GSEAlens
This is the development version of GSEAlens; to use it, please install the devel version of Bioconductor.
Gene Set Enrichment Analysis Interactive Explorer
Bioconductor version: Development (3.24)
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.
Author: Shenhui Xu [aut, cre] 
, Yuanhang Zhao [ctb], Mireia Ramos-Rodríguez [rev] (URL: https://github.com/mireia-bioinfo)
Maintainer: Shenhui Xu <sealgod at qq.com>
citation("GSEAlens")):Shenhui Xu. GSEAlens: Gene Set Enrichment Analysis Interactive Explorer. doi:10.18129/B9.bioc.GSEAlens, R package version 0.99.35, https://bioconductor.org/packages/GSEAlens.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GSEAlens")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GSEAlens")| GSEAlens：准备输入数据 | HTML | R Script |
| GSEAlens: Preparing Input Data | HTML | R Script |
| GSEAlens（中文版）：基因集富集分析的交互式探索平台 | HTML | R Script |
| GSEAlens: An Interactive Exploration Platform for Gene Set Enrichment Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneSetEnrichment, ShinyApps, Software, Visualization |
| Version | 0.99.35 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| 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 |
| System Requirements | |
| URL | https://github.com/DDL095/GSEAlens |
| Bug Reports | https://github.com/DDL095/GSEAlens/issues |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, airway, ggrepel |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GSEAlens_0.99.35.tar.gz |
| Windows Binary (x86_64) | GSEAlens_0.99.35.zip |
| macOS Binary (big-sur-x86_64) | GSEAlens_0.99.35.tgz |
| macOS Binary (sonoma-arm64) | GSEAlens_0.99.35.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GSEAlens |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GSEAlens |
| Package Short Url | https://bioconductor.org/packages/GSEAlens/ |
| Package Downloads Report | Download Stats |