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

Question

[Guangchuang Yu]

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. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.

GOSemSim is released within the Bioconductor project and the source code is hosted in GitHub.

Homepage: https://guangchuangyu.github.io/GOSemSim/

Documentation: https://guangchuangyu.github.io/GOSemSim/documentation/

Issue/Question: https://guangchuangyu.github.io/GOSemSim/#feedback

Citation

Yu G^†, Li F^†, Qin Y, Bo X^\*, Wu Y and Wang S^\*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010, 26(7):976-978. doi:10.1093/bioinformatics/btq064

Example

http://www.pnas.org/content/111/13/4892.short

[Guangchuang Yu]

new version of vignette is out. Now it supports all species that have OrgDb object which can be queried online by AnnotationHub.