cosmiq

DOI: 10.18129/B9.bioc.cosmiq    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see cosmiq.

cosmiq - COmbining Single Masses Into Quantities

Bioconductor version: 3.8

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 <dajofischer at googlemail.com>, Christian Panse <cp at fgcz.ethz.ch>, Endre Laczko <endre.laczko at fgcz.uzh.ch>

Maintainer: David Fischer <dajofischer at googlemail.com>, Christian Panse <cp at fgcz.ethz.ch>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	cosmiq primer
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	1.16.1
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 years)
License	GPL-3
Depends	R (>= 3.0.2), 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

Package Archives

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

Source Package	cosmiq_1.16.1.tar.gz
Windows Binary	cosmiq_1.16.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	cosmiq_1.16.1.tgz
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	http://bioconductor.org/packages/cosmiq/
Package Downloads Report	Download Stats