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Oxford University Press, Bioinformatics, 5(29), p. 666-668, 2013

DOI: 10.1093/bioinformatics/bts708

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RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface

Journal article published in 2013 by Markus S. Schröder ORCID, Daniel Gusenleitner, John Quackenbush, Aedı́n C. Culhane ORCID, Benjamin Haibe-Kains
This paper is available in a repository.
This paper is available in a repository.

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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.