RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 23297033.
- Also identified by DOI 10.1093/bioinformatics/bts708 and PMC identifier 3582261.
- No licence information is recorded for this record.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
Abstract
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. 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
Medical subject headings
- Genes
- Software
- Vocabulary, Controlled