To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("cosmiq")
In most cases, you don't need to download the package archive at all.
cosmiq
cosmiq - COmbining Single Masses Into Quantities
Bioconductor version: 3.0
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 (from within R,
enter citation("cosmiq")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("cosmiq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cosmiq")
| R Script | cosmiq primer | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | MassSpectrometry, Metabolomics, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | cosmiq_1.0.0.tar.gz |
| Windows Binary | cosmiq_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | cosmiq_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | cosmiq_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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