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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("EnrichmentBrowser")
In most cases, you don't need to download the package archive at all.
EnrichmentBrowser
Seamless navigation through combined results of set-based and network-based enrichment analysis
Bioconductor version: 3.0
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. In addition, the package facilitates the visualization and exploration of such sets and pathways.
Author: Ludwig Geistlinger
Maintainer: Ludwig Geistlinger <Ludwig.Geistlinger at bio.ifi.lmu.de>
Citation (from within R,
enter citation("EnrichmentBrowser")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("EnrichmentBrowser")
Documentation
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 |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Pathways, ReportWriting, Software, Visualization |
| Version | 1.0.3 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.0), Biobase, KEGGgraph |
| Imports | KEGGREST, MASS, RColorBrewer, Rgraphviz, SPIA, graph, limma, mixtools, neaGUI, qvalue, safe, stringr |
| LinkingTo | |
| Suggests | ALL, BiocStyle, hgu95av2.db |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | EnrichmentBrowser_1.0.3.tar.gz |
| Windows Binary | EnrichmentBrowser_1.0.3.zip |
| Mac OS X 10.6 (Snow Leopard) | EnrichmentBrowser_1.0.3.tgz |
| Mac OS X 10.9 (Mavericks) | EnrichmentBrowser_1.0.3.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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