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environment \u003chttps://github.com/ComPath\u003e`_ for pathway database comparison.\n\nIf you find this package useful, please consider citing [domingofernandez2018]_:\n\n.. [domingofernandez2018] Domingo-Fernandez, D., *et al* (2018). `ComPath: an ecosystem for exploring, analyzing,\n   and curating mappings across pathway databases \u003chttps://doi.org/10.1038/s41540-018-0078-8\u003e`_.\n   *Npj Systems Biology and Applications*, __5__(1), 3.\n\n**Warning** This package creates ``partOf`` relationships in BEL. MSigDB does not contain mechanistic relationships,\nbut it include simplifications of several sources (KEGG, WikiPathways, Reactome, PID) that do have mechanistic\nrelationships. Those sources can be converted to BEL with the\n`PathMe project \u003chttps://github.com/pathwaymerger/pathme\u003e`_.\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\n``bio2bel_msig`` can be installed easily from `PyPI \u003chttps://pypi.python.org/pypi/bio2bel_msig\u003e`_ with the\nfollowing code in your favorite terminal:\n\n.. code-block:: sh\n\n    $ pip install bio2bel_msig\n\nor from the latest code on `GitHub \u003chttps://github.com/bio2bel/msig\u003e`_ in development mode with:\n\n.. code-block:: sh\n\n    $ git clone https://github.com/bio2bel/msig.git\n    $ cd msig\n    $ pip install -e .\n\nSetup\n-----\nThe package expects you have downloaded the gene sets from MSigDB following the instructions and terms stated in\ntheir `website \u003chttp://software.broadinstitute.org/gsea/downloads.jsp\u003e`_.\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    \u003e\u003e\u003e import bio2bel_msig\n    \u003e\u003e\u003e msig_manager = bio2bel_msig.Manager()\n    \u003e\u003e\u003e 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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio2bel%2Fmsig","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbio2bel%2Fmsig","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio2bel%2Fmsig/lists"}