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

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

bioconductor-curatedmetagenomicdata
===================================

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

   Curated Metagenomic Data of the Human Microbiome

   :homepage: https://bioconductor.org/packages/3.18/data/experiment/html/curatedMetagenomicData.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-curatedmetagenomicdata <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-curatedmetagenomicdata>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-curatedmetagenomicdata/meta.yaml>`_

   The curatedMetagenomicData package provides standardized\, curated human microbiome data for novel analyses. It includes gene families\, marker abundance\, marker presence\, pathway abundance\, pathway coverage\, and relative abundance for samples collected from different body sites. The bacterial\, fungal\, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3\, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as \(Tree\)SummarizedExperiment objects.


.. conda:package:: bioconductor-curatedmetagenomicdata

   |downloads_bioconductor-curatedmetagenomicdata| |docker_bioconductor-curatedmetagenomicdata|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>3.10.0-0</code>,  <code>3.8.0-0</code>,  <code>3.6.0-0</code>,  <code>3.4.1-0</code>,  <code>3.2.3-0</code>,  <code>3.2.1-0</code>,  <code>3.0.1-0</code>,  <code>1.20.0-1</code>,  <code>1.20.0-0</code>,  </span></summary>
      

      ``3.10.0-0``,  ``3.8.0-0``,  ``3.6.0-0``,  ``3.4.1-0``,  ``3.2.3-0``,  ``3.2.1-0``,  ``3.0.1-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.1-0``,  ``1.12.3-0``,  ``1.10.2-0``,  ``1.8.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationhub: ``>=3.10.0,<3.11.0``
   :depends bioconductor-data-packages: ``>=20231203``
   :depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0``
   :depends bioconductor-mia: ``>=1.10.0,<1.11.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends bioconductor-treesummarizedexperiment: ``>=2.10.0,<2.11.0``
   :depends curl: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-dplyr: 
   :depends r-magrittr: 
   :depends r-purrr: 
   :depends r-rlang: 
   :depends r-stringr: 
   :depends r-tibble: 
   :depends r-tidyr: 
   :depends r-tidyselect: 
   :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-curatedmetagenomicdata

   and update with::

      mamba update bioconductor-curatedmetagenomicdata

  To create a new environment, run::

      mamba create --name myenvname bioconductor-curatedmetagenomicdata

  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-curatedmetagenomicdata:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-curatedmetagenomicdata";
        var versions = ["3.10.0","3.8.0","3.6.0","3.4.1","3.2.3"];
    </script>






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

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