Metadata-Version: 2.1
Name: bio2bel-msig
Version: 0.1.0
Summary: A wrapper around MSIGDB
Home-page: https://github.com/bio2bel/MSIG
Author: Daniel Domingo-Fernández and Charles Tapley Hoyt
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
Maintainer: Daniel Domingo-Fernández and Charles Tapley Hoyt
Maintainer-email: daniel.domingo.fernandez@scai.fraunhofer.de
License: MIT License
Description: Bio2BEL MSigDB |build| |coverage| |documentation| |zenodo|
        ==========================================================
        This package allows the enrichment of BEL networks with MSigDB information.
        Furthermore, it is integrated in the `ComPath environment <https://github.com/ComPath>`_ for pathway database comparison.
        
        Installation |pypi_version| |python_versions| |pypi_license|
        ------------------------------------------------------------
        ``bio2bel_msig`` can be installed easily from `PyPI <https://pypi.python.org/pypi/bio2bel_msig>`_ with the
        following code in your favorite terminal:
        
        .. code-block:: sh
        
            $ python3 -m pip install bio2bel_msig
        
        or from the latest code on `GitHub <https://github.com/bio2bel/msig>`_ with:
        
        .. code-block:: sh
        
            $ python3 -m pip install git+https://github.com/bio2bel/msig.git@master
        
        Setup
        -----
        The package expects you have downloaded the gene sets from MSigDB following the instructions and terms stated in
        their `website <http://software.broadinstitute.org/gsea/downloads.jsp>`_.
        
        The environment variable `BIO2BEL_MSIG_PATH` should be set to the directory where the gene set files in the GMT format
        are stored. Optionally, this can be directly overridden with the keyword argument to `populate()` in the REPL or as
        a flag in the command line utility.
        
        Python REPL
        ~~~~~~~~~~~
        .. code-block:: python
        
            >>> import bio2bel_msig
            >>> msig_manager = bio2bel_msig.Manager()
            >>> msig_manager.populate()
        
        Command Line Utility
        ~~~~~~~~~~~~~~~~~~~~
        .. code-block:: bash
        
            bio2bel_msig populate
        
        Other Command Line Utilities
        ----------------------------
        - Run an admin site for simple querying and exploration :code:`python3 -m bio2bel_msig web` (http://localhost:5000/admin/)
        - Export gene sets for programmatic use :code:`python3 -m bio2bel_msig export`
        
        Citation
        --------
        - 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.
        - Liberzon, A., *et al* (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739-1740.
        
        .. |build| image:: https://travis-ci.org/bio2bel/msig.svg?branch=master
            :target: https://travis-ci.org/bio2bel/msig
            :alt: Build Status
        
        .. |coverage| image:: https://codecov.io/gh/bio2bel/msig/coverage.svg?branch=master
            :target: https://codecov.io/gh/bio2bel/msig?branch=master
            :alt: Coverage Status
        
        .. |documentation| image:: http://readthedocs.org/projects/bio2bel-msig/badge/?version=latest
            :target: http://bio2bel.readthedocs.io/projects/msig/en/latest/?badge=latest
            :alt: Documentation Status
        
        .. |climate| image:: https://codeclimate.com/github/bio2bel/msig/badges/gpa.svg
            :target: https://codeclimate.com/github/bio2bel/msig
            :alt: Code Climate
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_msig.svg
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_msig.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_msig.svg
            :alt: MIT License
        
        .. |zenodo| image:: https://zenodo.org/badge/123948554.svg
            :target: https://zenodo.org/badge/latestdoi/123948554
Platform: UNKNOWN
Provides-Extra: web
