markeR/DESCRIPTION at default · DiseaseTranscriptomicsLab/markeR · GitHub

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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