netReg

DOI: 10.18129/B9.bioc.netReg    

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 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see netReg.

Network-Regularized Regression Models

Bioconductor version: 3.12

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 "4.0") 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

Details

biocViews	FeatureExtraction, GraphAndNetwork, Network, Regression, Software, StatisticalMethod
Version	1.14.0
In Bioconductor since	BioC 3.5 (R-3.4) (4 years)
License	GPL-3
Depends	R (>= 3.4), tensorflow (>= 1.14.0), tfprobability (>= 0.7.0)
Imports	Rcpp, stats, reticulate, nloptr, methods
LinkingTo	Rcpp, RcppArmadillo
Suggests	BiocStyle, testthat, knitr, rmarkdown, lintr, styler, LaplacesDemon, grplasso
SystemRequirements	C++11
Enhances
URL	https://github.com/dirmeier/netReg
BugReports	https://github.com/dirmeier/netReg/issues
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	netReg_1.14.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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	https://bioconductor.org/packages/netReg/
Package Downloads Report	Download Stats