meshes

DOI: 10.18129/B9.bioc.meshes  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see meshes.

MeSH Enrichment and Semantic analyses

Bioconductor version: 3.16

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.

Author: Guangchuang Yu [aut, cre], Erqiang Hu [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("meshes")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("meshes")

 

HTML	R Script	meshes
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Clustering, MultipleComparison, Software
Version	1.24.0
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0)
Imports	AnnotationDbi, DOSE, enrichplot, GOSemSim, methods, utils, AnnotationHub, MeSHDbi, yulab.utils
LinkingTo
Suggests	knitr, rmarkdown, prettydoc
SystemRequirements
Enhances
URL	https://yulab-smu.top/biomedical-knowledge-mining-book/
BugReports	https://github.com/GuangchuangYu/meshes/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	meshes_1.24.0.tar.gz
Windows Binary	meshes_1.24.0.zip
macOS Binary (x86_64)	meshes_1.24.0.tgz
macOS Binary (arm64)	meshes_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/meshes
Source Repository (Developer Access)	git clone [email protected]:packages/meshes
Bioc Package Browser	https://code.bioconductor.org/browse/meshes/
Package Short Url	https://bioconductor.org/packages/meshes/
Package Downloads Report	Download Stats