meshes: MeSH Enrichment and Semantic analyses

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]
Date of publication
None
Maintainer
Guangchuang Yu <guangchuangyu@gmail.com>
License
Artistic-2.0
Version
1.0.0
URLs

View on Bioconductor

Man pages

enrichMeSH
enrichMeSH
geneSim
geneSim
gseMeSH
gseMeSH
meshdata
meshdata
meshSim
meshSim
mesh_term_table
DATA Sets

Files in this package

meshes/.svnignore
meshes/DESCRIPTION
meshes/NAMESPACE
meshes/NEWS
meshes/R
meshes/R/DOSE.R
meshes/R/enrichMeSH.R
meshes/R/geneSim.R
meshes/R/gseMeSH.R
meshes/R/meshSim.R
meshes/R/meshes.R
meshes/R/utilities.R
meshes/R/zzz.R
meshes/README.md
meshes/build
meshes/build/vignette.rds
meshes/data
meshes/data/hsamd.rda
meshes/data/meshtbl.rda
meshes/inst
meshes/inst/doc
meshes/inst/doc/meshes.R
meshes/inst/doc/meshes.Rmd
meshes/inst/doc/meshes.html
meshes/inst/extdata
meshes/inst/extdata/build_meshtbl.R
meshes/man
meshes/man/enrichMeSH.Rd
meshes/man/geneSim.Rd
meshes/man/gseMeSH.Rd
meshes/man/meshSim.Rd
meshes/man/mesh_term_table.Rd
meshes/man/meshdata.Rd
meshes/vignettes
meshes/vignettes/meshes.Rmd
meshes/vignettes/meshes.bib
meshes/vignettes/nature.csl