GOSemSim

DOI: 10.18129/B9.bioc.GOSemSim    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GOSemSim.

GO-terms Semantic Similarity Measures

Bioconductor version: 3.13

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], Chuanle Xiao [ctb], LluĂ­s Revilla Sancho [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Citation (from within R, enter citation("GOSemSim")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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 2.18.1
In Bioconductor since BioC 2.4 (R-2.9) (12.5 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
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_2.18.1.tar.gz
Windows Binary GOSemSim_2.18.1.zip
macOS 10.13 (High Sierra) GOSemSim_2.18.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/GOSemSim
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GOSemSim
Package Short Url https://bioconductor.org/packages/GOSemSim/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: