Name Mode Size
..
GOSemSim-package.R 100644 3 kb
ICMethods.R 100644 4 kb
RcppExports.R 100644 0 kb
TCSSMethod.R 100644 5 kb
TCSScutoff.R 100644 8 kb
WangMethod.R 100644 3 kb
buildGOmap.R 100644 2 kb
clusterSim.R 100644 2 kb
combineMethods.R 100644 2 kb
computeIC.R 100644 1 kb
gene2GO.R 100644 0 kb
geneSim.R 100644 2 kb
goSim.R 100644 1 kb
godata.R 100644 3 kb
mclusterSim.R 100644 3 kb
mgeneSim.R 100644 2 kb
mgoSim.R 100644 2 kb
parseGAF.R 100644 2 kb
processTCSS.R 100644 7 kb
readBlast2go.R 100644 1 kb
termSim.R 100644 1 kb
utilities.R 100644 3 kb
zzz.R 100644 1 kb
README.md
# GOSemSim: GO semantic similarity measurement [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/GOSemSim.svg)](https://www.bioconductor.org/packages/devel/bioc/html/GOSemSim.html#since) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![platform](http://www.bioconductor.org/shields/availability/devel/GOSemSim.svg)](https://www.bioconductor.org/packages/devel/bioc/html/GOSemSim.html#archives) [![codecov](https://codecov.io/gh/GuangchuangYu/GOSemSim/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/GOSemSim/) [![](https://img.shields.io/badge/release%20version-2.12.0-green.svg)](https://www.bioconductor.org/packages/GOSemSim) [![](https://img.shields.io/badge/devel%20version-2.13.1-green.svg)](https://github.com/guangchuangyu/GOSemSim) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/GOSemSim/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/GOSemSim) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/GOSemSim/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/GOSemSim) [![](https://img.shields.io/badge/download-176874/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/GOSemSim) [![](https://img.shields.io/badge/download-5604/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/GOSemSim) [![download](http://www.bioconductor.org/shields/downloads/release/GOSemSim.svg)](https://bioconductor.org/packages/stats/bioc/GOSemSim) 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. [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=GOSemSim&url=http://bioinformatics.oxfordjournals.org/content/26/7/976&screen_name=guangchuangyu) [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu) [![](https://img.shields.io/badge/follow%20me%20on-WeChat-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) ## :writing\_hand: Authors Guangchuang YU <https://guangchuangyu.github.io> School of Basic Medical Sciences, Southern Medical University If you use [GOSemSim](http://bioconductor.org/packages/GOSemSim) in published research, please cite: - **Yu G**. [Gene Ontology Semantic Similarity Analysis Using GOSemSim](http://dx.doi.org/10.1007/978-1-0716-0301-7_11). In: Kidder B. (eds) Stem Cell Transcriptional Networks. ***Methods in Molecular Biology***, 2020, 2117:207-215. Humana, New York, NY. - **Yu G**<sup>\#</sup>, Li F<sup>\#</sup>, Qin Y, Bo X<sup>\*</sup>, Wu Y and Wang S<sup>\*</sup>. [GOSemSim: an R package for measuring semantic similarity among GO terms and gene products](http://dx.doi.org/10.1093/bioinformatics/btq064). ***Bioinformatics***. 2010, 26(7):976-978. ## :arrow\_double\_down: Installation Get the released version from Bioconductor: ``` r ## try http:// if https:// URLs are not supported if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") ## BiocManager::install("BiocUpgrade") ## you may need this BiocManager::install("GOSemSim") ``` Or the development version from github: ``` r ## install.packages("remotes") remotes::install_github("GuangchuangYu/GOSemSim") ``` ## :sparkling\_heart: Contributing We welcome any contributions\! By participating in this project you agree to abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).