AHWikipathwaysDbs

This is the released version of AHWikipathwaysDbs; for the devel version, see AHWikipathwaysDbs.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

Metabolites linked to WikiPathways pathways (for AnnotationHub)

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-8501-7319

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

Citation (from within R, enter citation("AHWikipathwaysDbs")):

Kozo Nishida. AHWikipathwaysDbs: Metabolites linked to WikiPathways pathways (for AnnotationHub). doi:10.18129/B9.bioc.AHWikipathwaysDbs, R package version 0.99.4, https://bioconductor.org/packages/AHWikipathwaysDbs.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AnnotationData, AnnotationHub, CustomDBSchema, FunctionalAnnotation
Version	0.99.4
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0)
Imports	AnnotationHub (>= 2.23.0)
System Requirements
URL	https://github.com/kozo2/AHWikipathwaysDbs

Suggests	BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown
Linking To
Enhances
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 (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Package Short Url	https://bioconductor.org/packages/AHWikipathwaysDbs/
Package Downloads Report	Download Stats