EnrichmentBrowser

DOI: 10.18129/B9.bioc.EnrichmentBrowser    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see EnrichmentBrowser.

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

Bioconductor version: 3.9

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], Marcel Ramos [ctb], Levi Waldron [ctb], Ralf Zimmer [aut]

Maintainer: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	EnrichmentBrowser Manual
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization
Version	2.14.3
In Bioconductor since	BioC 3.0 (R-3.1) (5 years)
License	Artistic-2.0
Depends	SummarizedExperiment, graph
Imports	AnnotationDbi, BiocFileCache, BiocManager, ComplexHeatmap, DESeq2, EDASeq, GSEABase, GO.db, KEGGREST, KEGGgraph, MASS, ReportingTools, Rgraphviz, S4Vectors, SPIA, biocGraph, edgeR, geneplotter, graphite, hwriter, limma, methods, pathview, rappdirs, safe, topGO
LinkingTo
Suggests	ALL, BiocStyle, airway, hgu95av2.db, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	GSEABenchmarkeR, PathwaySplice
Suggests Me	ToPASeq
Links To Me
Build Report

Package Archives

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

Source Package	EnrichmentBrowser_2.14.3.tar.gz
Windows Binary	EnrichmentBrowser_2.14.3.zip
Mac OS X 10.11 (El Capitan)	EnrichmentBrowser_2.14.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EnrichmentBrowser
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EnrichmentBrowser
Package Short Url	https://bioconductor.org/packages/EnrichmentBrowser/
Package Downloads Report	Download Stats