cosmiq
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see cosmiq.
cosmiq - COmbining Single Masses Into Quantities
Bioconductor version: 3.7
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>
citation("cosmiq")
):
Installation
To install this package, start R (version "3.5") 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")
13th Annual Conference of the Metabolomics Society 2017 poster P-32 | R Script | |
cosmiq primer | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | MassSpectrometry, Metabolomics, Software |
Version | 1.13.0 |
In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
License | GPL-3 |
Depends | R (>= 3.0.2), Rcpp |
Imports | pracma, xcms, MassSpecWavelet, faahKO |
System Requirements | |
URL | http://www.bioconductor.org/packages/devel/bioc/html/cosmiq.html |
See More
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_1.13.0.tar.gz |
Windows Binary | cosmiq_1.14.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | cosmiq_1.13.0.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 | https://bioconductor.org/packages/cosmiq/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.7 | Source Archive |