Package: meshes 1.31.0
Guangchuang Yu
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.
Authors:
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meshes.pdf |meshes.html✨
meshes/json (API)
NEWS
| # Install 'meshes' in R: |
| install.packages('meshes', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/guangchuangyu/meshes/issues
On BioConductor:meshes-1.31.0(bioc 3.20)meshes-1.30.0(bioc 3.19)
Last updated 2 months agofrom:77d300a2e6
Exports:cnetplotdotplotemapplotenrichMeSHgeneIDgeneInCategorygeneSimgseaplotgseMeSHheatplotmeshdatameshSimridgeplot
Dependencies:AnnotationDbiAnnotationHubapeaplotaskpassBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobcachemclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrdigestDOSEdplyrenrichplotfansifarverfastmapfastmatchfgseafilelockformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeglueGO.dbGOSemSimgraphlayoutsgridExtragridGraphicsgtableHDO.dbhttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixmemoiseMeSHDbimgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplyrpngpolyclippurrrqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangRSQLiteS4VectorsscalesscatterpieshadowtextsnowstringistringrsyssystemfontstibbletidygraphtidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8vctrsviridisviridisLitewithrXVectoryamlyulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| enrichMeSH | enrichMeSH |
| geneSim | geneSim |
| gseMeSH | gseMeSH |
| DATA Sets | hsamd meshtbl mesh_term_table |
| meshdata | meshdata |
| meshSim | meshSim |
