Metadata-Version: 1.1
Name: dreamtools
Version: 0.10.4
Summary: Scoring functions for the dream / sage challenges
Home-page: ['https://github.com/dreamtools/dreamtools']
Author: Thomas Cokelaer
Author-email: cokelaer@gmail.com
License: BSD
Download-URL: ['http://pypi.python.org/pypi/dreamtools']
Description: DREAMTools
        ==========
        
        
        .. image:: https://badge.fury.io/py/dreamtools.svg
            :target: https://pypi.python.org/pypi/dreamtools
        
        .. image:: https://secure.travis-ci.org/dreamtools/dreamtools.png
            :target: http://travis-ci.org/dreamtools/dreamtools
        
        .. image:: https://coveralls.io/repos/dreamtools/dreamtools/badge.png?branch=master 
           :target: https://coveralls.io/r/dreamtools/dreamtools?branch=master 
        
        .. image:: https://badge.waffle.io/dreamtools/dreamtools.png?label=issues&title=issues
           :target: https://waffle.io/dreamtools/dreamtools
        
        :note: DREAMTools is tested for Python 2.7
        :Contributions: Please join https://github.com/dreamtools/dreamtools and share your notebooks https://github.com/dreamtools/dreamtools/notebooks
        
        :Online documentation: `On pypi website <http://pythonhosted.org/dreamtools/>`_,
        :Issues and bug reports: `On github <https://github.com/dreamtools/dreamtools/issues>`_,
        
        
        .. image:: doc/dreamtools_logo.png
            :width: 50%
        
        .. contents::
        
        Overview
        ----------------
        
        **DREAMTools** aims at sharing code used in the scoring of `DREAM <http://dreamchallenges.org>`_ challenges.
        
        The main goals are to provide:
        
        #. scoring functions for the Dream challenges for **end-users** via the **dreamtools-scoring** standalone
           application.
        #. a place for **developers** involved in the dream challenges to share code
        
        **DREAMTools** does not provide code related to aggregation,
        leaderboards, or more complex analysis even though such code
        can be provided (e.g. D8C1 challenge). Note that some functionalities
        may be restricted with some access to synapse platform. Indeed, 
        some challenges will require to download public data sets from `Synapse
        <www.synapse.org>`_ (in which case you will need to register).
        
        Installation
        ---------------
        
        **DREAMTools** depends on a few libraries such as Pandas, Numpy, Matplotlib. They should be automatically
        installed with **dreamtools** using pip executable::
        
            pip install dreamtools
            
        From source, download the source code and install the package with Python::
        
           git clone git@github.com:dreamtools/dreamtools.git
           cd dreamtools
           sudo python setup.py install
        
        
        The **dreamtools-scoring** executable
        ------------------------------------------
        
        For users, **DREAMTools** provides an executable called **dreamtools**, which should be installed automatically. Knowing the name of the challenge (and possibly sub-challenge), it works as  follows::
        
            dreamtools --challenge d8c1 --sub-challenge sc1a --submission example.zip
        
        It prints some information and the score of the submision for instance for the example above::
        
             Solution for alphabeta-Network.zip in challenge d8c1 (sub-challenge sc1a) is :
             AUROC: 0.803628919403
             Rank LB: 1
        
        
        Available challenges
        -------------------------
        
        **DREAMTools** includes about 80% of DREAM challenges from DREAM2 to DREAM9.5
        
        
        Templates
        -------------
        
        All template location can be retrieved using **dreamtools** executable::
        
            dreamtools --challenge d5c2 --download-template
        
        
        Gold standard
        --------------
        
        All gold standard are retrieved automatically. You can obtain a GS location as
        follows::
        
            dreamtools --challenge d5c2 --download-goldstandard
        
        Issues
        -----------
        
        Please fill bug report in https://github.com/dreamtools/dreamtools/issues
        
        
        Contributions
        ---------------
        
        Please join https://github.com/dreamtools/dreamtools
        
        
        For developers
        ----------------
        
        Please see doc/source/developers.rst
        
        Credits
        -----------
        
        Please see doc/source/credits.rst
        
        
        
        
        
        
        
Keywords: DREAM challenges,DREAM,System Biology,Leaderboard
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
