genphen
This package is for version 3.12 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: 3.12
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("genphen")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Classification, FeatureExtraction, Genetics, GenomeWideAssociation, Regression, SequenceMatching, Sequencing, Software, SupportVectorMachine |
| Version | 1.18.0 |
| 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_1.18.0.tar.gz |
| Windows Binary | genphen_1.17.0.zip |
| macOS 10.13 (High Sierra) | genphen_1.18.0.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 3.12 | Source Archive |