genphen

This package is for version 3.9 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 in genome wide association studies (GWAS) with Bayesian inference and statistical learning


Bioconductor version: 3.9

Genetic association studies are an essential tool for studying the relationship between genotypes and phenotypes. With genphen we can jointly study multiple phenotypes of different types, by quantifying the association between different genotypes and each phenotype using a hybrid method which uses statistical learning techniques such as random forest and support vector machines, and Bayesian inference using hierarchical models.

Author: Simo Kitanovski [aut, cre]

Maintainer: Simo Kitanovski <simo.kitanovski at uni-due.de>

Citation (from within R, enter citation("genphen")):

Installation

To install this package, start R (version "3.6") 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 PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, Classification, FeatureExtraction, Genetics, GenomeWideAssociation, Regression, SequenceMatching, Sequencing, Software, SupportVectorMachine
Version 1.12.1
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL (>= 2)
Depends R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics
Imports rstan (>= 2.17.3), ranger, parallel, foreach, doParallel, e1071, Biostrings, rPref
System Requirements
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Suggests testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape, xtable
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package genphen_1.12.1.tar.gz
Windows Binary genphen_1.12.1.zip
Mac OS X 10.11 (El Capitan) genphen_1.12.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/genphen
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/genphen
Bioc Package Browser https://code.bioconductor.org/browse/genphen/
Package Short Url https://bioconductor.org/packages/genphen/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive