To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

EnrichmentBrowser

This package is for version 3.2 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: 3.2

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, Gergely Csaba, Ralf Zimmer

Maintainer: Ludwig Geistlinger <Ludwig.Geistlinger at bio.ifi.lmu.de>

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 EnrichmentBrowser Manual
PDF Reference Manual
Text NEWS

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization
Version 2.0.15
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License Artistic-2.0
Depends R (>= 3.0.0), Biobase, GSEABase, pathview
Imports AnnotationDbi, ComplexHeatmap, DESeq2, EDASeq, GO.db, KEGGREST, KEGGgraph, MASS, PathNet, ReportingTools, Rgraphviz, S4Vectors, SparseM, SPIA, SummarizedExperiment, biocGraph, biomaRt, edgeR, geneplotter, graph, hwriter, limma, mixtools, neaGUI, npGSEA, safe, stringr, topGO
LinkingTo
Suggests ALL, BiocStyle, airway, hgu95av2.db, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source EnrichmentBrowser_2.0.15.tar.gz
Windows Binary EnrichmentBrowser_2.0.15.zip
Mac OS X 10.6 (Snow Leopard) EnrichmentBrowser_2.0.0.tgz
Mac OS X 10.9 (Mavericks) EnrichmentBrowser_2.0.15.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/EnrichmentBrowser/tree/release-3.2
Package Short Url http://bioconductor.org/packages/EnrichmentBrowser/
Package Downloads Report Download Stats

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