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.
|Author||Guangchuang Yu <firstname.lastname@example.org> with contributions from Alexey Stukalov and Chuanle Xiao.|
|Date of publication||None|
|Maintainer||Guangchuang Yu <email@example.com>|
clusterSim: Semantic Similarity Between Two Gene Clusters
combineScores: combining similarity matrix to similarity score
geneSim: Semantic Similarity Between two Genes
GOSemSimDATA-class: Class "GOSemSimDATA" This class stores IC and gene to go...
GOSemSim-package: Gene Ontology-based Sematic Similarity Measures
goSim: Semantic Similarity Between Two GO Terms
go_term_table: Information content of GO terms
infoContentMethod: information content based methods
mclusterSim: Pairwise Semantic Similarities for a List of Gene Clusters
mgeneSim: Pairwise Semantic Similarity for a List of Genes
mgoSim: Semantic Similarity Between two GO terms lists