EnrichmentBrowser
This is the released version of EnrichmentBrowser; for the devel version, see EnrichmentBrowser.
Seamless navigation through combined results of set-based and network-based enrichment analysis
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 2.42.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 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, roastgsa, bugphyzz |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EnrichmentBrowser_2.42.0.tar.gz |
| Windows Binary (x86_64) | EnrichmentBrowser_2.42.0.zip |
| macOS Binary (big-sur-x86_64) | EnrichmentBrowser_2.42.0.tgz |
| macOS Binary (sonoma-arm64) | EnrichmentBrowser_2.42.0.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 |