AHPathbankDbs

DOI: 10.18129/B9.bioc.AHPathbankDbs    

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

Metabolites and proteins linked to PathBank pathways (for AnnotationHub)

Bioconductor version: Development (3.14)

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>

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
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")

 

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 10.13 (High Sierra)
Package Short Url https://bioconductor.org/packages/AHPathbankDbs/
Package Downloads Report Download Stats

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