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AHWikipathwaysDbs

This is the development version of AHWikipathwaysDbs; for the stable release version, see AHWikipathwaysDbs.

Metabolites linked to WikiPathways pathways (for AnnotationHub)


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews AnnotationData, AnnotationHub, CustomDBSchema, FunctionalAnnotation
Version 0.99.4
License Artistic-2.0
Depends R (>= 4.1.0)
Imports AnnotationHub(>= 2.23.0)
System Requirements
URL https://github.com/kozo2/AHWikipathwaysDbs
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Suggests BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown
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Depends On Me
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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)
macOS Binary (arm64)
Package Short Url https://bioconductor.org/packages/AHWikipathwaysDbs/
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