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: Dudali Lab [aut], Dudali Lab [cre]
Maintainer: Dudali Lab <sealgod at qq.com>
citation("GSEAlens")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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: An Interactive Exploration Platform for Gene Set Enrichment Analysis | 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：准备输入数据 | HTML | R Script |
| Reference Manual |
Details
| biocViews | GeneSetEnrichment, ShinyApps, Software, Visualization |
| Version | 0.99.33 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GSEAlens_0.99.33.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | GSEAlens_0.99.33.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GSEAlens |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GSEAlens |
| Bioc Package Browser | https://code.bioconductor.org/browse/GSEAlens/ |
| Package Short Url | https://bioconductor.org/packages/GSEAlens/ |
| Package Downloads Report | Download Stats |