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GOSemSim

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

GO-terms Semantic Similarity Measures


Bioconductor version: Development (3.19)

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], 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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
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 R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Clustering, GO, Network, Pathways, Software
Version 2.29.1
In Bioconductor since BioC 2.4 (R-2.9) (15 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports AnnotationDbi, GO.db, methods, rlang, stats, utils, yulab.utils
System Requirements
URL https://yulab-smu.top/biomedical-knowledge-mining-book/
Bug Reports https://github.com/YuLab-SMU/GOSemSim/issues
See More
Suggests AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR
Linking To Rcpp
Enhances
Depends On Me tRanslatome
Imports Me clusterProfiler, DOSE, enrichplot, meshes, Rcpi, rrvgo, simplifyEnrichment, 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_2.29.1.tar.gz
Windows Binary GOSemSim_2.29.1.zip
macOS Binary (x86_64) GOSemSim_2.29.1.tgz
macOS Binary (arm64) GOSemSim_2.29.1.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