This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see cosmiq.
Bioconductor version: 3.17
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 (from within R,
enter citation("cosmiq")
):
To install this package, start R (version "4.3") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cosmiq")
R Script | cosmiq primer | |
Reference Manual | ||
Text | NEWS |
biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
Version | 1.34.0 |
In Bioconductor since | BioC 3.0 (R-3.1) (9 years) |
License | GPL-3 |
Depends | R (>= 3.6), Rcpp |
Imports | pracma, xcms, MassSpecWavelet, faahKO |
LinkingTo | |
Suggests | RUnit, BiocGenerics, BiocStyle |
SystemRequirements | |
Enhances | |
URL | http://www.bioconductor.org/packages/devel/bioc/html/cosmiq.html |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | cosmiq_1.34.0.tar.gz |
Windows Binary | cosmiq_1.34.0.zip |
macOS Binary (x86_64) | cosmiq_1.34.0.tgz |
macOS Binary (arm64) | cosmiq_1.34.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/cosmiq |
Source Repository (Developer Access) | git clone [email protected]:packages/cosmiq |
Bioc Package Browser | https://code.bioconductor.org/browse/cosmiq/ |
Package Short Url | https://bioconductor.org/packages/cosmiq/ |
Package Downloads Report | Download Stats |
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