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

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

bioconductor-rtcgatoolbox
=========================

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

   A new tool for exporting TCGA Firehose data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/RTCGAToolbox.html
   :license: GPL-2
   :recipe: /`bioconductor-rtcgatoolbox <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-rtcgatoolbox>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-rtcgatoolbox/meta.yaml>`_
   :links: biotools: :biotools:`rtcgatoolbox`

   Managing data from large scale projects such as The Cancer Genome Atlas \(TCGA\) for further analysis is an important and time consuming step for research projects. Several efforts\, such as Firehose project\, make TCGA pre\-processed data publicly available via web services and data portals but it requires managing\, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre\-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition\, it can be integrated with other analysis pipelines for following data analysis.


.. conda:package:: bioconductor-rtcgatoolbox

   |downloads_bioconductor-rtcgatoolbox| |docker_bioconductor-rtcgatoolbox|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.32.1-0</code>,  <code>2.30.0-0</code>,  <code>2.28.0-0</code>,  <code>2.24.0-0</code>,  <code>2.22.0-0</code>,  <code>2.20.0-1</code>,  <code>2.20.0-0</code>,  <code>2.18.0-0</code>,  <code>2.16.0-0</code>,  </span></summary>
      

      ``2.32.1-0``,  ``2.30.0-0``,  ``2.28.0-0``,  ``2.24.0-0``,  ``2.22.0-0``,  ``2.20.0-1``,  ``2.20.0-0``,  ``2.18.0-0``,  ``2.16.0-0``,  ``2.14.0-1``,  ``2.12.1-0``,  ``2.10.0-0``,  ``2.8.0-0``,  ``2.6.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-raggedexperiment: ``>=1.26.0,<1.27.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends bioconductor-tcgautils: ``>=1.22.0,<1.23.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-httr: 
   :depends r-rcurl: 
   :depends r-rjsonio: 
   :depends r-rvest: 
   :depends r-stringr: 
   :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-rtcgatoolbox

   and update with::

      mamba update bioconductor-rtcgatoolbox

  To create a new environment, run::

      mamba create --name myenvname bioconductor-rtcgatoolbox

  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-rtcgatoolbox:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-rtcgatoolbox";
        var versions = ["2.32.1","2.30.0","2.28.0","2.24.0","2.22.0"];
    </script>






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

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

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

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