AHPathbankDbs

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

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 and proteins linked to PathBank pathways (for AnnotationHub)

Bioconductor version: Development (3.24)

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] ORCID: 0000-0001-8501-7319

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

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

Kozo Nishida. AHPathbankDbs: Metabolites and proteins linked to PathBank pathways (for AnnotationHub). doi:10.18129/B9.bioc.AHPathbankDbs, R package version 0.99.5, https://bioconductor.org/packages/AHPathbankDbs.

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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

Provide PathbankDb 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	0.99.5
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/AHPathbankDbs

Suggests	BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown
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Package Archives

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

Source Package	AHPathbankDbs_0.99.5.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Package Short Url	https://bioconductor.org/packages/AHPathbankDbs/
Package Downloads Report	Download Stats