GOSemSim: GO-terms Semantic Similarity Measures
Version 2.2.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorGuangchuang Yu [aut, cre], Alexey Stukalov [ctb], Chuanle Xiao [ctb]
Bioconductor views Annotation Clustering GO Network Pathways Software
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version2.2.0
URL https://guangchuangyu.github.io/GOSemSim
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GOSemSim")

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

Functions

GO Man page
GOSemSim Man page
GOSemSim-package Man page
GOSemSimDATA-class Man page
clusterSim Man page Source code
combineScores Man page Source code
computeIC Source code
gene2GO Source code
geneSim Man page Source code
getAncestors Source code
getParents Source code
getSV Source code
goSim Man page Source code
go_term_table Man page
godata Man page Source code
gotbl Man page
infoContentMethod Man page Source code
infoContentMethod_cpp Source code
load_OrgDb Man page Source code
mclusterSim Man page Source code
mgeneSim Man page Source code
mgoSim Man page Source code
nitial Source code
onAttach Source code
prepare_relation_df Source code
show,GOSemSimDATA-method Man page
termSim Man page Source code
wangMethod Source code
wangMethod_internal Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GOSemSim-package.R
R/ICMethods.R
R/RcppExports.R
R/WangMethod.R
R/clusterSim.R
R/combineMethods.R
R/computeIC.R
R/gene2GO.R
R/geneSim.R
R/goSim.R
R/godata.R
R/mclusterSim.R
R/mgeneSim.R
R/mgoSim.R
R/termSim.R
R/utilities.R
R/zzz.R
README.md
build
build/vignette.rds
data
data/gotbl.rda
inst
inst/CITATION
inst/doc
inst/doc/GOSemSim.R
inst/doc/GOSemSim.Rmd
inst/doc/GOSemSim.html
man
man/GOSemSim-package.Rd
man/GOSemSimDATA-class.Rd
man/clusterSim.Rd
man/combineScores.Rd
man/geneSim.Rd
man/goSim.Rd
man/go_term_table.Rd
man/godata.Rd
man/infoContentMethod.Rd
man/load_OrgDb.Rd
man/mclusterSim.Rd
man/mgeneSim.Rd
man/mgoSim.Rd
man/termSim.Rd
man/wangMethod_internal.Rd
src
src/ICmethod.cpp
src/RcppExports.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/test-GO.R
tests/testthat/test-Wang.R
tests/testthat/test-load_OrgDb.R
vignettes
vignettes/GOSemSim.Rmd
vignettes/GOSemSim.bib
vignettes/nature.csl
GOSemSim documentation built on May 20, 2017, 9:18 p.m.