MetaboAnnotation
This is the development version of MetaboAnnotation; for the stable release version, see MetaboAnnotation.
Utilities for Annotation of Metabolomics Data
Bioconductor version: Development (3.24)
High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.
Author: Michael Witting [aut]
, Johannes Rainer [aut, cre]
, Andrea Vicini [aut]
, Carolin Huber [aut]
, Philippine Louail [aut]
, Nir Shachaf [ctb]
Maintainer: Johannes Rainer <Johannes.Rainer at eurac.edu>
citation("MetaboAnnotation")):
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("MetaboAnnotation")
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("MetaboAnnotation")| Annotation of MS-based Metabolomics Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, 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 (>= 4.0.0) |
| Imports | BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra(>= 1.21.5), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb |
| System Requirements | |
| URL | https://github.com/RforMassSpectrometry/MetaboAnnotation |
| Bug Reports | https://github.com/RforMassSpectrometry/MetaboAnnotation/issues |
See More
| Suggests | testthat, knitr, MsDataHub, BiocStyle, rmarkdown, plotly, shiny, shinyjs, msentropy, DT, microbenchmark, mzR |
| Linking To | |
| Enhances | RMariaDB, RSQLite |
| 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 | MetaboAnnotation_1.17.0.tar.gz |
| Windows Binary (x86_64) | MetaboAnnotation_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | MetaboAnnotation_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | MetaboAnnotation_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MetaboAnnotation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MetaboAnnotation |
| Bioc Package Browser | https://code.bioconductor.org/browse/MetaboAnnotation/ |
| Package Short Url | https://bioconductor.org/packages/MetaboAnnotation/ |
| Package Downloads Report | Download Stats |