hmdbQuery
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see hmdbQuery.
utilities for exploration of human metabolome database
Bioconductor version: Release (3.23)
Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease).
Author: Vince Carey <stvjc at channing.harvard.edu>
Maintainer: VJ Carey <stvjc at channing.harvard.edu>
citation("hmdbQuery")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("hmdbQuery")
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("hmdbQuery")| hmdbQuery: working with Human Metabolome Database (hmdb.ca) | HTML | R Script |
| Reference Manual |
Details
| biocViews | Infrastructure, Metabolomics, Software |
| Version | 1.31.1 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5), XML |
| Imports | S4Vectors, methods, utils |
| System Requirements | |
| URL |
See More
| Suggests | knitr, annotate, gwascat, testthat, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | hmdbQuery_1.31.1.tar.gz |
| Windows Binary (x86_64) | hmdbQuery_1.31.1.zip |
| macOS Binary (big-sur-x86_64) | hmdbQuery_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/hmdbQuery |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/hmdbQuery |
| Package Short Url | https://bioconductor.org/packages/hmdbQuery/ |
| Package Downloads Report | Download Stats |