GSEABenchmarkeR

Reproducible GSEA Benchmarking

Bioconductor version: Release (3.19)

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.

Author: Ludwig Geistlinger [aut, cre], Gergely Csaba [aut], Mara Santarelli [ctb], Lucas Schiffer [ctb], Marcel Ramos [ctb], Ralf Zimmer [aut], Levi Waldron [aut]

Maintainer: Ludwig Geistlinger <ludwig.geistlinger at gmail.com>

Citation (from within R, enter citation("GSEABenchmarkeR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GSEABenchmarkeR")

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("GSEABenchmarkeR")

Reproducible GSEA Benchmarking	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization
Version	1.24.0
In Bioconductor since	BioC 3.7 (R-3.5) (6.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), Biobase, SummarizedExperiment
Imports	AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils
System Requirements
URL	https://github.com/waldronlab/GSEABenchmarkeR
Bug Reports	https://github.com/waldronlab/GSEABenchmarkeR/issues

Suggests	BiocStyle, GSE62944, knitr, rappdirs, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	pareg, roastgsa
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GSEABenchmarkeR_1.24.0.tar.gz
Windows Binary (x86_64)	GSEABenchmarkeR_1.24.0.zip (64-bit only)
macOS Binary (x86_64)	GSEABenchmarkeR_1.24.0.tgz
macOS Binary (arm64)	GSEABenchmarkeR_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GSEABenchmarkeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GSEABenchmarkeR
Bioc Package Browser	https://code.bioconductor.org/browse/GSEABenchmarkeR/
Package Short Url	https://bioconductor.org/packages/GSEABenchmarkeR/
Package Downloads Report	Download Stats