GOSemSim: GO semantic similarity measurement

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.

:writing_hand: Authors

Guangchuang YU https://yulab-smu.top

School of Basic Medical Sciences, Southern Medical University

Learn more at https://yulab-smu.top/contribution-knowledge-mining/.

If you use GOSemSim in published research, please cite:

• Yu G. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, 2020, 2117:207-215. Humana, New York, NY.
• Yu G^#, Li F^#, Qin Y, Bo X^*, Wu Y and Wang S^*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010, 26(7):976-978.

:arrow_double_down: Installation

Get the released version from Bioconductor:

## 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:

## 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.