AHWikipathwaysDbs

DOI: 10.18129/B9.bioc.AHWikipathwaysDbs    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see AHWikipathwaysDbs.

Metabolites linked to WikiPathways pathways (for AnnotationHub)

Bioconductor version: 3.15

The package provides a comprehensive mapping table of metabolites linked to Wikipathways pathways. The tables include HMDB, KEGG, ChEBI, Drugbank, PubChem compound, ChemSpider, KNApSAcK, and Wikidata IDs plus CAS and InChIKey. The tables are provided for each of the 25 species ("Anopheles gambiae", "Arabidopsis thaliana", "Bacillus subtilis", "Bos taurus", "Caenorhabditis elegans", "Canis familiaris", "Danio rerio", "Drosophila melanogaster", "Equus caballus", "Escherichia coli", "Gallus gallus", "Gibberella zeae", "Homo sapiens", "Hordeum vulgare", "Mus musculus", "Mycobacterium tuberculosis", "Oryza sativa", "Pan troglodytes", "Plasmodium falciparum", "Populus trichocarpa", "Rattus norvegicus", "Saccharomyces cerevisiae", "Solanum lycopersicum", "Sus scrofa", "Zea mays"). These table information can be used for Metabolite Set Enrichment Analysis.

Author: Kozo Nishida [aut, cre]

Maintainer: Kozo Nishida <kozo.nishida at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AHWikipathwaysDbs")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("AHWikipathwaysDbs")

 

HTML	R Script	Provide WikipathwaysDb databases for AnnotationHub
PDF		Reference Manual
Text		NEWS

Details

biocViews	AnnotationData, AnnotationHub, CustomDBSchema, FunctionalAnnotation
Version	0.99.4
License	Artistic-2.0
Depends	R (>= 4.1.0)
Imports	AnnotationHub(>= 2.23.0)
LinkingTo
Suggests	BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/kozo2/AHWikipathwaysDbs
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	AHWikipathwaysDbs_0.99.4.tar.gz
Windows Binary
macOS Binary (x86_64)
Package Short Url	https://bioconductor.org/packages/AHWikipathwaysDbs/
Package Downloads Report	Download Stats