GSEABenchmarkeR

DOI: 10.18129/B9.bioc.GSEABenchmarkeR    

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

Reproducible GSEA Benchmarking

Bioconductor version: Development (3.9)

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 sph.cuny.edu>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GSEABenchmarkeR", version = "3.9")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GSEABenchmarkeR")

 

HTML R Script Reproducible GSEA Benchmarking
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization
Version 1.3.0
License Artistic-2.0
Depends R (>= 3.5.0), Biobase, SummarizedExperiment
Imports AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, GEOquery, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, rappdirs, S4Vectors, stats, utils
LinkingTo
Suggests BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL https://github.com/waldronlab/GSEABenchmarkeR
BugReports https://github.com/waldronlab/GSEABenchmarkeR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package GSEABenchmarkeR_1.3.0.tar.gz
Windows Binary GSEABenchmarkeR_1.3.0.zip
Mac OS X 10.11 (El Capitan) GSEABenchmarkeR_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GSEABenchmarkeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GSEABenchmarkeR
Package Short Url http://bioconductor.org/packages/GSEABenchmarkeR/
Package Downloads Report Download Stats

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