Metadata-Version: 2.1
Name: xlmhg
Version: 2.5.3
Summary: XL-mHG: A Semiparametric Test for Enrichment
Home-page: https://github.com/flo-compbio/xlmhg
Author: Florian Wagner
Author-email: florian.wagner@duke.edu
License: GPLv3
Description: XL-mHG
        ======
        
        | |pypi| |versions| |license|
        
        ===========  ====================================================================
        **master**   |codecov-master| |travis-master| |appveyor-master| |docs-latest|
        **develop**  |codecov-develop| |travis-develop| |appveyor-develop| |docs-develop|
        ===========  ====================================================================
        
        This is an efficient Python/Cython implementation of the semiparametric
        `XL-mHG test`__ for enrichment in ranked lists. The XL-mHG test is an extension
        of the nonparametric `mHG test`__, which was developed by `Dr. Zohar
        Yakhini`__ and colleagues.
        
        __ xlmhg_paper_
        __ mhg_paper_
        __ zohar_
        
        Installation
        ------------
        
        .. code-block:: bash
        
            $ pip install xlmhg
        
        Getting started
        ---------------
        
        The `xlmhg` package provides two functions (one simple and more more advanced)
        for performing XL-mHG tests. These functions are documented in the
        `User Manual`__. Here's a quick example using the "simple" test function:
        
        .. code-block:: python
        
            import xlmhg
            stat, cutoff, pval = xlmhg.xlmhg_test(v, X, L)
        
        Where: ``v`` is the ranked list of 0's and 1's, represented by a NumPy array of
        integers, ``X`` and ``L`` are the XL-mHG parameters, and the return values have
        the following meanings:
        
        - ``stat``: The XL-mHG test statistic
        - ``cutoff``: The cutoff at which XL-mHG test statistic was attained
        - ``pval``: The XL-mHG p-value
        
        __ user_manual_
        
        Documentation
        -------------
        
        Please refer to the `XL-mHG User Manual`__ (hosted on ReadTheDocs).
        
        __ user_manual_
        
        Citing XL-mHG
        -------------
        
        If you use the XL-mHG test in your research, please cite `Eden et al. (PLoS
        Comput Biol, 2007)`__ and `Wagner (PLoS One, 2015)`__.
        
        __ mhg_paper_
        __ go_pca_paper_
        
        Copyright and License
        ---------------------
        
        Copyright (c) 2015-2019 Florian Wagner
        
        ::
        
            Redistribution and use in source and binary forms, with or without
            modification, are permitted provided that the following conditions are met:
        
            * Redistributions of source code must retain the above copyright notice, this
            list of conditions and the following disclaimer.
        
            * Redistributions in binary form must reproduce the above copyright notice,
            this list of conditions and the following disclaimer in the documentation
            and/or other materials provided with the distribution.
        
            * Neither the name of the copyright holder nor the names of its
            contributors may be used to endorse or promote products derived from
            this software without specific prior written permission.
        
            THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
            AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
            IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
            DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
            FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
            DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
            SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
            CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
            OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
            OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
        
        .. _xlmhg_paper: https://doi.org/10.7287/peerj.preprints.1962v2
        
        .. _zohar: http://bioinfo.cs.technion.ac.il/people/zohar
        
        .. _mhg_paper: https://dx.doi.org/10.1371/journal.pcbi.0030039
        
        .. _go_pca_paper: https://dx.doi.org/10.1371/journal.pone.0143196
        
        .. _user_manual: https://xl-mhg.readthedocs.io
        
        .. |pypi| image:: https://img.shields.io/pypi/v/xlmhg.svg
            :target: https://pypi.python.org/pypi/xlmhg
            :alt: PyPI version
        
        .. |versions| image:: https://img.shields.io/pypi/pyversions/xlmhg.svg
            :target: https://pypi.python.org/pypi/xlmhg
            :alt: Python versions supported
        
        .. |license| image:: https://img.shields.io/pypi/l/xlmhg.svg
            :target: https://pypi.python.org/pypi/xlmhg
            :alt: License
        
        .. |travis-master| image:: https://travis-ci.org/flo-compbio/xlmhg.svg?branch=master
            :alt: Travis-CI build Status (master branch)
            :scale: 100%
            :target: https://travis-ci.org/flo-compbio/xlmhg.svg?branch=master
        
        .. |travis-develop| image:: https://travis-ci.org/flo-compbio/xlmhg.svg?branch=develop
            :alt: Travis-CI build Status (develop branch)
            :scale: 100%
            :target: https://travis-ci.org/flo-compbio/xlmhg.svg?branch=develop
        
        .. |appveyor-master| image:: https://ci.appveyor.com/api/projects/status/wpon7qkwpxx3fe6q/branch/master?svg=true
            :alt: Appveyor build Status (master branch)
            :scale: 100%
            :target: https://ci.appveyor.com/project/flo-compbio/xlmhg/branch/master
        
        .. |appveyor-develop| image:: https://ci.appveyor.com/api/projects/status/wpon7qkwpxx3fe6q/branch/develop?svg=true
            :alt: Appveyor build Status (develop branch)
            :scale: 100%
            :target: https://ci.appveyor.com/project/flo-compbio/xlmhg/branch/develop
        
        .. |codecov-master| image:: https://codecov.io/gh/flo-compbio/xlmhg/branch/master/graph/badge.svg
            :alt: Coverage (master branch)
            :target: https://codecov.io/gh/flo-compbio/xlmhg/branch/master
        
        .. |codecov-develop| image:: https://codecov.io/gh/flo-compbio/xlmhg/branch/develop/graph/badge.svg
            :alt: Coverage (develop branch)
            :target: https://codecov.io/gh/flo-compbio/xlmhg/branch/develop
        
        .. |docs-latest| image:: https://readthedocs.org/projects/xl-mhg/badge/?version=latest
            :alt: Documentation Status (master branch)
            :target: https://xl-mhg.readthedocs.io/en/latest
        
        .. |docs-develop| image:: https://readthedocs.org/projects/xl-mhg/badge/?version=develop
            :alt: Documentation Status (develop branch)
            :target: https://xl-mhg.readthedocs.io/en/develop
        
Keywords: statistics nonparametric semiparametric enrichment test ranked lists
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Cython
Provides-Extra: docs
Provides-Extra: tests
