---
title: "GO Semantic Similarity Analysis"
format: 
    html:
        theme: none
        embed-resources: true
        fontsize: 1.1em
        linestretch: 1.7
author: "Guangchuang Yu\

        School of Basic Medical Sciences, Southern Medical University"
date: "`r Sys.Date()`"
vignette: >
  %\VignetteIndexEntry{GOSemSim}
  %\VignetteEngine{quarto::html}
  %\VignetteEncoding{UTF-8}
---

```{r style, echo=FALSE, results="asis", message=FALSE}
knitr::opts_chunk$set(tidy = FALSE,
                      warning = FALSE,
                      message = FALSE)
```

```{r echo=FALSE, results="hide", message=FALSE}
Biocpkg <- yulab.utils::Biocpkg
```

# Vignette

`r Biocpkg('GOSemSim')` provides methods and utilities for semantic similarity analysis of Gene Ontology annotations, including:

+ semantic similarity measurement among GO terms, gene products, and gene clusters;
+ support for multiple similarity methods, including Wang, Resnik, Lin, Rel, Jiang, and TCSS;
+ preparation of GO annotation data from OrgDb objects or user-supplied annotation data frames;
+ score combination strategies for comparing sets of GO terms or genes.

Please go to <https://yulab-smu.top/biomedical-knowledge-mining-book/> for the full vignette.


# Citation


If you use `r Biocpkg('GOSemSim')` in published research, please cite the most appropriate paper(s) from this list:

1. **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. 
2. **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](http://dx.doi.org/10.1093/bioinformatics/btq064). **_Bioinformatics_**. 2010, 26(7):976-978. 



# Need helps?


For questions, please post to [Bioconductor support site](https://support.bioconductor.org/) and tag your post with *GOSemSim*.