EnrichmentBrowser

DOI: 10.18129/B9.bioc.EnrichmentBrowser    

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

Bioconductor version: Release (3.7)

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
        source("https://bioconductor.org/biocLite.R")
        biocLite("EnrichmentBrowser")

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, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization
Version 2.10.4
In Bioconductor since BioC 3.0 (R-3.1) (4 years)
License Artistic-2.0
Depends R (>= 3.4.0), SummarizedExperiment, graph
Imports AnnotationDbi, BiocFileCache, 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
Build Report  

Package Archives

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

Source Package EnrichmentBrowser_2.10.4.tar.gz
Windows Binary EnrichmentBrowser_2.10.4.zip
Mac OS X 10.11 (El Capitan) EnrichmentBrowser_2.10.4.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 http://bioconductor.org/packages/EnrichmentBrowser/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive

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