genphen
This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see genphen.
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
Bioconductor version: 3.6
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.
Author: Simo Kitanovski
Maintainer: Simo Kitanovski <simo.kitanovski at uni-due.de>
citation("genphen")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("genphen")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("genphen")| genphen overview | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Classification, FeatureExtraction, Genetics, GenomeWideAssociation, Regression, SequenceMatching, Sequencing, Software, SupportVectorMachine |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.3), randomForest, e1071, ggplot2, effsize, Biostrings, rjags |
| Imports | |
| System Requirements | |
| URL |
See More
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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | genphen_1.6.0.tar.gz |
| Windows Binary | genphen_1.6.0.zip |
| Mac OS X 10.11 (El Capitan) | genphen_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/genphen |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/genphen |
| Package Short Url | https://bioconductor.org/packages/genphen/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |