GOSemSim

DOI: 10.18129/B9.bioc.GOSemSim  

GO-terms Semantic Similarity Measures

Bioconductor version: Release (3.16)

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 [aut, cre], Alexey Stukalov [ctb], Pingfan Guo [ctb], Chuanle Xiao [ctb], Lluís Revilla Sancho [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GOSemSim")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GOSemSim")

 

HTML	R Script	GOSemSim
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Clustering, GO, Network, Pathways, Software
Version	2.24.0
In Bioconductor since	BioC 2.4 (R-2.9) (14 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	AnnotationDbi, GO.db, methods, utils
LinkingTo	Rcpp
Suggests	AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat, ROCR
SystemRequirements
Enhances
URL	https://yulab-smu.top/biomedical-knowledge-mining-book/
BugReports	https://github.com/YuLab-SMU/GOSemSim/issues
Depends On Me	tRanslatome
Imports Me	clusterProfiler, DOSE, enrichplot, GAPGOM, meshes, Rcpi, rrvgo, simplifyEnrichment, ViSEAGO
Suggests Me	BioCor, epiNEM, FELLA, SemDist
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GOSemSim_2.24.0.tar.gz
Windows Binary	GOSemSim_2.24.0.zip
macOS Binary (x86_64)	GOSemSim_2.24.0.tgz
macOS Binary (arm64)	GOSemSim_2.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GOSemSim
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GOSemSim
Bioc Package Browser	https://code.bioconductor.org/browse/GOSemSim/
Package Short Url	https://bioconductor.org/packages/GOSemSim/
Package Downloads Report	Download Stats