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        "author": "Simon H\u00e9bert-Deschamps",
        "author_email": "simon.hebert-deschamps@usherbrooke.ca",
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            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# epiGeEC Analysis #\n\nThe **epiGenomic Efficient Correlator (epiGeEC) Analysis** is a suite of tools to process, annotate and analyse correlation matrices generated by [**epiGeEC**](https://bitbucket.org/labjacquespe/epigeec/src/master/). A galaxy implementation featuring these tools and including thousands of pre-computed public epigenomic datasets is availalble at <http://epigeec.genap.ca/galaxy/>.\n\n### Installation\n\nLinux/x64 is the only OS currently supported, but it can work on any platform with python and pip installed.\n\n#### Dependencies\n\nYou will need pip to install the python package, use the following command if not already installed\n\n\tsudo apt-get install python-pip\n\nPip will attempt to install all dependencies but most likely will fail\n\nSee documentation on how to install [pandas](https://github.com/svaksha/PyData-Workshop-Sprint/wiki/linux-install-pandas).\n\nYou might have more success with\n\n\tsudo apt-get install python-pandas\n\n#### Install epiGeEC Analysis\n\n    sudo pip install epigeec-analysis\n\n### How To Use\n\nThis tool suite provide multiple analysis program.\n\nFor more info on each parameter use the help flag\n\n\tepigeec-analysis [tool] --help\n\n#### Annotate matrix\n\nEssentialy, this tool apply a hierachical cluster method on a correlation matrix to\nregroup datasets in clusters associated with their metadatas.\n\n![Hierarchical clustering](images/img5.jpg)\n\n\n\n    epigeec-analysis annotate --pdf output.pdf --tsv output.tsv epiGeEC_Correlate.mat epiGeEC_Datasets.json assay cell_type timepoint\n\n#### Evaluate clusters\n\n    epigeec-analysis evaluate epiGeEC_Correlate.mat epiGeEC_Datasets.json -b assay cell_type timepoint -r assay cell_type timepoint > output.ari\n\n### License\n\n[GNU General Public License v3](LICENSE)\n\n",
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