioconductor-biocgenerics: ``>=0.40.0,<0.41.0``
   :depends bioconductor-biocparallel: ``>=1.28.0,<1.29.0``
   :depends bioconductor-chipseeker: ``>=1.30.0,<1.31.0``
   :depends bioconductor-complexheatmap: ``>=2.10.0,<2.11.0``
   :depends bioconductor-enrichedheatmap: ``>=1.24.0,<1.25.0``
   :depends bioconductor-genomeinfodb: ``>=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-org.hs.eg.db: ``>=3.14.0,<3.15.0``
   :depends bioconductor-org.mm.eg.db: ``>=3.14.0,<3.15.0``
   :depends bioconductor-rgreat: ``>=1.26.0,<1.27.0``
   :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-soggi: ``>=1.26.0,<1.27.0``
   :depends bioconductor-summarizedexperiment: ``>=1.24.0,<1.25.0``
   :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.0,<3.3.0``
   :depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene: ``>=3.14.0,<3.15.0``
   :depends bioconductor-txdb.mmusculus.ucsc.mm10.knowngene: ``>=3.10.0,<3.11.0``
   :depends bioconductor-txdb.mmusculus.ucsc.mm9.knowngene: ``>=3.2.0,<3.3.0``
   :depends r-base: ``>=4.1,<4.2.0a0``
   :depends r-cairo: 
   :depends r-circlize: 
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-magrittr: 
   :depends r-pheatmap: 
   :depends r-r.utils: 
   :depends r-rjson: 
   :depends r-rlang: 
   :depends r-tidyr: 
   :depends r-tiff: 
   :requirements:

   .. rubric:: Installation

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

      conda install bioconductor-profileplyr

   and update with::

      conda update bioconductor-profileplyr

   or use the docker container::

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

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


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


.. raw:: html

    <script>
        var package = "bioconductor-profileplyr";
        var versions = ["1.10.0","1.8.0","1.6.0","1.6.0","1.4.3"];
    </script>






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

.. raw:: html
    :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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