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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 (3.20)

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 "4.4") and enter:


if (!require("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")
Provide PathbankDb databases for AnnotationHub HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AnnotationData, AnnotationHub, CustomDBSchema, FunctionalAnnotation
Version 0.99.5
License Artistic-2.0
Depends R (>= 4.1.0)
Imports AnnotationHub(>= 2.23.0)
System Requirements
URL https://github.com/kozo2/AHPathbankDbs
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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
macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url https://bioconductor.org/packages/AHPathbankDbs/
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