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        "description": "Bio2BEL MSigDB |build| |coverage| |documentation| |zenodo|\n==========================================================\nThis package allows the enrichment of BEL networks with MSigDB information.\nFurthermore, it is integrated in the `ComPath environment <https://github.com/ComPath>`_ for pathway database comparison.\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\n``bio2bel_msig`` can be installed easily from `PyPI <https://pypi.python.org/pypi/bio2bel_msig>`_ with the\nfollowing code in your favorite terminal:\n\n.. code-block:: sh\n\n    $ python3 -m pip install bio2bel_msig\n\nor from the latest code on `GitHub <https://github.com/bio2bel/msig>`_ with:\n\n.. code-block:: sh\n\n    $ python3 -m pip install git+https://github.com/bio2bel/msig.git@master\n\nSetup\n-----\nThe package expects you have downloaded the gene sets from MSigDB following the instructions and terms stated in\ntheir `website <http://software.broadinstitute.org/gsea/downloads.jsp>`_.\n\nThe environment variable `BIO2BEL_MSIG_PATH` should be set to the directory where the gene set files in the GMT format\nare stored. Optionally, this can be directly overridden with the keyword argument to `populate()` in the REPL or as\na flag in the command line utility.\n\nPython REPL\n~~~~~~~~~~~\n.. code-block:: python\n\n    >>> import bio2bel_msig\n    >>> msig_manager = bio2bel_msig.Manager()\n    >>> msig_manager.populate()\n\nCommand Line Utility\n~~~~~~~~~~~~~~~~~~~~\n.. code-block:: bash\n\n    bio2bel_msig populate\n\nOther Command Line Utilities\n----------------------------\n- Run an admin site for simple querying and exploration :code:`python3 -m bio2bel_msig web` (http://localhost:5000/admin/)\n- Export gene sets for programmatic use :code:`python3 -m bio2bel_msig export`\n\nCitation\n--------\n- Subramanian, A., *et al.* (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545-15550.\n- Liberzon, A., *et al* (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739-1740.\n\n.. |build| image:: https://travis-ci.org/bio2bel/msig.svg?branch=master\n    :target: https://travis-ci.org/bio2bel/msig\n    :alt: Build Status\n\n.. |coverage| image:: https://codecov.io/gh/bio2bel/msig/coverage.svg?branch=master\n    :target: https://codecov.io/gh/bio2bel/msig?branch=master\n    :alt: Coverage Status\n\n.. |documentation| image:: http://readthedocs.org/projects/bio2bel-msig/badge/?version=latest\n    :target: http://bio2bel.readthedocs.io/projects/msig/en/latest/?badge=latest\n    :alt: Documentation Status\n\n.. |climate| image:: https://codeclimate.com/github/bio2bel/msig/badges/gpa.svg\n    :target: https://codeclimate.com/github/bio2bel/msig\n    :alt: Code Climate\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_msig.svg\n    :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_msig.svg\n    :alt: Current version on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_msig.svg\n    :alt: MIT License\n\n.. |zenodo| image:: https://zenodo.org/badge/123948554.svg\n    :target: https://zenodo.org/badge/latestdoi/123948554",
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