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

.. title:: Package Recipe 'r-bulkanalyser'
.. highlight: bash

r-bulkanalyser
==============

.. conda:recipe:: r-bulkanalyser
   :replaces_section_title:
   :noindex:

   Given an expression matrix from a bulk sequencing experiment\, pre\-processes it and creates a shiny app for interactive data analysis and visualisation. The app contains quality checks\, differential expression analysis\, volcano and cross plots\, enrichment analysis and gene regulatory network inference\, and can be customised to contain more panels by the user.

   :homepage: https://github.com/Core-Bioinformatics/bulkAnalyseR
   :license: GPL2 / GPL-2.0-only
   :recipe: /`r-bulkanalyser <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-bulkanalyser>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-bulkanalyser/meta.yaml>`_

   


.. conda:package:: r-bulkanalyser

   |downloads_r-bulkanalyser| |docker_r-bulkanalyser|

   :versions:
      
      

      ``1.1.0-2``,  ``1.1.0-1``,  ``1.1.0-0``,  ``1.0.0-1``,  ``1.0.0-0``

      

   
   :depends bioconductor-complexheatmap: 
   :depends bioconductor-deseq2: 
   :depends bioconductor-edger: 
   :depends bioconductor-genie3: 
   :depends bioconductor-preprocesscore: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-circlize: 
   :depends r-dplyr: 
   :depends r-dt: 
   :depends r-ggforce: 
   :depends r-ggnewscale: 
   :depends r-ggplot2: 
   :depends r-ggrastr: 
   :depends r-ggrepel: 
   :depends r-ggvenndiagram: 
   :depends r-glue: 
   :depends r-gprofiler2: 
   :depends r-magrittr: 
   :depends r-matrixstats: 
   :depends r-noisyr: 
   :depends r-rcolorbrewer: 
   :depends r-rlang: 
   :depends r-scales: 
   :depends r-shiny: 
   :depends r-shinyjqui: 
   :depends r-shinyjs: 
   :depends r-shinylp: 
   :depends r-shinywidgets: 
   :depends r-stringr: 
   :depends r-tibble: 
   :depends r-tidyr: 
   :depends r-upsetr: 
   :depends r-visnetwork: 
   :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 r-bulkanalyser

   and update with::

      mamba update r-bulkanalyser

  To create a new environment, run::

      mamba create --name myenvname r-bulkanalyser

  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/r-bulkanalyser:<tag>

   (see `r-bulkanalyser/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "r-bulkanalyser";
        var versions = ["1.1.0","1.1.0","1.1.0","1.0.0","1.0.0"];
    </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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