AHPathbankDbs

DOI: 10.18129/B9.bioc.AHPathbankDbs  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see AHPathbankDbs.

Metabolites and proteins linked to PathBank pathways (for AnnotationHub)

Bioconductor version: 3.16

The package provides a comprehensive mapping table of metabolites and proteins linked to PathBank pathways. The tables include HMDB, KEGG, ChEBI, CAS, Drugbank, Uniprot IDs. The tables are provided for each of the 10 species ("Homo sapiens", "Escherichia coli", "Mus musculus", "Arabidopsis thaliana", "Saccharomyces cerevisiae", "Bos taurus", "Caenorhabditis elegans", "Rattus norvegicus", "Drosophila melanogaster", and "Pseudomonas aeruginosa"). These table information can be used for Metabolite Set (and other) 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("AHPathbankDbs")

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("AHPathbankDbs")

 

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

Details

biocViews	AnnotationData, AnnotationHub, CustomDBSchema, FunctionalAnnotation
Version	0.99.5
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/AHPathbankDbs
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	AHPathbankDbs_0.99.5.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url	https://bioconductor.org/packages/AHPathbankDbs/
Package Downloads Report	Download Stats