GSEABenchmarkeR
Reproducible GSEA Benchmarking
Bioconductor version: 3.23 · Package version: 1.32.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GSEABenchmarkeR")Details
| Maintainer | Ludwig Geistlinger <ludwig.geistlinger@gmail.com> |
| Author | Ludwig Geistlinger [aut, cre], Gergely Csaba [aut], Mara Santarelli [ctb], Lucas Schiffer [ctb], Marcel Ramos [ctb], Ralf Zimmer [aut], Levi Waldron [aut] |
| License | Artistic-2.0 |
| URL | https://github.com/waldronlab/GSEABenchmarkeR |
| Bug Reports | https://github.com/waldronlab/GSEABenchmarkeR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/GSEABenchmarkeR/ |
Citation
From within R, enter citation("GSEABenchmarkeR"):
Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer, Levi Waldron. GSEABenchmarkeR: Reproducible GSEA Benchmarking. doi:10.18129/B9.bioc.GSEABenchmarkeR, R package version 1.32.0, https://bioconductor.org/packages/GSEABenchmarkeR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | GSEABenchmarkeR_1.32.0.tar.gz |
| Windows binary (x86_64) | GSEABenchmarkeR_1.32.0.zip |
| macOS binary (arm64) | GSEABenchmarkeR_1.32.0.tgz |
| macOS binary (x86_64) | GSEABenchmarkeR_1.32.0.tgz |
Dependencies
Depends: R (>= 4.5.0), Biobase, SummarizedExperiment
Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils
Reverse dependencies
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