Package: markeR
Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic
        Markers
Version: 1.3.1
Authors@R: 
    c(
      person("Rita", "Martins-Silva", 
             email = "rita.silva@gimm.pt", 
             role = c("aut", "cre"),
             comment = c(ORCID = "0000-0002-1067-7993")), 
            person("Alexandre", "Kaizeler",  
             role = c("aut", "ctb"),
             comment = c(ORCID = "0000-0002-9117-6073")),
        person(c("Nuno", "Luís"), "Barbosa-Morais", role=c("aut", "led", "ths"),
               comment=c(ORCID="0000-0002-1215-0538"))
    )
Description: markeR is an R package that provides a modular and
        extensible framework for the systematic evaluation of gene sets
        as phenotypic markers using transcriptomic data. The package is
        designed to support both quantitative analyses and visual
        exploration of gene set behaviour across experimental and
        clinical phenotypes. It implements multiple methods, including
        score-based and enrichment approaches, and also allows the
        exploration of expression behaviour of individual genes. In
        addition, users can assess the similarity of their own gene
        sets against established collections (e.g., those from MSigDB),
        facilitating biological interpretation.
License: Artistic-2.0
biocViews: GeneExpression, Transcriptomics, Visualization, Software,
        GeneSetEnrichment, Classification
Encoding: UTF-8
Language: en-GB
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Additional_repositories: https://bioconductor.org/packages/release/bioc
Imports: circlize, edgeR, ComplexHeatmap, ggh4x, ggplot2, ggpubr, grid,
        gridExtra, pROC, RColorBrewer, reshape2, rstatix, scales,
        stats, utils, fgsea, limma, ggrepel, effectsize, msigdbr,
        tibble
Suggests: devtools, markdown, renv, testthat, BiocManager, knitr,
        rmarkdown, roxygen2, mockery, covr, magick, BiocStyle
Config/testthat/edition: 3
Depends: R (>= 4.5.0)
URL: https://diseasetranscriptomicslab.github.io/markeR/,
        https://github.com/DiseaseTranscriptomicsLab/markeR,
        https://doi.org/10.1093/nargab/lqag057
BugReports: https://github.com/DiseaseTranscriptomicsLab/markeR/issues
VignetteBuilder: knitr
Config/Needs/website: rmarkdown
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libssl-dev perl
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-08 11:23:21 UTC
RemoteUrl: https://github.com/bioc/markeR
RemoteRef: HEAD
RemoteSha: 60afe2786e79c490ebb50f269dc1a4e1c4fafbf8
NeedsCompilation: no
Packaged: 2026-07-08 17:16:30 UTC; root
Author: Rita Martins-Silva [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1067-7993>),
  Alexandre Kaizeler [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-9117-6073>),
  Nuno Luís Barbosa-Morais [aut, led, ths] (ORCID:
    <https://orcid.org/0000-0002-1215-0538>)
Maintainer: Rita Martins-Silva <rita.silva@gimm.pt>