Metadata-Version: 1.1
Name: staNMF
Version: 1.1
Summary: python 2.7 implementation of stability NMF (Siqi Wu 2016)
Home-page: https://github.com/greenelab/staNMF
Author: Greene Lab
Author-email: team@greenelab.com
License: LICENSE.txt
Description: Amy Campbell, 2016
        
        
        staNMF
        ------
        Python 2.7 implementation of `Siqi Wu et al.'s 2016 stability NMF (staNMF)
        <http://doi.org/10.1073/pnas.1521171113>`_
        
        Package Contents
        ----------------
        
        =========
        staNMF.py
        =========
        staNMF.py class includes the necessary methods to perform stability
        NMF on a user-specified .csv datase (see sourcecode/staNMF_Example for precise
        usage instructions)
        
        =================
        staNMF_Example.py
        =================
        Example of staNMF demonstrated on Wu et al.'s 2016
        drosophila spatial expression data between K=15 and K=30; Generates
        sample factorizations, calculates instability index, and plots instability
        against K
        
        ================
        staNMF_driver.py
        ================
        Driver script to run staNMF in parallel; can be called from the command line
        using:
        python staNMF_driver.py <k1> <k2> <reps1> <reps2> <folder> <filename> <function>
        (See docstring for more specific instructions) 
        
        ============================
        data/WuExampleExpression.csv
        ============================
        sample dataset (also available for download `here
        <http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl?t=html&p=downloads>`_)
        
        
        Installation
        -------------
        $ pip install staNMF
        
        *Please note that staNMF requires SPAMs package (version 2.5), which is
        available from* `Julien Mairal et al.
        <http://spams-devel.gforge.inria.fr/downloads.html>`_ , or from Anaconda
        using:
        
        $ conda install -c conda-forge python-spams=2.5
        
        
        Acknowledgements
        ----------------
        This work was supported by The Gordon and Betty Moore Foundation’s Data-Driven
        Discovery Initiative (GBMF 4552 to C.S.G.) and a grant from the National
        Institutes of Health (R01 CA200854)
        
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
