cosmiq

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

cosmiq - COmbining Single Masses Into Quantities

Bioconductor version: Development (3.21)

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] (ORCID: ), 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 "4.5") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	1.41.0
In Bioconductor since	BioC 3.0 (R-3.1) (10 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

Suggests	RUnit, BiocGenerics, BiocStyle
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/cosmiq/
Package Downloads Report	Download Stats