GSEABenchmarkeR
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GSEABenchmarkeR.
Reproducible GSEA Benchmarking
Bioconductor version: 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("GSEABenchmarkeR")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | Artistic-2.0 |
| Depends | Biobase, SummarizedExperiment |
| Imports | AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, GEOquery, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, rappdirs, S4Vectors, stats, utils |
| System Requirements | |
| URL | https://github.com/waldronlab/GSEABenchmarkeR |
| Bug Reports | https://github.com/waldronlab/GSEABenchmarkeR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| 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 | GSEABenchmarkeR_1.4.0.tar.gz |
| Windows Binary | GSEABenchmarkeR_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | GSEABenchmarkeR_1.4.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |