meshes
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see meshes.
MeSH Enrichment and Semantic analyses
Bioconductor version: 3.12
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]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
citation("meshes")):
Installation
To install this package, start R (version "4.0") 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")| meshes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Clustering, MultipleComparison, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.6.0) |
| Imports | AnnotationDbi, DOSE, enrichplot, GOSemSim, MeSH.db, methods, rvcheck, utils |
| System Requirements | |
| URL | https://yulab-smu.top/biomedical-knowledge-mining-book/ |
| Bug Reports | https://github.com/GuangchuangYu/meshes/issues |
See More
| Suggests | knitr, MeSH.Cel.eg.db, MeSH.Hsa.eg.db, prettydoc |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | meshes_1.16.0.tar.gz |
| Windows Binary | meshes_1.16.0.zip |
| macOS 10.13 (High Sierra) | meshes_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/meshes |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/meshes |
| Bioc Package Browser | https://code.bioconductor.org/browse/meshes/ |
| Package Short Url | https://bioconductor.org/packages/meshes/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |