genphen

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.15 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see genphen.

genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)


Bioconductor version: 3.15

Genetic association studies help us discover relationships between genotypes and phenotype. genphen is a computational tool for quantification of genotype-phenotype associations using a hybrid approach based on statistical learning techniques and probabilistic models that are analyzed computationally by Bayes inference.

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 "4.2") 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 1.24.0
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
URL
Bug Reports https://github.com/snaketron/genphen/issues
See More
Suggests testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape, xtable
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package genphen_1.24.0.tar.gz
Windows Binary
macOS Binary (x86_64) genphen_1.24.0.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 3.15 Source Archive