waldronlab/GSEABenchmarkeR: Reproducible GSEA Benchmarking

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.

Getting started

Package details

Author Ludwig Geistlinger [aut, cre], Gergely Csaba [aut], Mara Santarelli [ctb], Lucas Schiffer [ctb], Marcel Ramos [ctb], Ralf Zimmer [aut], Levi Waldron [aut]
Bioconductor views DifferentialExpression GeneExpression GeneSetEnrichment GraphAndNetwork ImmunoOncology Microarray Network NetworkEnrichment Pathways RNASeq ReportWriting Visualization
MaintainerLudwig Geistlinger <ludwig.geistlinger@gmail.com>
URL https://github.com/waldronlab/GSEABenchmarkeR
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
waldronlab/GSEABenchmarkeR documentation built on Nov. 3, 2023, 10:59 p.m.