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 (>= 4.5.0)
VignetteBuilder: knitr
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev perl libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-19 04:12:16 UTC
RemoteUrl: https://github.com/bioc/GSEAlens
RemoteRef: HEAD
RemoteSha: d1807abe23fdacd7d9ebaf212e545abf0b471fd3
NeedsCompilation: no
Packaged: 2026-09-18 08:50:57 UTC; root
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>