Metadata-Version: 1.1
Name: limix
Version: 0.8.5
Summary: A flexible and fast mixed model toolbox.
Home-page: http://pmbio.github.io/limix/
Author: Limix Developers
Author-email: stegle@ebi.ac.uk
License: Apache License 2.0
Description: Limix
        =====
        
        |PyPIl| |PyPIv| |Anaconda| |Travis|
        
        Limix is a flexible and efficient linear mixed model library with
        interfaces to Python. Genomic analyses require flexible models that can
        be adapted to the needs of the user. Limix is smart about how particular
        models are fitted to save computational cost.
        
        LATEST: `iSet, interaction set tests for gene-context interactions, is
        now in
        Limix. <https://github.com/PMBio/limix-tutorials/tree/master/iSet>`__
        
        Installation
        ------------
        
        Using Conda package manager
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Conda is a package manager designed for Python and R users/developers of
        scientific tools, and comes with the `Anaconda
        distribution <https://www.continuum.io/downloads>`__. Currently we
        support this installation for Linux 64 bits and OSX operating systems.
        
        ::
        
            conda install -c conda-forge limix
        
        Using Pip
        ~~~~~~~~~
        
        If you don't have Conda (or don't want to use the above method), Limix
        can be installed via Pip package manager.
        
        ::
        
            pip install limix
        
        This approach is not as straightforward as the first one because it
        requires compilation of C/C++ and (potentially) Fortran code, and some
        understanding of dependency resolution is likely to be required. We
        provide bellow recipes for some popular Limix distributions, assuming
        you have the ``wget`` command line tool.
        
        -  Ubuntu
        
           ::
        
               bash <(wget -O - https://raw.githubusercontent.com/PMBio/limix/master/deploy/apt_limix_install)
        
        -  Fedora
        
           ::
        
               bash <(wget -O - https://raw.githubusercontent.com/PMBio/limix/master/deploy/dnf_limix_install)
        
        -  OpenSUSE
        
           ::
        
               bash <(wget -O - https://raw.githubusercontent.com/PMBio/limix/master/deploy/zypper_limix_install)
        
        From source
        ~~~~~~~~~~~
        
        This is more tricky in terms of dependency resolution but useful for
        developers.
        
        ::
        
            git clone https://github.com/PMBio/limix.git
            cd limix
            python setup.py install # or python setup.py develop
        
        Usage
        -----
        
        A good starting point is our package Vignettes. These tutorials are
        available from this repository:
        https://github.com/PMBio/limix-tutorials.
        
        The main package vignette can also be viewed using the ipython notebook
        viewer:
        http://nbviewer.ipython.org/github/pmbio/limix-tutorials/blob/master/index.ipynb.
        
        Alternatively, the source file is available in the separate Limix
        tutorial repository: https://github.com/PMBio/limix-tutorials
        
        Problems
        --------
        
        If you want to use Limix and encounter any issues, please contact us via
        ``limix@mixed-models.org``.
        
        Authors
        -------
        
        -  ``Franceso Paolo Casale`` (``casale@ebi.ac.uk``)
        -  ``Danilo Horta`` (``horta@ebi.ac.uk``)
        -  ``Christoph Lippert`` (``christoph.a.lippert@gmail.com``)
        -  ``Oliver Stegle`` (``stegle@ebi.ac.uk``)
        
        License
        -------
        
        See `Apache License (Version 2.0, January
        2004) <https://github.com/PMBio/limix/blob/master/LICENSE>`__.
        
        .. |PyPIl| image:: https://img.shields.io/pypi/l/limix.svg?style=flat-square
           :target: https://pypi.python.org/pypi/limix/
        .. |PyPIv| image:: https://img.shields.io/pypi/v/limix.svg?style=flat-square
           :target: https://pypi.python.org/pypi/limix/
        .. |Anaconda| image:: https://anaconda.org/conda-forge/limix/badges/version.svg
           :target: https://anaconda.org/conda-forge/limix
        .. |Travis| image:: https://img.shields.io/travis/PMBio/limix.svg?style=flat-square
           :target: https://travis-ci.org/PMBio/limix
        
Keywords: linear mixed models,GWAS,QTL,Variance component modelling
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
