EnrichmentBrowser
This package is for version 3.10 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: 3.10
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("EnrichmentBrowser")):
Installation
To install this package, start R (version "3.6") 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")| EnrichmentBrowser Manual | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization |
| Version | 2.16.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | Artistic-2.0 |
| Depends | SummarizedExperiment, graph |
| Imports | AnnotationDbi, BiocFileCache, BiocManager, ComplexHeatmap, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, biocGraph, edgeR, geneplotter, graphite, hwriter, limma, methods, pathview, rappdirs, safe, topGO |
| System Requirements | |
| URL |
See More
| Suggests | ALL, BiocStyle, ReportingTools, airway, hgu95av2.db, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | GSEABenchmarkeR, PathwaySplice |
| Suggests Me | ToPASeq |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EnrichmentBrowser_2.16.1.tar.gz |
| Windows Binary | EnrichmentBrowser_2.16.1.zip |
| Mac OS X 10.11 (El Capitan) | EnrichmentBrowser_2.16.1.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 3.10 | Source Archive |