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 (3.9)

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

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 (!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 1.12.0
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, rPref
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_1.12.0.tar.gz
Windows Binary genphen_1.12.0.zip
Mac OS X 10.11 (El Capitan) genphen_1.12.0.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 http://bioconductor.org/packages/genphen/
Package Downloads Report Download Stats

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