meshes

This is the development version of meshes; for the stable release version, see meshes.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

MeSH Enrichment and Semantic analyses

Bioconductor version: Development (3.24)

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.

Author: Guangchuang Yu [aut, cre]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Citation (from within R, enter citation("meshes")):

Guangchuang Yu. meshes: MeSH Enrichment and Semantic analyses. doi:10.18129/B9.bioc.meshes, R package version 1.39.3, https://bioconductor.org/packages/meshes.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

meshes.html	HTML
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Clustering, MultipleComparison, Software
Version	1.39.3
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
License	Artistic-2.0
Depends	R (>= 4.1.0)
Imports	enrichit (>= 0.2.2), gson, AnnotationDbi, GOSemSim (> 2.37.0), methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5)
System Requirements
URL	https://yulab-smu.top/biomedical-knowledge-mining-book/
Bug Reports	https://github.com/YuLab-SMU/meshes/issues

Suggests	knitr, quarto
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	meshes_1.39.3.tar.gz
Windows Binary (x86_64)	meshes_1.39.3.zip
macOS Binary (big-sur-x86_64)	meshes_1.39.3.tgz
macOS Binary (sonoma-arm64)	meshes_1.39.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/meshes
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/meshes
Package Short Url	https://bioconductor.org/packages/meshes/
Package Downloads Report	Download Stats