Smoother
--------


.. image:: ../biosmoother/static/favicon.png
    :width: 200
    :align: center


Smoother is an interactive analysis and visualization software for nucleic acid interactome data that allows the change of parameters such as normalization, bin size or MAPQ on-the-fly. Smoother can load multiple samples which can be grouped and compared. Smoother also allows filtering by annotations and the display of coverage for additional sequencing data.

Smoother is centered around an index including the genome, annotations, and datasets to be analyzed and visualized. Using this index, Smoother allows changing analysis parameters on-the-fly.

Manuscript
----------

Smoother has been published in Nucleic Acids Research. If you use Smoother in your research, please cite:

Markus R Schmidt, Anna Barcons-Simon, Claudia Rabuffo, T Nicolai Siegel, Smoother: on-the-fly processing of interactome data using prefix sums, Nucleic Acids Research, 2024; gkae008, https://doi.org/10.1093/nar/gkae008

Smoothers source code is available at `GitHub <https://github.com/Siegel-Lab/BioSmoother>`_.

Table of Contents
-----------------

* :ref:`QuickStart <quickstart_target>`
* :ref:`Overview <overview_target>`
* :ref:`Taking a Tour <tour_target>`
* :ref:`Installation <installation_target>`
* :ref:`Command organization <command_organization_target>`
* :ref:`Creating an index <creating_an_index_target>`
* :ref:`Using the graphical interface <using_graphical_target>`
* :ref:`Using the command line interface <using_cli_target>`
* :ref:`Citing Smoother <citing_target>`
* :ref:`References and acknowledgments <ref_and_ack_target>`
* :ref:`Command line API reference <cli_target>`

.. toctree::
   :hidden:

   Manual
   Cli
   genindex