Package: markeR
Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic
        Markers
Version: 1.1.2
Authors@R: 
    c(
      person("Rita", "Martins-Silva", 
             email = "rita.silva@medicina.ulisboa.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
BugReports: https://github.com/DiseaseTranscriptomicsLab/markeR/issues
VignetteBuilder: knitr
Config/Needs/website: rmarkdown
git_url: https://git.bioconductor.org/packages/markeR
git_branch: devel
git_last_commit: 3356098
git_last_commit_date: 2026-03-12
Repository: Bioconductor 3.23
Date/Publication: 2026-03-12
NeedsCompilation: no
Packaged: 2026-03-12 20:23:29 UTC; biocbuild
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@medicina.ulisboa.pt>
Built: R 4.6.0; ; 2026-03-13 01:07:01 UTC; unix
