anhima - Exploration and analysis of genetic variation data¶
This package is intended to provide convenience for those working with genetic variation data who need quick access to some exploratory analysis and plotting functions.
This package is mostly an extremely thin wrapper around numpy, scipy, numexpr, matplotlib, sklearn and other generic scientific libraries. Viewing the source code is recommended, as this may suggest ways that generic libraries like numpy could be used or adapted for other purposes beyond the limited set of functionalities supported here.
N.B., this package is in a very early stage of development. Please report any bugs to the GitHub issue tracker.
- Documentation: http://anhima.readthedocs.org
- Examples: http://nbviewer.ipython.org/github/alimanfoo/anhima/tree/master/examples/
- Source: http://github.com/alimanfoo/anhima
- Mailing list: https://groups.google.com/forum/#!forum/anhima
- Release notes: https://github.com/alimanfoo/anhima/releases
See also information for developers.
Install latest stable release from PyPI:
pip install -U anhima
Install from GitHub:
git clone https://github.com/alimanfoo/anhima.git cd anhima python setup.py install
- Locating samples and variants
- Allele frequencies
- Site frequencies
- Doubleton sharing
- Linkage disequilibrium
- Genetic distance
- Principal components analysis
- Multidimensional scaling
- Pedigrees (families and crosses)
- Input/output utilities
- HDF5 utilities
- Miscellaneous utilities
Indices and tables