meshes: MeSH Enrichment and Semantic analyses
Version 1.2.0

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.

AuthorGuangchuang Yu [aut, cre]
Bioconductor views Annotation Clustering MultipleComparison Software
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version1.2.0
URL https://guangchuangyu.github.io/meshes
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("meshes")

Getting started

README.md
MeSH Enrichment and Semantic Analyses

Popular man pages

enrichMeSH: enrichMeSH
geneSim: geneSim
gseMeSH: gseMeSH
meshdata: meshdata
meshSim: meshSim
mesh_term_table: DATA Sets
See all...

All man pages Function index File listing

Man pages

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

Functions

computeIC Source code
enrichMeSH Man page Source code
gene2MeSH Source code
geneSim Man page Source code
getAncestors Source code
getOffsprings Source code
get_MeSH_data Source code
gseMeSH Man page Source code
hsamd Man page
meshSim Man page Source code
mesh_term_table Man page
meshdata Man page Source code
meshtbl Man page
nitial Source code
onLoad Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/DOSE.R
R/enrichMeSH.R
R/geneSim.R
R/gseMeSH.R
R/meshSim.R
R/meshes.R
R/utilities.R
R/zzz.R
README.Rmd
README.md
build
build/vignette.rds
data
data/hsamd.rda
data/meshtbl.rda
inst
inst/doc
inst/doc/meshes.R
inst/doc/meshes.Rmd
inst/doc/meshes.html
inst/extdata
inst/extdata/build_meshtbl.R
man
man/enrichMeSH.Rd
man/geneSim.Rd
man/gseMeSH.Rd
man/meshSim.Rd
man/mesh_term_table.Rd
man/meshdata.Rd
vignettes
vignettes/meshes.Rmd
vignettes/meshes.bib
vignettes/nature.csl
meshes documentation built on May 20, 2017, 9:51 p.m.

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