GOSemSim

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see GOSemSim.

GO-terms Semantic Similarity Measures

Bioconductor version: 3.10

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], Lluís 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 "3.6") 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")

An introduction to GOSemSim	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Clustering, GO, Network, Pathways, Software
Version	2.12.1
In Bioconductor since	BioC 2.4 (R-2.9) (15 years)
License	Artistic-2.0
Depends	R (>= 3.4.0)
Imports	AnnotationDbi, GO.db, methods, utils
System Requirements
URL	https://guangchuangyu.github.io/software/GOSemSim
Bug Reports	https://github.com/YuLab-SMU/GOSemSim/issues

Suggests	AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, testthat
Linking To	Rcpp
Enhances
Depends On Me	tRanslatome
Imports Me	clusterProfiler, DOSE, enrichplot, GAPGOM, meshes, Rcpi, ViSEAGO
Suggests Me	BioCor, epiNEM, FELLA, SemDist
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	GOSemSim_2.12.1.tar.gz
Windows Binary	GOSemSim_2.12.1.zip
Mac OS X 10.11 (El Capitan)	GOSemSim_2.12.1.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
Old Source Packages for BioC 3.10	Source Archive