This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see EnrichmentBrowser.
Bioconductor version: 3.8
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 (from within R,
enter citation("EnrichmentBrowser")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("EnrichmentBrowser")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("EnrichmentBrowser")
R Script | EnrichmentBrowser Manual | |
Reference Manual | ||
Text | NEWS |
biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization |
Version | 2.12.1 |
In Bioconductor since | BioC 3.0 (R-3.1) (4.5 years) |
License | Artistic-2.0 |
Depends | R (>= 3.5.0), SummarizedExperiment, graph |
Imports | AnnotationDbi, BiocFileCache, BiocManager, ComplexHeatmap, DESeq2, EDASeq, GSEABase, GO.db, KEGGREST, KEGGgraph, MASS, ReportingTools, Rgraphviz, S4Vectors, SPIA, biocGraph, edgeR, geneplotter, graphite, hwriter, limma, methods, pathview, rappdirs, safe, topGO |
LinkingTo | |
Suggests | ALL, BiocStyle, airway, hgu95av2.db, knitr |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | GSEABenchmarkeR, PathwaySplice |
Suggests Me | ToPASeq |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | EnrichmentBrowser_2.12.1.tar.gz |
Windows Binary | EnrichmentBrowser_2.12.1.zip |
Mac OS X 10.11 (El Capitan) | EnrichmentBrowser_2.12.1.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/EnrichmentBrowser |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/EnrichmentBrowser |
Package Short Url | http://bioconductor.org/packages/EnrichmentBrowser/ |
Package Downloads Report | Download Stats |
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