scikit-allel - Explore and analyse genetic variation

This package provides utility functions for working with large scale genetic variation data using numpy, scipy and other Python scientific libraries.

allel is in an early stage of development, if you have any questions please email Alistair Miles <alimanfoo@googlemail.com>.

• GitHub repository: https://github.com/cggh/scikit-allel

Installation

This package requires numpy, scipy and numexpr. Install these dependencies first, then:

$ pip install -U scikit-allel

Contents

• Data structures
  • GenotypeArray
  • HaplotypeArray
  • PositionIndex
  • LabelIndex
• Miscellaneous utilities
  • Windowed counting functions

Acknowledgments

Development of this package is supported by the MRC Centre for Genomics and Global Health.

Indices and tables

• Index
• Module Index
• Search Page