GRridge

DOI: 10.18129/B9.bioc.GRridge  

Better prediction by use of co-data: Adaptive group-regularized ridge regression

Bioconductor version: Release (3.17)

This package allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation) to improve prediction of binary, continuous and survival response using (logistic, linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction diagnostics by cross-validation using ROC curves and AUC.

Author: Mark A. van de Wiel <mark.vdwiel at vumc.nl>, Putri W. Novianti <p.novianti at vumc.nl>

Maintainer: Mark A. van de Wiel <mark.vdwiel at vumc.nl>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GRridge")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	Bayesian, Classification, GO, GeneExpression, GenePrediction, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, KEGG, Pathways, RNASeq, Regression, Software, Survival
Version	1.23.0
In Bioconductor since	BioC 3.5 (R-3.4) (6.5 years)
License	GPL-3
Depends	R (>= 3.2), penalized, Iso, survival, methods, graph, stats, glmnet, mvtnorm
Imports
LinkingTo
Suggests	testthat
SystemRequirements
Enhances
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Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)	GRridge_1.23.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GRridge
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GRridge
Bioc Package Browser	https://code.bioconductor.org/browse/GRridge/
Package Short Url	https://bioconductor.org/packages/GRridge/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive