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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../html/EnrichmentBrowser.html below:

Bioconductor - EnrichmentBrowser (development version)

EnrichmentBrowser

This is the development version of EnrichmentBrowser; for the stable release version, see EnrichmentBrowser.

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

Bioconductor version: Development (3.22)

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF NEWS Text Details biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization Version 2.39.0 In Bioconductor since BioC 3.0 (R-3.1) (10.5 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 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.


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