GOSemSim-package: Gene Ontology-based Sematic Similarity Measures

GOSemSim-packageR Documentation

Gene Ontology-based Sematic Similarity Measures


Implementation of semantic similarity measures to estimate the functional similarities among Gene Ontology terms and gene products


Quantitative measure of functional similarities among gene products is important for post-genomics study. and widely used in gene function prediction, cluster analysis and pathway modeling. This package is designed to estimate the GO terms' and genes' semantic similarities. Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively. Support many species, including Anopheles, Arabidopsis, Bovine, Canine, Chicken, Chimp, E coli strain K12 and strain Sakai, Fly, Human, Malaria, Mouse, Pig, Rhesus, Rat, Worm, Xenopus, Yeast, Zebrafish.

Package: GOSemSim
Type: Package
Version: 2.0.0
Date: 09-11-2012
biocViews: GO, Clustering, Pathways, Anopheles_gambiae, Arabidopsis_thaliana, Bos_taurus, Caenorhabditis_elegans, Canis_familiaris, Danio_rerio, Drosophila_melanogaster, Escherichia_coli, Gallus_gallus, Homo_sapiens, Mus_musculus, Pan_troglodytes, Plasmodium_falciparum, Rattus_norvegicus, Saccharomyces_cerevisiae, Streptomyces_coelicolor, Sus_scrofa, Xenopus_laevis
Imports: methods, AnnotationDbi, GO.db
Suggests: clusterProfiler, DOSE
License: Artistic-2.0


Guangchuang Yu

Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>


Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976–978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

See Also

goSim mgoSim geneSim mgeneSim clusterSim mclusterSim

YuLab-SMU/GOSemSim documentation built on Nov. 2, 2022, 2:57 p.m.