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("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 | ||
| 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 |