Metadata-Version: 1.0
Name: deepTools
Version: 2.3.2
Summary: Useful tools for exploring deep sequencing data 
Home-page: http://pypi.python.org/pypi/deepTools/
Author: Fidel Ramirez,  Devon P Ryan, Björn Grüning, Friederike Dündar, Sarah Diehl, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Thomas Manke
Author-email: deeptools@googlegroups.com
License: LICENSE.txt
Description: ======================================================================
        deepTools
        ======================================================================
        |Build Status| |Documentation Status| |PyPI version| |bioconda-badge|
        
        User-friendly tools for exploring deep-sequencing data
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        deepTools addresses the challenge of handling the large amounts of data
        that are now routinely generated from DNA sequencing centers. deepTools
        contains useful modules to process the mapped reads data for multiple
        quality checks, creating **normalized coverage files** in standard
        bedGraph and bigWig file formats, that allow comparison between
        different files (for example, treatment and control). Finally, using
        such normalized and standardized files, deepTools can create many
        publication-ready **visualizations** to identify enrichments and for
        functional annotations of the genome.
        
        For support, questions, or feature requests contact:
        deeptools@googlegroups.com
        
        Citation:
        ^^^^^^^^^
        
        Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne
        S, Dündar F, Manke T. `deepTools2: a next generation web server for
        deep-sequencing data
        analysis. <https://nar.oxfordjournals.org/content/early/2016/04/12/nar.gkw257.abstract>`__
        Nucleic Acids Research. 2016 Apr 13:gkw257.
        
        Documentation:
        ^^^^^^^^^^^^^^
        
        Our `documentation <http://deeptools.readthedocs.org/>`__ contains more
        details on the `individual tool scopes and
        usages <http://deeptools.readthedocs.org/en/latest/content/list_of_tools.html>`__
        and an `introduction to our deepTools Galaxy web
        server <http://deeptools.readthedocs.org/en/latest/content/help_galaxy_intro.html>`__
        including `step-by-step
        protocols <http://deeptools.readthedocs.org/en/latest/content/example_usage.html>`__.
        
            Please see also the
            `FAQ <http://deeptools.readthedocs.org/en/latest/content/help_faq.html>`__,
            which we update regularly. Our
            `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html>`__
            may give you some more ideas about the scope of deepTools.
        
            For more specific **troubleshooting, feedback, and tool
            suggestions**, contact us via deeptools@googlegroups.com.
        
        --------------
        
        Installation
        ^^^^^^^^^^^^
        
        deepTools are available for:
        
        -  Command line usage (via pip/anaconda/github)
        -  Integration into Galaxy servers (via toolshed/API/web-browser)
        
        There are many easy ways to install deepTools. Details can be found
        `here <https://deeptools.readthedocs.io/en/latest/content/installation.html>`__
        
        **Install by cloning this repository:**
        
        You can install any one of the deepTools branches on command line
        (linux/mac) by cloning this git repository :
        
        ::
        
            $ git clone https://github.com/fidelram/deepTools
            $ cd deepTools
            $ python setup.py install
        
        By default, the script will install the python library and executable
        codes globally, which means you need to be root or administrator of the
        machine to complete the installation. If you need to provide a
        nonstandard install prefix, or any other nonstandard options, you can
        provide many command line options to the install script.
        
        ::
        
            $ python setup.py --help
        
        For example, to install under a specific location use:
        
        ::
        
            $ python setup.py install --prefix <target directory>
        
        To install into your home directory, use:
        
        ::
        
            $ python setup.py install --user
        
        **Note:** From version 2.3 onwards, deepTools support **python3**. In
        case of any problems running with python3/python2, contact our user
        group : deeptools@googlegroups.com.
        
        --------------
        
        This tool suite is developed by the `Bioinformatics
        Facility <http://www1.ie-freiburg.mpg.de/bioinformaticsfac>`__ at the
        `Max Planck Institute for Immunobiology and Epigenetics,
        Freiburg <http://www1.ie-freiburg.mpg.de/>`__.
        
        `Documentation <http://deeptools.readthedocs.org/en/latest/index.html>`__
        \| `deepTools Galaxy <http://deeptools.ie-freiburg.mpg.de>`__ \|
        `FAQ <http://deeptools.readthedocs.org/en/latest/content/help_faq.html>`__
        
        .. |Build Status| image:: https://travis-ci.org/fidelram/deepTools.svg?branch=master
           :target: https://travis-ci.org/fidelram/deepTools
        .. |Documentation Status| image:: https://readthedocs.org/projects/deeptools/badge/
           :target: http://deeptools.readthedocs.org/
        .. |PyPI version| image:: https://badge.fury.io/py/deeptools.svg
           :target: https://badge.fury.io/py/deeptools
        .. |bioconda-badge| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
           :target: http://bioconda.github.io
        
Platform: UNKNOWN
