genphen

DOI: 10.18129/B9.bioc.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: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") 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	1.20.0
In Bioconductor since	BioC 3.3 (R-3.3) (5.5 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
LinkingTo
Suggests	testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape, xtable
SystemRequirements
Enhances
URL
BugReports	https://github.com/snaketron/genphen/issues
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_1.20.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	genphen_1.20.0.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