Metadata-Version: 2.1
Name: bel_enrichment
Version: 0.0.2
Summary: A package for generating curation sheets for rationally enriching a BEL graph using INDRA and PyBEL.
Home-page: https://github.com/bel-enrichment/bel-enrichment
Author: Charles Tapley Hoyt
Author-email: charles.hoyt@scai.fraunhofer.de
Maintainer: Charles Tapley Hoyt
Maintainer-email: charles.hoyt@scai.fraunhofer.de
License: MIT License
Download-URL: https://github.com/bel-enrichment/bel-enrichment/releases
Project-URL: Bug Tracker, https://github.com/bel-enrichment/bel-enrichment/issues
Project-URL: Source Code, https://github.com/bel-enrichment/bel-enrichment
Description: BEL Enrichment |build|
        ======================
        A package for generating curation sheets for rationally enriching a BEL graph.
        
        If you find ``bel_enrichment`` useful in your work, please consider citing [1]_:
        
        .. [1] Hoyt, C. T., *et al* (2019). `Re-curation and Rational Enrichment of Knowledge Graphs in
               Biological Expression Language <https://doi.org/10.1101/536409>`_. *bioRxiv*, 536409.
        
        Additionally, this package also heavily builds on INDRA [2]_ and PyBEL [3]_.
        
        Installation |pypi_version| |python_versions| |pypi_license|
        ------------------------------------------------------------
        ``bel_enrichment`` can be installed from PyPI with the following command:
        
        .. code-block:: bash
        
           $ pip install bel_enrichment
        
        The latest version can be installed from GitHub with:
        
        .. code-block:: bash
        
           $ pip install git+https://github.com/bel-enrichment/bel-enrichment.git
        
        Usage
        -----
        Generate a folder full of curation sheets based on the given BEL graph that has been pre-compiled by PyBEL.
        Use ``--info-cutoff`` to specify the minimum information density cutoff. 1.0 means that the node has no edges, .5 means
        one edge, and so on. Use ``--belief-cutoff`` to specify the minimum belief score from INDRA for adding the statement
        to the sheet. Higher belief means the more chance a statement is already right.
        
        .. code-block:: bash
        
           $ bel-enrichment make_sheet zhang2011.bel --directory ~/Desktop/zhang-enrichment
        
        Generate a ranking for genes based on the information content in a given BEL graph that has been pre-compiled by PyBEL.
        
        .. code-block:: bash
        
           $ bel-enrichment ranks zhang2011.bel
        
        References
        ----------
        .. [2] Gyori, B. M., *et al.* (2017). `From word models to executable models of signaling networks using automated
               assembly <https://doi.org/10.15252/msb.20177651>`_. Molecular Systems Biology, 13(11), 954.
        .. [3] Hoyt, C. T., Konotopez, A., Ebeling, C., (2017). `PyBEL: a computational framework for Biological Expression
               Language <https://doi.org/10.1093/bioinformatics/btx660>`_. Bioinformatics (Oxford, England), 34(4), 703–704.
        
        .. |build| image:: https://travis-ci.com/bel-enrichment/bel-enrichment.svg?branch=master
            :target: https://travis-ci.com/bel-enrichment/bel-enrichment
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/bel_enrichment.svg
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/bel_enrichment.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/bel_enrichment.svg
            :alt: License
        
Keywords: Biological Expression Language,BEL,Domain Specific Language,DSL,Systems Biology,Networks Biology
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.6
Provides-Extra: docs
