yamss
This is the development version of yamss; for the stable release version, see yamss.
Tools for high-throughput metabolomics
Bioconductor version: Development (3.24)
Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis. At the core of these methods is a peak detection phase that pools information across all samples simultaneously. This is in contrast to other methods that detect peaks in a sample-by-sample basis.
Author: Leslie Myint [cre, aut]
, Kasper Daniel Hansen [aut]
Maintainer: Leslie Myint <leslie.myint at gmail.com>
citation("yamss")):
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("yamss")
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("yamss")| yamss User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Metabolomics, PeakDetection, Software |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0), methods, BiocGenerics(>= 0.15.3), SummarizedExperiment |
| Imports | IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma |
| System Requirements | |
| URL | https://github.com/hansenlab/yamss |
| Bug Reports | https://github.com/hansenlab/yamss/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat |
| 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 | yamss_1.39.0.tar.gz |
| Windows Binary (x86_64) | yamss_1.39.0.zip |
| macOS Binary (big-sur-x86_64) | yamss_1.39.0.tgz |
| macOS Binary (sonoma-arm64) | yamss_1.39.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/yamss |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/yamss |
| Bioc Package Browser | https://code.bioconductor.org/browse/yamss/ |
| Package Short Url | https://bioconductor.org/packages/yamss/ |
| Package Downloads Report | Download Stats |