GOSemSim: GO-terms Semantic Similarity Measures

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 <guangchuangyu@gmail.com> with contributions from Alexey Stukalov and Chuanle Xiao.
Date of publication
None
Maintainer
Guangchuang Yu <guangchuangyu@gmail.com>
License
Artistic-2.0
Version
2.0.2
URLs

View on Bioconductor

Man pages

clusterSim
Semantic Similarity Between Two Gene Clusters
combineScores
combining similarity matrix to similarity score
geneSim
Semantic Similarity Between two Genes
godata
godata
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
load_OrgDb
load_OrgDb
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
termSim
termSim
wangMethod_internal
wangMethod

Files in this package

GOSemSim/DESCRIPTION
GOSemSim/NAMESPACE
GOSemSim/NEWS
GOSemSim/R
GOSemSim/R/GOSemSim-package.R
GOSemSim/R/ICMethods.R
GOSemSim/R/RcppExports.R
GOSemSim/R/WangMethod.R
GOSemSim/R/clusterSim.R
GOSemSim/R/combineMethods.R
GOSemSim/R/computeIC.R
GOSemSim/R/gene2GO.R
GOSemSim/R/geneSim.R
GOSemSim/R/goSim.R
GOSemSim/R/godata.R
GOSemSim/R/mclusterSim.R
GOSemSim/R/mgeneSim.R
GOSemSim/R/mgoSim.R
GOSemSim/R/termSim.R
GOSemSim/R/utilities.R
GOSemSim/R/zzz.R
GOSemSim/README.md
GOSemSim/build
GOSemSim/build/vignette.rds
GOSemSim/data
GOSemSim/data/gotbl.rda
GOSemSim/inst
GOSemSim/inst/CITATION
GOSemSim/inst/doc
GOSemSim/inst/doc/GOSemSim.R
GOSemSim/inst/doc/GOSemSim.Rmd
GOSemSim/inst/doc/GOSemSim.html
GOSemSim/man
GOSemSim/man/GOSemSim-package.Rd
GOSemSim/man/GOSemSimDATA-class.Rd
GOSemSim/man/clusterSim.Rd
GOSemSim/man/combineScores.Rd
GOSemSim/man/geneSim.Rd
GOSemSim/man/goSim.Rd
GOSemSim/man/go_term_table.Rd
GOSemSim/man/godata.Rd
GOSemSim/man/infoContentMethod.Rd
GOSemSim/man/load_OrgDb.Rd
GOSemSim/man/mclusterSim.Rd
GOSemSim/man/mgeneSim.Rd
GOSemSim/man/mgoSim.Rd
GOSemSim/man/termSim.Rd
GOSemSim/man/wangMethod_internal.Rd
GOSemSim/src
GOSemSim/src/ICmethod.cpp
GOSemSim/src/RcppExports.cpp
GOSemSim/tests
GOSemSim/tests/testthat
GOSemSim/tests/testthat.R
GOSemSim/tests/testthat/test-GO.R
GOSemSim/tests/testthat/test-Wang.R
GOSemSim/tests/testthat/test-load_OrgDb.R
GOSemSim/vignettes
GOSemSim/vignettes/GOSemSim.Rmd
GOSemSim/vignettes/GOSemSim.bib
GOSemSim/vignettes/nature.csl