cosmiq
This is the development version of cosmiq; for the stable release version, see cosmiq.
cosmiq - COmbining Single Masses Into Quantities
Bioconductor version: Development (3.24)
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("cosmiq")):David Fischer, Christian Panse. cosmiq: cosmiq - COmbining Single Masses Into Quantities. doi:10.18129/B9.bioc.cosmiq, R package version 1.47.0, https://bioconductor.org/packages/cosmiq.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.47.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 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 |
See More
| Suggests | RUnit, BiocGenerics, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cosmiq_1.47.0.tar.gz |
| Windows Binary (x86_64) | cosmiq_1.47.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | cosmiq_1.47.0.tgz |
| macOS Binary (sonoma-arm64) | cosmiq_1.47.0.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 |