CompoundDb
This is the development version of CompoundDb; for the stable release version, see CompoundDb.
Creating and Using (Chemical) Compound Annotation Databases
Bioconductor version: Development (3.24)
CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.
Author: Jan Stanstrup [aut]
, Johannes Rainer [aut, cre]
, Josep M. Badia [ctb]
, Roger Gine [aut]
, Andrea Vicini [aut]
, Prateek Arora [ctb]
Maintainer: Johannes Rainer <johannes.rainer at eurac.edu>
citation("CompoundDb")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("CompoundDb")
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("CompoundDb")| Creating CompoundDb annotation resources | HTML | R Script |
| Usage of Annotation Resources with the CompoundDb Package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, MassSpectrometry, Metabolomics, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1), methods, AnnotationFilter, S4Vectors |
| Imports | BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics(>= 1.35.3), xml2, IRanges, Spectra(>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel, stringi, data.table |
| System Requirements | |
| URL | https://github.com/RforMassSpectrometry/CompoundDb |
| Bug Reports | https://github.com/RforMassSpectrometry/CompoundDb/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle(>= 2.5.19), MsBackendMgf |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MetaboAnnotation, pubchem.bio |
| Suggests Me | AHMassBank, AnnotationHub, MetMashR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CompoundDb_1.17.0.tar.gz |
| Windows Binary (x86_64) | CompoundDb_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | CompoundDb_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | CompoundDb_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CompoundDb |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CompoundDb |
| Bioc Package Browser | https://code.bioconductor.org/browse/CompoundDb/ |
| Package Short Url | https://bioconductor.org/packages/CompoundDb/ |
| Package Downloads Report | Download Stats |