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Bioconductor - glmSparseNet

glmSparseNet

This is the released version of glmSparseNet; for the devel version, see glmSparseNet.

Network Centrality Metrics for Elastic-Net Regularized Models

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-2212-339X , Susana Vinga [aut], Eunice Carrasquinha [ctb], Marta Lopes [ctb]

Maintainer: André Veríssimo <andre.verissimo at tecnico.ulisboa.pt>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("glmSparseNet")

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("glmSparseNet")
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 NEWS Text Details biocViews Classification, DimensionReduction, GraphAndNetwork, Network, Regression, Software, StatisticalMethod, Survival Version 1.26.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 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 System Requirements URL https://www.github.com/sysbiomed/glmSparseNet Bug Reports https://www.github.com/sysbiomed/glmSparseNet/issues See More Suggests BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC, rmarkdown, survival, testthat, VennDiagram, withr Linking To Enhances Depends On Me Imports Me priorityelasticnet Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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