genphen

DOI: 10.18129/B9.bioc.genphen    

This package is for version 3.8 of Bioconductor; for the 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: 3.8

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

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	genphen overview
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Classification, FeatureExtraction, Genetics, GenomeWideAssociation, Regression, SequenceMatching, Sequencing, Software, SupportVectorMachine
Version	1.10.3
In Bioconductor since	BioC 3.3 (R-3.3) (3 years)
License	GPL (>= 2)
Depends	R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics
Imports	rstan (>= 2.17.3), rstantools (>= 1.5.0), ranger, parallel, foreach, doParallel, e1071, Biostrings
LinkingTo	StanHeaders (>= 2.17.2), rstan (>= 2.17.3), BH (>= 1.66.0-1), Rcpp (>= 0.12.17), RcppEigen (>= 0.3.3.4.0)
Suggests	testthat
SystemRequirements	GNU make
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	genphen_1.10.3.tar.gz
Windows Binary	genphen_1.10.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	genphen_1.10.3.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	http://bioconductor.org/packages/genphen/
Package Downloads Report	Download Stats