Type: Package
Package: glmSparseNet
Title: Network Centrality Metrics for Elastic-Net Regularized Models
Version: 1.22.0
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
git_url: https://git.bioconductor.org/packages/glmSparseNet
git_branch: RELEASE_3_19
git_last_commit: 7b32a0f
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
Packaged: 2024-05-01 23:20:12 UTC; biocbuild
Author: André Veríssimo [aut, cre] (<https://orcid.org/0000-0002-2212-339X>),
  Susana Vinga [aut],
  Eunice Carrasquinha [ctb],
  Marta Lopes [ctb]
Maintainer: André Veríssimo <andre.verissimo@tecnico.ulisboa.pt>
Built: R 4.4.0; ; 2024-05-02 12:54:12 UTC; windows
