Type: Package
Package: glmSparseNet
Title: Network Centrality Metrics for Elastic-Net Regularized Models
Version: 1.31.0
Authors@R: c(
    person("André", "Veríssimo", , "andre.verissimo@tecnico.ulisboa.pt", 
           role = c("aut", "cre"), comment = c(ORCID = "0000-0002-2212-339X")),
    person("Susana", "Vinga", , "susanavinga@tecnico.ulisboa.pt", role = "aut"),
    person("Eunice", "Carrasquinha", , "eunice.trigueirao@tecnico.ulisboa.pt", 
           role = "ctb"),
    person("Marta", "Lopes", , "marta.lopes@tecnico.ulisboa.pt", role = "ctb")
  )
Description: 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".
License: GPL-3
URL: https://www.github.com/sysbiomed/glmSparseNet
BugReports: https://www.github.com/sysbiomed/glmSparseNet/issues
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
Suggests: BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC,
        rmarkdown, survival, testthat, VennDiagram, withr
VignetteBuilder: knitr
RdMacros: lifecycle
biocViews: Software, StatisticalMethod, DimensionReduction, Regression,
        Classification, Survival, Network, GraphAndNetwork
Encoding: UTF-8
Language: en-US
LazyData: false
NeedsCompilation: no
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev libx11-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:48:45 UTC
RemoteUrl: https://github.com/bioc/glmSparseNet
RemoteRef: HEAD
RemoteSha: f9c60d0cc3a82fa4ce8c6886e7d24538e506a9f0
Packaged: 2026-07-02 10:03:32 UTC; root
Author: André Veríssimo [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2212-339X>),
  Susana Vinga [aut],
  Eunice Carrasquinha [ctb],
  Marta Lopes [ctb]
Maintainer: André Veríssimo <andre.verissimo@tecnico.ulisboa.pt>