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>

Citation (from within R, enter citation("netReg")):

Installation

To install this package, start R (version "4.0") and enter:


if (!require("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")
netReg HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews FeatureExtraction, GraphAndNetwork, Network, Regression, Software, StatisticalMethod
Version 1.14.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends R (>= 3.4), tensorflow (>= 1.14.0), tfprobability (>= 0.7.0)
Imports Rcpp, stats, reticulate, nloptr, methods
System Requirements C++11
URL https://github.com/dirmeier/netReg
Bug Reports https://github.com/dirmeier/netReg/issues
See More
Suggests BiocStyle, testthat, knitr, rmarkdown, lintr, styler, LaplacesDemon, grplasso
Linking To Rcpp, RcppArmadillo
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 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
Old Source Packages for BioC 3.12 Source Archive