cosmiq
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see cosmiq.
cosmiq - COmbining Single Masses Into Quantities
Bioconductor version: 3.9
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 "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
| Version | 1.18.0 |
| 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_1.18.0.tar.gz |
| Windows Binary | cosmiq_1.18.0.zip |
| Mac OS X 10.11 (El Capitan) | cosmiq_1.18.0.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 3.9 | Source Archive |