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

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

bioconductor-transcriptogramer
==============================

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

   Transcriptional analysis based on transcriptograms

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/transcriptogramer.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-transcriptogramer <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-transcriptogramer>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-transcriptogramer/meta.yaml>`_

   R package for transcriptional analysis based on transcriptograms\, a method to analyze transcriptomes that projects expression values on a set of ordered proteins\, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are\, hence\, genome wide gene expression profiles that provide a global view for the cellular metabolism\, while indicating gene sets whose expressions are altered.


.. conda:package:: bioconductor-transcriptogramer

   |downloads_bioconductor-transcriptogramer| |docker_bioconductor-transcriptogramer|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-1</code>,  <code>1.12.0-0</code>,  <code>1.10.0-0</code>,  <code>1.8.0-0</code>,  </span></summary>
      

      ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.4.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0``
   :depends bioconductor-limma: ``>=3.58.0,<3.59.0``
   :depends bioconductor-reder: ``>=2.6.0,<2.7.0``
   :depends bioconductor-topgo: ``>=2.54.0,<2.55.0``
   :depends openjdk: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-dosnow: 
   :depends r-foreach: 
   :depends r-ggplot2: 
   :depends r-igraph: 
   :depends r-progress: 
   :depends r-snow: 
   :depends r-tidyr: 
   :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 bioconductor-transcriptogramer

   and update with::

      mamba update bioconductor-transcriptogramer

  To create a new environment, run::

      mamba create --name myenvname bioconductor-transcriptogramer

  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-transcriptogramer:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-transcriptogramer";
        var versions = ["1.24.0","1.22.0","1.20.0","1.16.0","1.14.0"];
    </script>






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

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

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

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

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