netReg

DOI: 10.18129/B9.bioc.netReg    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see netReg.

Network-Regularized Regression Models

Bioconductor version: 3.8

netReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the loss function of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.

Author: Simon Dirmeier [aut, cre]

Maintainer: Simon Dirmeier <simon.dirmeier at web.de>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("netReg")

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("netReg")

 

HTML	R Script	netReg
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	FeatureExtraction, GraphAndNetwork, Network, Regression, Software, StatisticalMethod
Version	1.6.0
In Bioconductor since	BioC 3.5 (R-3.4) (2 years)
License	GPL-3 | BSL-1.0 + file LICENSE
Depends	R (>= 3.4)
Imports	Rcpp, stats
LinkingTo	Rcpp, RcppArmadillo
Suggests	testthat, knitr, rmarkdown, BiocStyle, lintr, lassoshooting
SystemRequirements	C++11
Enhances
URL	https://github.com/dirmeier/netReg
BugReports	https://github.com/dirmeier/netReg/issues
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	netReg_1.6.0.tar.gz
Windows Binary	netReg_1.6.0.zip
Mac OS X 10.11 (El Capitan)	netReg_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/netReg
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/netReg
Package Short Url	http://bioconductor.org/packages/netReg/
Package Downloads Report	Download Stats