Package: pathMED
Title: Scoring Personalized Molecular Portraits
Version: 1.1.4
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 (>= 4.5.0)
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
git_url: https://git.bioconductor.org/packages/pathMED
git_branch: devel
git_last_commit: 07a5010
git_last_commit_date: 2025-07-29
Repository: Bioconductor 3.22
Date/Publication: 2025-07-29
NeedsCompilation: no
Packaged: 2025-07-30 01:13:00 UTC; biocbuild
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 4.5.1; ; 2025-07-30 13:55:59 UTC; windows
