meshes
MeSH Enrichment and Semantic analyses
Bioconductor version: 3.23 · Package version: 1.38.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("meshes")Details
| Maintainer | Guangchuang Yu <guangchuangyu@gmail.com> |
| Author | Guangchuang Yu [aut, cre] |
| License | Artistic-2.0 |
| URL | https://yulab-smu.top/biomedical-knowledge-mining-book/ |
| Bug Reports | https://github.com/GuangchuangYu/meshes/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Clustering, MultipleComparison, Software |
| Package Short Url | https://bioconductor.org/packages/meshes/ |
Citation
From within R, enter citation("meshes"):
Guangchuang Yu. meshes: MeSH Enrichment and Semantic analyses. doi:10.18129/B9.bioc.meshes, R package version 1.38.0, https://bioconductor.org/packages/meshes.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | meshes_1.38.0.tar.gz |
| Windows binary (x86_64) | meshes_1.38.0.zip |
| macOS binary (arm64) | meshes_1.38.0.tgz |
| macOS binary (x86_64) | meshes_1.38.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: enrichit, gson, AnnotationDbi, GOSemSim (> 2.37.0), methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5)