Package: GSEAlens
Type: Package
Title: Gene Set Enrichment Analysis Interactive Explorer
Version: 0.99.35
Authors@R: c(person(given = "Shenhui", family = "Xu", role = c("aut", "cre"), email = "sealgod@qq.com", comment = c(ORCID = "0000-0002-2616-5132")), person(given = "Yuanhang", family = "Zhao", role = "ctb", email = "zy0928hang@163.com"), person(given = "Mireia", family = "Ramos-Rodríguez", role = "rev", comment = c(URL = "https://github.com/mireia-bioinfo")))
Description: GSEAlens provides an interactive exploration layer on top of
    standard Bioconductor RNA-seq workflows. It consumes fitted model objects
    from limma (MArrayLM) or DESeq2 (DESeqDataSet) as input and accepts
    expression matrices and sample metadata as SummarizedExperiment objects,
    ensuring interoperability with core Bioconductor data containers. For core
    computation, GSEAlens wraps clusterProfiler::GSEA() as its statistical
    engine (thereby inheriting the fgsea fast GSEA methodology) and draws on
    MSigDB gene set collections via the msigdbr package from CRAN; multi-contrast
    parallel computation is handled by future (future::multisession).
    Visualization output relies on Bioconductor graphics packages including
    enrichplot, ComplexHeatmap, and circlize, producing figures suitable for
    publication pipelines. The package also includes a built-in Shiny application
    for interactive exploration of enrichment results after DEG analysis, with
    the ability to export self-contained reproducible R scripts.
License: MIT + file LICENSE
URL: https://github.com/DDL095/GSEAlens
BugReports: https://github.com/DDL095/GSEAlens/issues
Encoding: UTF-8
RoxygenNote: 8.0.0
biocViews: GeneSetEnrichment, Visualization, ShinyApps, Software
Imports: stats, utils, enrichplot, enrichit, grDevices, graphics,
        methods, shiny, shinycssloaders, DT, plotly, ggplot2, rlang,
        igraph, dplyr, tidyr, tibble, stringr, patchwork,
        ComplexHeatmap, circlize, grid, clusterProfiler, limma, edgeR,
        DESeq2, SummarizedExperiment, S4Vectors, msigdbr, future,
        future.apply, htmltools, htmlwidgets, jsonlite, clipr,
        progressr, visNetwork, shinyjs, withr
Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, airway,
        ggrepel
Depends: R (>= 4.6.0)
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GSEAlens
git_branch: devel
git_last_commit: d1807ab
git_last_commit_date: 2026-08-19
Repository: Bioconductor 3.24
Date/Publication: 2026-08-19
NeedsCompilation: no
Packaged: 2026-08-19 22:25:37 UTC; biocbuild
Author: Shenhui Xu [aut, cre] (ORCID: <https://orcid.org/0000-0002-2616-5132>),
  Yuanhang Zhao [ctb],
  Mireia Ramos-Rodríguez [rev] (URL: https://github.com/mireia-bioinfo)
Maintainer: Shenhui Xu <sealgod@qq.com>
