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Bioinformatics. 2010 Apr 1;26(7):976-8. doi: 10.1093/bioinformatics/btq064. Epub 2010 Feb 23.

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products.

Author information

1
Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China.

Abstract

SUMMARY:

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four information content (IC)- and a graph-based methods are implemented in the GOSemSim package, multiple species including human, rat, mouse, fly and yeast are also supported. The functions provided by the GOSemSim offer flexibility for applications, and can be easily integrated into high-throughput analysis pipelines.

AVAILABILITY:

GOSemSim is released under the GNU General Public License within Bioconductor project, and freely available at http://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html.

PMID:
20179076
DOI:
10.1093/bioinformatics/btq064
[Indexed for MEDLINE]

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