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

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

bioconductor-knowseq
====================

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

   KnowSeq R\/Bioc package \- The Smart Transcriptomic Pipeline

   :homepage: https://bioconductor.org/packages/3.22/bioc/html/KnowSeq.html
   :license: GPL-2.0-or-later
   :recipe: /`bioconductor-knowseq <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-knowseq>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-knowseq/meta.yaml>`_

   KnowSeq proposes a novel methodology that comprises the most relevant steps in the Transcriptomic gene expression analysis. KnowSeq expects to serve as an integrative tool that allows to process and extract relevant biomarkers\, as well as to assess them through a Machine Learning approaches. Finally\, the last objective of KnowSeq is the biological knowledge extraction from the biomarkers \(Gene Ontology enrichment\, Pathway listing and Visualization and Evidences related to the addressed disease\). Although the package allows analyzing all the data manually\, the main strenght of KnowSeq is the possibilty of carrying out an automatic and intelligent HTML report that collect all the involved steps in one document. It is important to highligh that the pipeline is totally modular and flexible\, hence it can be started from whichever of the different steps. KnowSeq expects to serve as a novel tool to help to the experts in the field to acquire robust knowledge and conclusions for the data and diseases to study.


.. conda:package:: bioconductor-knowseq

   |downloads_bioconductor-knowseq| |docker_bioconductor-knowseq|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.24.0-0</code>,  <code>1.20.0-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  <code>1.8.0-0</code>,  <code>1.6.0-0</code>,  <code>1.4.4-0</code>,  <code>1.4.0-0</code>,  </span></summary>
      

      ``1.24.0-0``,  ``1.20.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.4-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1``

      
      .. raw:: html

         </details>
      

   
   :depends on bioconductor-cqn: ``>=1.56.0,<1.57.0``
   :depends on bioconductor-edger: ``>=4.8.0,<4.9.0``
   :depends on bioconductor-limma: ``>=3.66.0,<3.67.0``
   :depends on bioconductor-sva: ``>=3.58.0,<3.59.0``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-caret: 
   :depends on r-e1071: 
   :depends on r-ggplot2: ``>=3.3.0``
   :depends on r-gridextra: 
   :depends on r-hmisc: ``>=4.4.0``
   :depends on r-httr: 
   :depends on r-jsonlite: 
   :depends on r-kernlab: 
   :depends on r-praznik: 
   :depends on r-r.utils: 
   :depends on r-randomforest: 
   :depends on r-reshape2: 
   :depends on r-rlist: 
   :depends on r-rmarkdown: 
   :depends on r-stringr: 
   :depends on r-xml: 

   :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-knowseq

to add into an existing workspace instead, run::

    pixi add bioconductor-knowseq

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-knowseq

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

    conda create -n envname bioconductor-knowseq

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-knowseq:<tag>

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


.. raw:: html

    <script>
        var package = "bioconductor-knowseq";
        var versions = ["1.24.0","1.20.0","1.16.0","1.14.0","1.12.0"];
    </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-knowseq/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-knowseq/README.html