index.rst

.. module:: anhima

.. moduleauthor:: Alistair Miles <alimanfoo@googlemail.com>

anhima - Exploration and analysis of genetic variation data

N.B., this package is in a very early stage of development. Please report any bugs to the GitHub issue tracker.

Please note that this package is mostly an extremely thin wrapper around :mod:`numpy`, :mod:`scipy`, :mod:`numexpr`, :mod:`matplotlib`, :mod:`sklearn` and other generic scientific libraries. This package is intended to provide convenience for those working with genetic variation data who need quick access to some simple analysis and plotting functions. Viewing the source code is recommended, as this may suggest ways that generic libraries like :mod:`numpy` could be used or adapted for other purposes beyond the limited set of functionalities supported here.

• Documentation: http://anhima.readthedocs.org
• Examples: http://nbviewer.ipython.org/github/alimanfoo/anhima/tree/master/examples/
• Source: http://github.com/alimanfoo/anhima

Installation

Install from GitHub:

git clone https://github.com/alimanfoo/anhima.git
cd anhima
python setup.py install

Contents

.. toctree::
    :maxdepth: 2

    loc
    gt
    af
    ld
    dist
    pca
    mds
    tree
    ped
    h5
    sim

Indices and tables

• :ref:`genindex`
• :ref:`modindex`
• :ref:`search`