ASICS
This is the development version of ASICS; for the stable release version, see ASICS.
Automatic Statistical Identification in Complex Spectra
Bioconductor version: Development (3.24)
With a set of pure metabolite reference spectra, ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty. The method and its statistical properties are described in Tardivel et al. (2017)
Author: Gaëlle Lefort [aut, cre], Rémi Servien [aut], Patrick Tardivel [aut], Nathalie Vialaneix [aut]
Maintainer: Gaëlle Lefort <gaelle.lefort at inrae.fr>
citation("ASICS")):
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("ASICS")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Cheminformatics, DataImport, Metabolomics, Software |
| Version | 2.29.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5) |
| Imports | BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat, ASICSdata |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | AlpsNMR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | ASICS_2.29.0.zip |
| macOS Binary (big-sur-x86_64) | ASICS_2.29.0.tgz |
| macOS Binary (sonoma-arm64) | ASICS_2.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ASICS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ASICS |
| Package Short Url | https://bioconductor.org/packages/ASICS/ |
| Package Downloads Report | Download Stats |