Metadata-Version: 1.2
Name: MAnorm
Version: 1.1.4
Summary: A robust model for quantitative comparison of ChIP-Seq data sets.
Home-page: https://github.com/shao-lab/MAnorm
Author: Semal
Author-email: 
Maintainer: Hayden Sun
Maintainer-email: sunhongduo@picb.ac.cn
License: BSD
Description: MAnorm
        ======
        
        |travis-ci| |Documentation Status| |pypi| |install with bioconda| |license|
        
        .. |travis-ci| image:: https://travis-ci.org/shao-lab/MAnorm.svg?branch=master
           :target: https://travis-ci.org/shao-lab/MAnorm
        .. |Documentation Status| image:: https://readthedocs.org/projects/manorm/badge/?version=latest
           :target: http://manorm.readthedocs.io/en/latest/?badge=latest
        .. |pypi| image:: https://img.shields.io/pypi/v/MAnorm.svg
           :target: https://pypi.python.org/pypi/MAnorm
        .. |install with bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
           :target: http://bioconda.github.io/recipes/manorm/README.html
        .. |license| image:: https://img.shields.io/pypi/l/MAnorm.svg
           :target: https://github.com/shao-lab/MAnorm/blob/master/LICENSE
        
        Introduction
        ------------
        
        ChIP-Seq is widely used to characterize genome-wide binding patterns of
        transcription factors and other chromatin-associated proteins. Although
        comparison of ChIP-Seq data sets is critical for understanding cell
        type-dependent and cell state-specific binding, and thus the study of
        cell-specific gene regulation, few quantitative approaches have been
        developed.
        
        Here, we present a simple and effective method, MAnorm, for quantitative
        comparison of ChIP-Seq data sets describing transcription factor binding
        sites and epigenetic modifications. The quantitative binding differences
        inferred by MAnorm showed strong correlation with both the changes in
        expression of target genes and the binding of cell type-specific
        regulators.
        
        Citation
        --------
        
        `Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. MAnorm: a robust model for quantitative comparison of
        ChIP-Seq data sets. Genome biology. 2012 Mar 16;13(3):R16.
        <https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-3-r16>`__
        
        Documentation
        -------------
        
        To see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io/en/latest/
        
        Installation
        ------------
        
        The latest version release of MAnorm is available at
        `PyPI <https://pypi.python.org/pypi/MAnorm>`__:
        
        ::
        
            $ pip install manorm
        
        Or you can install MAnorm via conda:
        
        ::
        
            $ conda install -c bioconda manorm
        
        MAnorm uses `setuptools <https://setuptools.readthedocs.io/en/latest/>`__ for installation from source code.
        The source code of MAnorm is hosted on GitHub: https://github.com/shao-lab/MAnorm
        
        You can clone the repo and execute the following command under source directory:
        
        ::
        
            $ python setup.py install
        
        Galaxy Installation
        -------------------
        MAnorm is available on Galaxy_, you can incorporate MAnorm into your own Galaxy instance.
        
        Please search and install MAnorm via the `Galaxy Tool Shed`_.
        
        .. _Galaxy: https://galaxyproject.org
        .. _`Galaxy Tool Shed`: https://toolshed.g2.bx.psu.edu/view/haydensun/manorm
        
        Usage
        -----
        
        ::
        
            $ manorm --p1 sample1_peaks.bed --p2 sample2_peaks.bed --r1 sample1_reads.bed --r2 sample2_reads.bed -o sample1_vs_sample2
        
        **Note:** Using -h/--help for the details of all arguments.
        
        License
        -------
        
        `BSD 3-Clause
        License <https://github.com/shao-lab/MAnorm/blob/master/LICENSE>`__
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
