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Network Centrality Metrics for Elastic-Net Regularized Models

Bioconductor version: Release (3.19)

glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".

Author: André Veríssimo [aut, cre] , Susana Vinga [aut], Eunice Carrasquinha [ctb], Marta Lopes [ctb]

Maintainer: André Veríssimo <andre.verissimo at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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


To view documentation for the version of this package installed in your system, start R and enter:

Breast survival dataset using network from STRING DB HTML R Script
Example for Classification -- Breast Invasive Carcinoma HTML R Script
Example for Survival Data -- Breast Invasive Carcinoma HTML R Script
Example for Survival Data -- Prostate Adenocarcinoma HTML R Script
Example for Survival Data -- Skin Melanoma HTML R Script
Separate 2 groups in Cox regression HTML R Script
Reference Manual PDF


biocViews Classification, DimensionReduction, GraphAndNetwork, Network, Regression, Software, StatisticalMethod, Survival
Version 1.22.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-3
Depends R (>= 4.3.0)
Imports biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2, glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet, Matrix, MultiAssayExperiment, SummarizedExperiment, survminer, TCGAutils, utils
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Source Package glmSparseNet_1.22.0.tar.gz
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