Package: genphen
Type: Package
Title: A tool for quantification of associations between genotypes and
        phenotypes with statistical learning techniques such as random
        forests and support vector machines as well as with Bayesian
        inference using hierarchical models
Version: 1.4.0
Date: 2016-09-28
Author: Simo Kitanovski
Maintainer: Simo Kitanovski <simo.kitanovski@uni-due.de>
Description: Genetic association studies have become an essential tool for
    studying the relationship between genotypes and phenotypes. They are
    necessary for the discovery of disease-causing genetic variants. Here we
    provide a tool for conducting genetic association studies, which uses
    statistical learning techniques such as random forests and support vector
    machines, as well as using Bayesian inference with Bayesian hierarchical
    models. These techniques are superior to the commonly used (frequentist)
    statistical approaches, alleviating the multiple hypothesis problems and
    the need for P value corrections, which often lead to massive numbers of
    false negatives. Thus, with genphen we provide a framework to compare the
    results obtained using frequentist methods with those obtained using the
    more sophisticated methods provided by this tool. The tool also provides a
    few visualization functions which enable the user to inspect the results of
    such genetic association study and conveniently select the genotypes which
    have the highest strength of association with the phenotype.
License: GPL (>= 2)
Depends: R(>= 3.3), randomForest, e1071, ggplot2, effsize, Biostrings,
        rjags
LazyLoad: yes
biocViews: GenomeWideAssociation, Regression, Classification,
        SupportVectorMachine, Genetics, SequenceMatching, Bayesian,
        FeatureExtraction, Sequencing
NeedsCompilation: no
Packaged: 2017-04-25 01:23:29 UTC; biocbuild
Built: R 3.4.0; ; 2017-04-25 04:21:24 UTC; windows
