cosmiq
This is the released version of cosmiq; for the devel version, see cosmiq.
cosmiq - COmbining Single Masses Into Quantities
Bioconductor version: Release (3.23)
cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.
Author: David Fischer [aut, cre], Christian Panse [aut]
, Endre Laczko [ctb]
Maintainer: David Fischer <dajofischer at googlemail.com>
citation("cosmiq")):
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("cosmiq")
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("cosmiq")| cosmiq primer | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
| Version | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | GPL-3 |
| Depends | R (>= 3.6), Rcpp |
| Imports | pracma, xcms, MassSpecWavelet, faahKO |
| System Requirements | |
| URL | http://www.bioconductor.org/packages/devel/bioc/html/cosmiq.html |
See More
| Suggests | RUnit, BiocGenerics, BiocStyle |
| 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 | cosmiq_1.46.0.tar.gz |
| Windows Binary (x86_64) | cosmiq_1.46.0.zip |
| macOS Binary (big-sur-x86_64) | cosmiq_1.46.0.tgz |
| macOS Binary (sonoma-arm64) | cosmiq_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cosmiq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cosmiq |
| Bioc Package Browser | https://code.bioconductor.org/browse/cosmiq/ |
| Package Short Url | https://bioconductor.org/packages/cosmiq/ |
| Package Downloads Report | Download Stats |