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

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

bioconductor-river
==================

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

   R package for RIVER \(RNA\-Informed Variant Effect on Regulation\)

   :homepage: https://bioconductor.org/packages/3.22/bioc/html/RIVER.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-river <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-river>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-river/meta.yaml>`_

   An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations\, such as the location of a variant with respect to regulatory elements\, determine the prior probability that variant is a functional regulatory variant\, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information\, documentation and examples.


.. conda:package:: bioconductor-river

   |downloads_bioconductor-river| |docker_bioconductor-river|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.34.0-0</code>,  <code>1.30.0-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-1</code>,  <code>1.14.0-0</code>,  </span></summary>
      

      ``1.34.0-0``,  ``1.30.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.6.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends on bioconductor-biobase: ``>=2.70.0,<2.71.0``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-ggplot2: 
   :depends on r-glmnet: 
   :depends on r-proc: 

   :additional platforms:
      

Installation
------------

You need a conda-compatible package manager
(currently either `pixi <https://pixi.sh>`__, `conda <https://docs.conda.io/projects/conda>`__, or `micromamba <https://mamba.readthedocs.io>`__)
and the Bioconda channel already activated (see :ref:`bioconda_setup`).
Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi
""""

With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`),
to install globally, run::

    pixi global install bioconductor-river

to add into an existing workspace instead, run::

    pixi add bioconductor-river

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace::

    pixi workspace channel add conda-forge
    pixi workspace channel add bioconda

Conda
"""""

With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run::

    conda install bioconductor-river

Alternatively, to install into a new environment, run::

    conda create -n envname bioconductor-river

with ``envname`` being the name of the desired environment.

Container
"""""""""

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime.
For e.g. docker, run::

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

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

Integrated deployment
"""""""""""""""""""""

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment.
Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency.
Check the documentation of your workflow management system to find out about the integration.

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


.. raw:: html

    <script>
        var package = "bioconductor-river";
        var versions = ["1.34.0","1.30.0","1.26.0","1.24.0","1.22.0"];
    </script>






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

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

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

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

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-river/README.html)

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