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EnrichmentBrowser

Seamless navigation through combined results of set-based and network-based enrichment analysis

Bioconductor version: 3.23 · Package version: 2.42.0

The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.

Installation

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

BiocManager::install("EnrichmentBrowser")

Details

MaintainerLudwig Geistlinger <ludwig.geistlinger@gmail.com>
AuthorLudwig Geistlinger [aut, cre], Gergely Csaba [aut], Mara Santarelli [ctb], Mirko Signorelli [ctb], Rohit Satyam [ctb], Marcel Ramos [ctb], Levi Waldron [ctb], Ralf Zimmer [aut]
LicenseArtistic-2.0
Bug Reportshttps://github.com/lgeistlinger/EnrichmentBrowser/issues
Downloads rank830
Source branchRELEASE_3_23
biocViewsDifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization

Documentation

Download

Dependencies

Depends: SummarizedExperiment, graph

Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe

Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod

Reverse dependencies

Imports Me (2): GSEABenchmarkeR, zenith

Suggests Me (3): bugphyzz, GenomicSuperSignature, roastgsa