Package: glmSparseNet
Type: Package
Title: Network Centrality Metrics for Elastic-Net Regularized Models
Version: 1.4.0
Authors@R: c(person("André", "Veríssimo", email = "andre.verissimo@tecnico.ulisboa.pt", role = c("aut", "cre")),
             person("Susana", "Vinga", email = "susanavinga@tecnico.ulisboa.pt", role = "aut"),
             person("Eunice", "Carrasquinha", email = "eunice.trigueirao@tecnico.ulisboa.pt", role = "ctb"),
             person("Marta", "Lopes", email = "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)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
biocViews: Software, StatisticalMethod, DimensionReduction, Regression,
        Classification, Survival, Network, GraphAndNetwork
Depends: R (>= 3.5), Matrix, MultiAssayExperiment, glmnet
Imports: SummarizedExperiment, STRINGdb, biomaRt, futile.logger,
        sparsebn, sparsebnUtils, forcats, dplyr, readr, ggplot2,
        survminer, reshape2, stats, stringr, rlang, parallel, methods,
        loose.rock (>= 1.0.12)
Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC,
        VennDiagram, BiocStyle, curatedTCGAData, TCGAutils
VignetteBuilder: knitr
RoxygenNote: 6.1.1
BugReports: https://www.github.com/sysbiomed/glmSparseNet/issues
URL: https://www.github.com/sysbiomed/glmSparseNet
git_url: https://git.bioconductor.org/packages/glmSparseNet
git_branch: RELEASE_3_10
git_last_commit: 91e41c0
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
Packaged: 2019-10-30 03:21:19 UTC; biocbuild
Author: André Veríssimo [aut, cre],
  Susana Vinga [aut],
  Eunice Carrasquinha [ctb],
  Marta Lopes [ctb]
Maintainer: André Veríssimo <andre.verissimo@tecnico.ulisboa.pt>
Built: R 3.6.1; ; 2019-11-03 17:10:41 UTC; unix
