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,
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
respectively and supports more than 70 species.
Guangchuang Yu, School of Public Health, The University of Hong Kong.
meshes is easy, follow the guide on the Bioconductor
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") ## biocLite("BiocUpgrade") ## you may need this biocLite("meshes")
- Over-representation analysis
- Gene set enrichment analysis
- MeSH term semantic similarity
- Gene semantic similarity
Find out details and examples on Documentation.
- clusterProfiler for Ontologies/pathways enrichment analyses
- DOSE for Disease Ontology Semantic and Enrichment analyses
- GOSemSim for GO semantic similarity measurement
- ReactomePA for Reactome pathway analysis
Find out more on projects.
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- For bugs or feature requests, please post to [github issue](https://github.com/GuangchuangYu/meshes/issues)
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