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GSEABenchmarkeR

This is the development version of GSEABenchmarkeR; for the stable release version, see GSEABenchmarkeR.

Reproducible GSEA Benchmarking


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization
Version 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
See More
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_1.23.0.tar.gz
Windows Binary GSEABenchmarkeR_1.23.0.zip
macOS Binary (x86_64) GSEABenchmarkeR_1.23.0.tgz
macOS Binary (arm64)
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