Package: asuri
Date: 2024-04-03
Type: Package
Title: Analysis of SUrvival and RIsk prediction in patients based on
        gene signatures
Version: 1.0.0
Description: The ASURI (Analysis of SUrvival and patients RIsk
        prediction based on gene signatures) package discovers marker
        genes that are related to risk prediction capabilities and to a
        clinical variable of interest. It uses two main steps,
        including subsampling glmnet and unicox. The package implements
        robust functions to discover survival markers related to a
        clinical phenotype and to predict a risk score, allowing to
        study the patient's risk based on the gene signatures. Several
        plots are provided to visualise the relevance of the genes, the
        risk score, and patient stratification, as well as a robust
        version of the Kaplan-Meier curves.
Authors@R: c(
  person(given = "Alberto",
         family = "Berral-Gonzalez",
         email = "aberralgonzalez@gmail.com",
         role = c("aut", "cre", "ctb"),
         comment = c(ORCID = "0000-0001-8388-6051")),
  person(given = "María",
         family = "Sanchez-Martin",
         email = "msanmar@usal.es",
         role = c("aut", "ctb"),
         comment = c(ORCID = "0009-0006-5549-6113")),
  person(given = "Santiago",
         family = "Bueno-Fortes",
         role = c("aut", "ctb"),
         comment = c(ORCID = "0000-0001-7141-2860")),
  person(given = "Natalia",
         family = "Alonso-Moreda",
         role = c("aut", "ctb"),
         comment = c(ORCID = "0000-0002-2347-5127")),
  person(given = "Jose Manuel",
         family = "Sanchez-Santos",
         role = c("aut", "ctb"),
         comment = c(ORCID = "0000-0002-7434-7598")),
  person(given = "Manuel",
         family = "Martin-Merino Acera",
         role = c("aut", "ctb"),
         comment = c(ORCID = "0000-0002-5914-2332")),
  person(given = "Javier", 
         family = "De Las Rivas",
         email = "jrivas@usal.es",
         role = c("aut", "ctb"),
         comment = c(ORCID = "0000-0002-0984-9946"))
  )
License: LGPL-3 + file LICENSE
Depends: R (>= 4.5.0), stats, methods
Imports: SummarizedExperiment, spsUtil, lubridate, survival, glmnet,
        siggenes, survcomp, scales, ROCR, ggplot2, grDevices, graphics,
        utils, Rdpack
Suggests: BiocStyle, knitr, formatR, rmarkdown, magick, devtools
biocViews: Software, StatisticalMethod, WorkflowStep, GeneExpression,
        Microarray, DifferentialExpression, GenePrediction, Regression,
        Survival, ExonArray, MultipleComparison
URL: https://github.com/jdelasrivas-lab/asuri
BugReports: https://github.com/jdelasrivas-lab/asuri/issues
BiocType: Software
ZipData: TRUE
RoxygenNote: 7.3.3
NeedsCompilation: no
RdMacros: Rdpack
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: false
Config/pak/sysreqs: libicu-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:05:58 UTC
RemoteUrl: https://github.com/bioc/asuri
RemoteRef: RELEASE_3_23
RemoteSha: 9c8ad9790f08014b94d0e08122de94fe9248740c
Packaged: 2026-04-29 18:12:08 UTC; root
Author: Alberto Berral-Gonzalez [aut, cre, ctb] (ORCID:
    <https://orcid.org/0000-0001-8388-6051>),
  María Sanchez-Martin [aut, ctb] (ORCID:
    <https://orcid.org/0009-0006-5549-6113>),
  Santiago Bueno-Fortes [aut, ctb] (ORCID:
    <https://orcid.org/0000-0001-7141-2860>),
  Natalia Alonso-Moreda [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-2347-5127>),
  Jose Manuel Sanchez-Santos [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-7434-7598>),
  Manuel Martin-Merino Acera [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-5914-2332>),
  Javier De Las Rivas [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-0984-9946>)
Maintainer: Alberto Berral-Gonzalez <aberralgonzalez@gmail.com>
Built: R 4.6.0; ; 2026-04-29 18:29:20 UTC; windows
