meshes: MeSH Enrichment and Semantic analyses

Provides tools for MeSH (Medical Subject Headings) enrichment and semantic similarity analysis. The package uses MeSH term annotations linked to Entrez Gene identifiers through gendoo, gene2pubmed and RBBH, enabling over-representation analysis, gene set enrichment analysis and semantic comparison of gene lists or ranked expression profiles. It implements Resnik, Schlicker, Jiang, Lin and Wang similarity methods for comparing MeSH terms, genes and gene groups across more than 70 species.

For details, please visit https://yulab-smu.top/biomedical-knowledge-mining-book/.

⏬ Installation

Get the released version from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("meshes")

Or install the development version from GitHub:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("YuLab-SMU/meshes")

Citation: G Yu. Using meshes for MeSH term enrichment and semantic analyses. Bioinformatics 2018, 34(21):3766-3767. https://dx.doi.org/10.1093/bioinformatics/bty410.

✍️ Authors

Guangchuang YU https://yulab-smu.top

School of Basic Medical Sciences, Southern Medical University

💖 Contributing

We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.