scikit-RARE

RARE: Relevant Association Rare-variant-bin Evolver is an evolutionary algorithm approach to binning rare variants as a rare variant association analysis tool. scikit-RARE is scikit compatible pypi package for the RARE algotithm.

RARE constructs bins of rare variant features with relevant association to class (univariate and/or multivariate interactions) through the following steps:

  1. Random bin initializaiton or expert knowledge input

  2. Repeated evolutionary cycles consisting of: - Candidate bin evaluation with univariate scoring (chi-square test) or Relief-based scoring (MultiSURF algorithm); note: new scoring options currently under testing - Genetic operations (parent selection, crossover, and mutation) to generate the next generation of candidate bins

  3. Final bin evaluation and summary of top bins

Installation

We can easily install scikit-rare using the following command:

pip install scikit-rare

Documentation for RARE Class:

Documentation for the RARE class can be found here.

Contact

Please email sdasariraju23@lawrenceville.org and Ryan.Urbanowicz@cshs.org for any inquiries related to RARE.