Package: meshr 2.13.0

Koki Tsuyuzaki

meshr: Tools for conducting enrichment analysis of MeSH

A set of annotation maps describing the entire MeSH assembled using data from MeSH.

Authors:Koki Tsuyuzaki, Itoshi Nikaido, Gota Morota

meshr_2.13.0.tar.gz
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meshr.pdf |meshr.html✨
meshr/json (API)
NEWS

# Install 'meshr' in R:

install.packages('meshr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rikenbit/meshr/issues

On BioConductor:meshr-2.11.0(bioc 3.20)meshr-2.10.0(bioc 3.19)

annotationdata functionalannotation bioinformatics statistics annotation multiplecomparisons meshdb

4.56 score 1 packages 9 scripts 279 downloads 6 mentions 22 exports 75 dependencies

Last updated 23 days agofrom:5a2870d44b. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:annotation annotation<-category category<-database database<-geneIds initialize makeValidParams meshAnnotation meshCategory meshDatabase meshHyperGTest meshIds pAdjust pAdjust<-pvalueCutoff pvalueCutoff<-show summary universeGeneIds universeGeneIds<-

Dependencies:annotate AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocManager BiocStyle Biostrings bit bit64 blob bookdown bslib cachem Category cli commonmark cpp11 crayon curl DBI digest evaluate fastmap fdrtool fontawesome fs genefilter GenomeInfoDb GenomeInfoDbData glue graph GSEABase highr htmltools httr IRanges jquerylib jsonlite KEGGREST knitr lattice lifecycle markdown Matrix MatrixGenerics matrixStats memoise MeSHDbi mime openssl pkgconfig plogr png R6 rappdirs RBGL rlang rmarkdown RSQLite S4Vectors sass survival sys tinytex UCSC.utils vctrs xfun XML xtable XVector yaml zlibbioc

AnnotationHub-style MeSH ORA Framework from BioC 3.14

Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Itoshi Nikaido

Rendered fromMeSH.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-10-18
Started: 2021-08-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Enrichment analysis for MeSH terms.	meshr-package meshr
A function to return the name of MeSH category	category category,MeSHHyperGParams-method category<- category<-,MeSHHyperGParams,character-method generic,category
A function to return the name of MeSH database	database database,MeSHHyperGParams-method database<- database<-,MeSHHyperGParams,character-method generic,database
Class "MeSHHyperGParams"	annotation,MeSHHyperGParams-method annotation<-,MeSHHyperGParams,character-method geneIds,MeSHHyperGParams-method geneIds<-,MeSHHyperGParams,ANY-method geneIds<-,MeSHHyperGParams,logical-method initialize,MeSHHyperGParams-method makeValidParams,MeSHHyperGParams-method MeSHHyperGParams-class pAdjust pAdjust,MeSHHyperGParams-method pAdjust<- pAdjust<-,MeSHHyperGParams,character-method pvalueCutoff,MeSHHyperGParams-method pvalueCutoff<-,MeSHHyperGParams-method universeGeneIds universeGeneIds,MeSHHyperGParams-method universeGeneIds<- universeGeneIds<-,MeSHHyperGParams,ANY-method universeGeneIds<-,MeSHHyperGParams,logical-method universeGeneIds<-,MeSHHyperGParams-method
Class "MeSHHyperGResult"	meshAnnotation meshAnnotation,MeSHHyperGResult-method meshCategory meshCategory,MeSHHyperGResult-method meshDatabase meshDatabase,MeSHHyperGResult-method MeSHHyperGResult-class meshIds meshIds,MeSHHyperGResult-method meshTerms meshTerms,MeSHHyperGResult-method pvalues pvalues,MeSHHyperGResult-method show show,MeSHHyperGResult-method summary summary,MeSHHyperGResult-method
Hypergeometric Tests for MeSH term association	meshHyperGTest meshHyperGTest,MeSHHyperGParams-method