EnrichmentBrowser
Seamless navigation through combined results of set-based and network-based enrichment analysis
Bioconductor version: Release (3.19)
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], Rohit Satyam [ctb], Marcel Ramos [ctb], Levi Waldron [ctb], Ralf Zimmer [aut]
Maintainer: Ludwig Geistlinger <ludwig.geistlinger at gmail.com>
citation("EnrichmentBrowser")):
Installation
To install this package, start R (version "4.4") 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")| Seamless navigation through combined results of set- & network-based enrichment analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization |
| Version | 2.34.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/lgeistlinger/EnrichmentBrowser/issues |
See More
| Suggests | ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | GSEABenchmarkeR, zenith |
| Suggests Me | GenomicSuperSignature, epiregulon.extra, roastgsa |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EnrichmentBrowser_2.34.1.tar.gz |
| Windows Binary (x86_64) | EnrichmentBrowser_2.34.1.zip (64-bit only) |
| macOS Binary (x86_64) | EnrichmentBrowser_2.34.1.tgz |
| macOS Binary (arm64) | EnrichmentBrowser_2.34.1.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 3.19 | Source Archive |