Package: pathMED
Title: Scoring Personalized Molecular Portraits
Version: 1.2.0
Authors@R: c(person("Jordi", "Martorell-Marugán", email="jmartorellm@gmail.com", role=c("cre", "aut"), comment = c(ORCID = "0000-0002-5186-0735")),
  person("Daniel", "Toro-Domínguez", email="danieltorodominguez@gmail.com", role=c("aut"), comment = c(ORCID = "0000-0001-8440-312X")),
  person("Raúl", "López-Domínguez", email="raul.lopez@genyo.es", role=c("aut"), comment = c(ORCID = "0000-0001-8634-117X")),
  person("Iván", "Ellson", email="ivan.ellson@genyo.es", role=c("aut"), comment = c(ORCID = "0000-0001-6307-3141")))
Description: PathMED is a collection of tools to facilitate precision
        medicine studies with omics data (e.g. transcriptomics). Among
        its funcionalities, genesets scores for individual samples may
        be calculated with several methods. These scores may be used to
        train machine learning models and to predict clinical features
        on new data. For this, several machine learning methods are
        evaluated in order to select the best method based on internal
        validation and to tune the hyperparameters. Performance metrics
        and a ready-to-use model to predict the outcomes for new
        patients are returned.
Depends: R (>= 4.4.0)
Suggests: ada, AUCell, Biobase, BiocGenerics, BiocStyle, fgsea (>=
        1.15.4), gam, GSEABase, import, kernlab, klaR, knitr, mboost,
        MLeval, randomForest, ranger, rmarkdown, RUnit,
        SummarizedExperiment, utils, xgboost
Imports: BiocParallel, caret, caretEnsemble, decoupleR, ggplot2, GSVA,
        factoextra, FactoMineR, magrittr, matrixStats, methods,
        metrica, pbapply, reshape2, singscore, stats, stringi, dplyr,
VignetteBuilder: knitr
biocViews: Pathways, Classification, FeatureExtraction, Transcriptomics
BugReports: https://github.com/jordimartorell/pathMED/issues
URL: https://github.com/jordimartorell/pathMED
License: GPL-2
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
Config/pak/sysreqs: cmake make libgsl0-dev libmagick++-dev gsfonts
        libicu-dev libpng-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:36:06 UTC
RemoteUrl: https://github.com/bioc/pathMED
RemoteRef: RELEASE_3_22
RemoteSha: b17f51cad424e5d64373a7806e3183f062f0cd55
NeedsCompilation: no
Packaged: 2026-02-03 08:29:05 UTC; root
Author: Jordi Martorell-Marugán [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-5186-0735>),
  Daniel Toro-Domínguez [aut] (ORCID:
    <https://orcid.org/0000-0001-8440-312X>),
  Raúl López-Domínguez [aut] (ORCID:
    <https://orcid.org/0000-0001-8634-117X>),
  Iván Ellson [aut] (ORCID: <https://orcid.org/0000-0001-6307-3141>)
Maintainer: Jordi Martorell-Marugán <jmartorellm@gmail.com>
Built: R 4.5.2; ; 2026-02-03 08:30:58 UTC; windows
