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

.. title:: Package Recipe 'bioconductor-seq2pathway'
.. highlight: bash

bioconductor-seq2pathway
========================

.. conda:recipe:: bioconductor-seq2pathway
   :replaces_section_title:
   :noindex:

   a novel tool for functional gene\-set \(or termed as pathway\) analysis of next\-generation sequencing data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/seq2pathway.html
   :license: GPL-2
   :recipe: /`bioconductor-seq2pathway <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-seq2pathway>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-seq2pathway/meta.yaml>`_
   :links: biotools: :biotools:`seq2pathway`

   Seq2pathway is a novel tool for functional gene\-set \(or termed as pathway\) analysis of next\-generation sequencing data\, consisting of \"seq2gene\" and \"gene2path\" components. The seq2gene links sequence\-level measurements of genomic regions \(including SNPs or point mutation coordinates\) to gene\-level scores\, and the gene2pathway summarizes gene scores to pathway\-scores for each sample. The seq2gene has the feasibility to assign both coding and non\-exon regions to a broader range of neighboring genes than only the nearest one\, thus facilitating the study of functional non\-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway\-level scores\, thus allowing one to functional interpret such datasets as RNA\-seq\, ChIP\-seq\, GWAS\, and derived from other next generational sequencing experiments.


.. conda:package:: bioconductor-seq2pathway

   |downloads_bioconductor-seq2pathway| |docker_bioconductor-seq2pathway|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.34.0-0</code>,  <code>1.32.0-0</code>,  <code>1.30.0-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-1</code>,  <code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-1</code>,  </span></summary>
      

      ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.16.0-1``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-seq2pathway.data: ``>=1.34.0,<1.35.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-gsa: 
   :depends r-nnet: 
   :depends r-wgcna: 
   :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-seq2pathway

   and update with::

      mamba update bioconductor-seq2pathway

  To create a new environment, run::

      mamba create --name myenvname bioconductor-seq2pathway

  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-seq2pathway:<tag>

   (see `bioconductor-seq2pathway/tags`_ for valid values for ``<tag>``)


.. |downloads_bioconductor-seq2pathway| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-seq2pathway.svg?style=flat
   :target: https://anaconda.org/bioconda/bioconductor-seq2pathway
   :alt:   (downloads)
.. |docker_bioconductor-seq2pathway| image:: https://quay.io/repository/biocontainers/bioconductor-seq2pathway/status
   :target: https://quay.io/repository/biocontainers/bioconductor-seq2pathway
.. _`bioconductor-seq2pathway/tags`: https://quay.io/repository/biocontainers/bioconductor-seq2pathway?tab=tags


.. raw:: html

    <script>
        var package = "bioconductor-seq2pathway";
        var versions = ["1.34.0","1.32.0","1.30.0","1.26.0","1.24.0"];
    </script>






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

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

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