EnrichmentBrowser

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

Bioconductor version: Release (3.17)

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.

Author: Ludwig Geistlinger [aut, cre], Gergely Csaba [aut], Mara Santarelli [ctb], Mirko Signorelli [ctb], Marcel Ramos [ctb], Levi Waldron [ctb], Ralf Zimmer [aut]

Maintainer: Ludwig Geistlinger <ludwig.geistlinger at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("EnrichmentBrowser")

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("EnrichmentBrowser")

EnrichmentBrowser Manual	PDF	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization
Version	2.30.2
In Bioconductor since	BioC 3.0 (R-3.1) (9 years)
License	Artistic-2.0
Depends	SummarizedExperiment, graph
Imports	AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe
Linking To
Suggests	ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod
System Requirements
Enhances
URL
Bug Reports	https://github.com/lgeistlinger/EnrichmentBrowser/issues

Depends On Me
Imports Me	GSEABenchmarkeR, zenith
Suggests Me	GenomicSuperSignature
Links To Me
Build Report

Package Archives

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

Source Package	EnrichmentBrowser_2.30.2.tar.gz
Windows Binary	EnrichmentBrowser_2.30.2.zip (64-bit only)
macOS Binary (x86_64)	EnrichmentBrowser_2.30.2.tgz
macOS Binary (arm64)	EnrichmentBrowser_2.30.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EnrichmentBrowser
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EnrichmentBrowser
Bioc Package Browser	https://code.bioconductor.org/browse/EnrichmentBrowser/
Package Short Url	https://bioconductor.org/packages/EnrichmentBrowser/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive