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RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.

ABSTRACT:

Summary

The R/Bioconductor package RamiGO is an R interface to AmiGO that enables visualization of Gene Ontology (GO) trees. Given a list of GO terms, RamiGO uses the AmiGO visualize API to import Graphviz-DOT format files into R, and export these either as images (SVG, PNG) or into Cytoscape for extended network analyses. RamiGO provides easy customization of annotation, highlighting of specific GO terms, colouring of terms by P-value or export of a simplified summary GO tree. We illustrate RamiGO functionalities in a genome-wide gene set analysis of prognostic genes in breast cancer.

Availability and implementation

RamiGO is provided in R/Bioconductor, is open source under the Artistic-2.0 License and is available with a user manual containing installation, operating instructions and tutorials. It requires R version 2.15.0 or higher. URL: http://bioconductor.org/packages/release/bioc/html/RamiGO.html

SUBMITTER: Schroder MS

PROVIDER: S-EPMC3582261 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.

Schröder Markus S MS Gusenleitner Daniel D Quackenbush John J Culhane Aedín C AC Haibe-Kains Benjamin B

Bioinformatics (Oxford, England) 20130106 5

<h4>Summary</h4>The R/Bioconductor package RamiGO is an R interface to AmiGO that enables visualization of Gene Ontology (GO) trees. Given a list of GO terms, RamiGO uses the AmiGO visualize API to import Graphviz-DOT format files into R, and export these either as images (SVG, PNG) or into Cytoscape for extended network analyses. RamiGO provides easy customization of annotation, highlighting of specific GO terms, colouring of terms by P-value or export of a simplified summary GO tree. We illust ...[more]

PMID: 23297033

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