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

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

bioconductor-proactiv
=====================

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

   Estimate Promoter Activity from RNA\-Seq data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/proActiv.html
   :license: MIT + file LICENSE
   :recipe: /`bioconductor-proactiv <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-proactiv>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-proactiv/meta.yaml>`_

   Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre\-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA\-seq data. proActiv uses aligned reads as input\, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular\, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active\, which promoter is inactive\, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.


.. conda:package:: bioconductor-proactiv

   |downloads_bioconductor-proactiv| |docker_bioconductor-proactiv|

   :versions:
      
      

      ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-2``,  ``1.0.0-1``

      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0``
   :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-gplots: 
   :depends r-rlang: 
   :depends r-scales: 
   :depends r-tibble: 
   :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-proactiv

   and update with::

      mamba update bioconductor-proactiv

  To create a new environment, run::

      mamba create --name myenvname bioconductor-proactiv

  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-proactiv:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-proactiv";
        var versions = ["1.12.0","1.10.0","1.8.0","1.4.0","1.2.0"];
    </script>






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-----------------

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

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