{ "info": { "author": "Semal", "author_email": "", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "MAnorm\n======\n\n|travis-ci| |Documentation Status| |pypi| |install with bioconda| |license|\n\n.. |travis-ci| image:: https://travis-ci.org/shao-lab/MAnorm.svg?branch=master\n :target: https://travis-ci.org/shao-lab/MAnorm\n.. |Documentation Status| image:: https://readthedocs.org/projects/manorm/badge/?version=latest\n :target: http://manorm.readthedocs.io/en/latest/?badge=latest\n.. |pypi| image:: https://img.shields.io/pypi/v/MAnorm.svg\n :target: https://pypi.python.org/pypi/MAnorm\n.. |install with bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square\n :target: http://bioconda.github.io/recipes/manorm/README.html\n.. |license| image:: https://img.shields.io/pypi/l/MAnorm.svg\n :target: https://github.com/shao-lab/MAnorm/blob/master/LICENSE\n\nIntroduction\n------------\n\nChIP-Seq is widely used to characterize genome-wide binding patterns of\ntranscription factors and other chromatin-associated proteins. Although\ncomparison of ChIP-Seq data sets is critical for understanding cell\ntype-dependent and cell state-specific binding, and thus the study of\ncell-specific gene regulation, few quantitative approaches have been\ndeveloped.\n\nHere, we present a simple and effective method, MAnorm, for quantitative\ncomparison of ChIP-Seq data sets describing transcription factor binding\nsites and epigenetic modifications. The quantitative binding differences\ninferred by MAnorm showed strong correlation with both the changes in\nexpression of target genes and the binding of cell type-specific\nregulators.\n\nCitation\n--------\n\n`Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. MAnorm: a robust model for quantitative comparison of\nChIP-Seq data sets. Genome biology. 2012 Mar 16;13(3):R16.\n`__\n\nDocumentation\n-------------\n\nTo see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io/en/latest/\n\nInstallation\n------------\n\nThe latest version release of MAnorm is available at\n`PyPI `__:\n\n::\n\n $ pip install manorm\n\nOr you can install MAnorm via conda:\n\n::\n\n $ conda install -c bioconda manorm\n\nMAnorm uses `setuptools `__ for installation from source code.\nThe source code of MAnorm is hosted on GitHub: https://github.com/shao-lab/MAnorm\n\nYou can clone the repo and execute the following command under source directory:\n\n::\n\n $ python setup.py install\n\nGalaxy Installation\n-------------------\nMAnorm is available on Galaxy_, you can incorporate MAnorm into your own Galaxy instance.\n\nPlease search and install MAnorm via the `Galaxy Tool Shed`_.\n\n.. _Galaxy: https://galaxyproject.org\n.. _`Galaxy Tool Shed`: 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