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

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

bioconductor-nadfinder
======================

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

   Call wide peaks for sequencing data

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/NADfinder.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-nadfinder <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-nadfinder>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-nadfinder/meta.yaml>`_

   Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes\, aka ribosome biogenesis. In addition\, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non\-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli \(NAD\- seq\) have shown that specific loci\, termed nucleolus\- associated domains \(NADs\) form frequent three\- dimensional associations with nucleoli. NAD\-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell \(ESC\) differentiation. Here\, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD\-seq data\, including baseline correction\, smoothing\, normalization\, peak calling\, and annotation.


.. conda:package:: bioconductor-nadfinder

   |downloads_bioconductor-nadfinder| |docker_bioconductor-nadfinder|

   :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``,  ``1.8.1-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends on bioconductor-atacseqqc: ``>=1.34.0,<1.35.0``
   :depends on bioconductor-biocgenerics: ``>=0.56.0,<0.57.0``
   :depends on bioconductor-csaw: ``>=1.44.0,<1.45.0``
   :depends on bioconductor-empiricalbrownsmethod: ``>=1.38.0,<1.39.0``
   :depends on bioconductor-genomeinfodb: ``>=1.46.0,<1.47.0``
   :depends on bioconductor-genomicalignments: ``>=1.46.0,<1.47.0``
   :depends on bioconductor-genomicranges: ``>=1.62.0,<1.63.0``
   :depends on bioconductor-iranges: ``>=2.44.0,<2.45.0``
   :depends on bioconductor-limma: ``>=3.66.0,<3.67.0``
   :depends on bioconductor-rsamtools: ``>=2.26.0,<2.27.0``
   :depends on bioconductor-rtracklayer: ``>=1.70.0,<1.71.0``
   :depends on bioconductor-s4vectors: ``>=0.48.0,<0.49.0``
   :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0``
   :depends on bioconductor-trackviewer: ``>=1.46.0,<1.47.0``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-baseline: 
   :depends on r-corrplot: 
   :depends on r-metap: 
   :depends on r-signal: 

   :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-nadfinder

to add into an existing workspace instead, run::

    pixi add bioconductor-nadfinder

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-nadfinder

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

    conda create -n envname bioconductor-nadfinder

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-nadfinder:<tag>

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


.. raw:: html

    <script>
        var package = "bioconductor-nadfinder";
        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-nadfinder/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-nadfinder/README.html