Package: gINTomics
Title: Multi-Omics data integration
Version: 1.7.0
Authors@R: c(person("Angelo", "Velle", role = c("cre", "aut"),
                    email = "angelo.velle@unipd.it",
                    comment = c(ORCID = "0000-0002-4010-6390")),
             person("Francesco", "Patane'", role = "aut",
                     email = "francesco.patane@unipd.it", 
                     comment = c(ORCID = "0009-0001-8619-447X")),
             person("Chiara", "Romualdi", role = "aut", 
                    email = "chiara.romualdi@unipd.it",
                    comment = c(ORCID = "0000-0003-4792-9047")))
Description: gINTomics is an R package for Multi-Omics data integration and 
            visualization.
            gINTomics is designed to detect the association between the 
            expression of a target and of its regulators, taking into account 
            also their genomics modifications such as Copy Number Variations 
            (CNV) and methylation. 
            What is more, gINTomics allows integration results visualization 
            via a Shiny-based interactive app.
License: AGPL-3
biocViews: GeneExpression, RNASeq, Microarray, 
    Visualization, CopyNumberVariation, GeneTarget
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: 
    BiocParallel,
    biomaRt,
    OmnipathR,
    edgeR,
    ggplot2,
    ggridges,
    gtools,
    MultiAssayExperiment,
    plyr,
    stringi,
    stringr,
    SummarizedExperiment,
    methods,
    stats,
    reshape2,
    randomForest,
    limma,
    org.Hs.eg.db,
    org.Mm.eg.db,
    BiocGenerics,
    GenomicFeatures,
    ReactomePA,
    clusterProfiler,
    dplyr,
    AnnotationDbi,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    TxDb.Mmusculus.UCSC.mm10.knownGene,
    shiny,
    GenomicRanges,
    ggtree,
    shinydashboard,
    plotly,
    DT,
    MASS,
    InteractiveComplexHeatmap,
    ComplexHeatmap,
    visNetwork,
    shiny.gosling,
    ggvenn,
    RColorBrewer,
    utils,
    grDevices,
    callr,
    circlize,
    MethylMix,
    shinyjs
Depends: 
    R (>= 4.4.0)
LazyData: false
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
BugReports: https://github.com/angelovelle96/gINTomics/issues
URL: https://github.com/angelovelle96/gINTomics
git_url: https://git.bioconductor.org/packages/gINTomics
git_branch: devel
git_last_commit: 4cacafe
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
