EnrichmentBrowser

DOI: 10.18129/B9.bioc.EnrichmentBrowser  

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

Bioconductor version: Release (3.16)

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 hms.harvard.edu>

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

Installation

To install this package, start R (version "4.2") 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")

 

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 2.28.2
In Bioconductor since BioC 3.0 (R-3.1) (8.5 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
LinkingTo
Suggests ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown
SystemRequirements
Enhances
URL
BugReports 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_2.28.2.tar.gz
Windows Binary EnrichmentBrowser_2.28.2.zip (64-bit only)
macOS Binary (x86_64) EnrichmentBrowser_2.28.2.tgz
macOS Binary (arm64) EnrichmentBrowser_2.28.2.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 3.16 Source Archive

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