cosmiq

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see cosmiq.

cosmiq - COmbining Single Masses Into Quantities

Bioconductor version: 3.15

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 "4.2") 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	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	1.30.0
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

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_1.30.0.tar.gz
Windows Binary	cosmiq_1.30.0.zip (64-bit only)
macOS Binary (x86_64)	cosmiq_1.30.0.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
Old Source Packages for BioC 3.15	Source Archive