GOSemSim

This is the development version of GOSemSim; for the stable release version, see GOSemSim.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

GO-terms Semantic Similarity Measures

Bioconductor version: Development (3.24)

Semantic similarity analysis of Gene Ontology (GO) annotations provides a quantitative framework for comparing GO terms, gene products, and gene clusters. GOSemSim implements widely used information content- and graph-based similarity measures, including the methods of Resnik, Schlicker, Jiang, Lin, Wang and TCSS. It also provides utilities for preparing annotation data and combining term-level similarities into gene- and cluster-level scores.

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>

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

Guangchuang Yu. GOSemSim: GO-terms Semantic Similarity Measures. doi:10.18129/B9.bioc.GOSemSim, R package version 2.39.3, https://bioconductor.org/packages/GOSemSim.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

GOSemSim.html	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	2.39.3
In Bioconductor since	BioC 2.4 (R-2.9) (17.5 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	AnnotationDbi, DBI, digest, GO.db, methods, Rcpp, rlang, stats, utils, yulab.utils (>= 0.2.3)
System Requirements
URL	https://yulab-smu.top/biomedical-knowledge-mining-book/
Bug Reports	https://github.com/YuLab-SMU/GOSemSim/issues

Suggests	AnnotationHub, BiocParallel, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, quarto, readr, testthat, tidyr, tidyselect, ROCR
Linking To	Rcpp
Enhances
Depends On Me	tRanslatome
Imports Me	clusterProfiler, DOSE, enrichplot, meshes, Rcpi, rrvgo, ViSEAGO
Suggests Me	BioCor, epiNEM, FELLA, genekitr, protr, scDiffCom, SemDist
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	GOSemSim_2.39.3.tar.gz
Windows Binary (x86_64)	GOSemSim_2.39.3.zip
macOS Binary (big-sur-x86_64)	GOSemSim_2.39.3.tgz
macOS Binary (sonoma-arm64)	GOSemSim_2.39.3.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