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cosmiq

This is the development version of cosmiq; for the stable release version, see cosmiq.

cosmiq - COmbining Single Masses Into Quantities


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
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Suggests RUnit, BiocGenerics, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cosmiq_1.37.0.tar.gz
Windows Binary cosmiq_1.37.0.zip
macOS Binary (x86_64) cosmiq_1.37.0.tgz
macOS Binary (arm64)
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