% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/GSEAlens-package.R
\docType{package}
\name{GSEAlens-package}
\alias{GSEAlens-package}
\alias{GSEAlens}
\title{GSEAlens: Gene Set Enrichment Analysis Interactive Explorer}
\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.
}
\details{
**Main entry points:**

- [setup_gsea_env()]: Initialize a GSEA analysis environment from limma or
  DESeq2 fitted objects.
- [batch_calc_gsea()]: Run GSEA across multiple contrasts in parallel.
- [build_gsea_pathways()]: Build MSigDB pathway database (interactive or
  automated selection).
- [extract_gsea_task()]: Extract a single contrast for downstream
  visualization and reporting.

**Built-in Shiny application:**

Launch the interactive explorer via [launch_gsea_app()] after DEG analysis.
The app provides pathway-level drill-down, multi-contrast joint canvases,
quadrant plots, hub-gene networks, and one-click export of self-contained
reproducible R scripts.

**Vignettes:**

- `vignette("GSEAlens", package = "GSEAlens")`: Main workflow
- `vignette("GSEAlens-preprocessing", package = "GSEAlens")`: Data
  preprocessing
}
\examples{
library(GSEAlens)
packageDescription("GSEAlens")$Version
}
\references{
<https://github.com/DDL095/GSEAlens>
}
\seealso{
Useful links:
\itemize{
  \item \url{https://github.com/DDL095/GSEAlens}
  \item Report bugs at \url{https://github.com/DDL095/GSEAlens/issues}
}

}
\author{
Shenhui Xu \email{sealgod@qq.com}
}
