Package: pairedGSEA
Title: Paired DGE and DGS analysis for gene set enrichment analysis
Version: 1.11.0
Authors@R: c(
    person(given = "Søren Helweg",
        family = "Dam",
        email = "sohdam@dtu.dk",
        role = c("cre", "aut"),
        comment = c(ORCID = "0000-0002-9895-0930")),
    person(given = "Lars Rønn",
        family = "Olsen",
        email = "lronn@dtu.dk",
        role = "aut",
        comment = c(ORCID = "0000-0002-6725-7850")),
    person(given = "Kristoffer",
        family = "Vitting-Seerup",
        email = "krivi@dtu.dk",
        role = "aut",
        comment = c(ORCID = "0000-0002-6450-0608"))
        )
Description: pairedGSEA makes it simple to run a paired Differential
    Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis.
    The package allows you to store intermediate results for further
    investiation, if desired.
    pairedGSEA comes with a wrapper function for running an
    Over-Representation Analysis (ORA) and functionalities for
    plotting the results.
License: MIT + file LICENSE
Imports: 
    DESeq2, DEXSeq,
    limma,
    fgsea,
    msigdbr, 
    sva,
    SummarizedExperiment,
    S4Vectors,
    BiocParallel,
    ggplot2,
    aggregation,
    stats,
    utils,
    methods,
    showtext
Suggests: 
    writexl, readxl, readr,
    rhdf5,
    plotly,
    testthat (>= 3.0.0),
    knitr,
    rmarkdown,
    BiocStyle,
    covr
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.2
VignetteBuilder: knitr
biocViews:
    DifferentialExpression,
    AlternativeSplicing,
    DifferentialSplicing,
    GeneExpression,
    ImmunoOncology,
    GeneSetEnrichment,
    Pathways,
    RNASeq,
    Software,
    Transcription,
URL: https://github.com/shdam/pairedGSEA
BugReports: https://github.com/shdam/pairedGSEA/issues
Depends:
    R (>= 4.4.0)
git_url: https://git.bioconductor.org/packages/pairedGSEA
git_branch: devel
git_last_commit: dcfda05
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
