recipe bioconductor-cosmiq

cosmiq - COmbining Single Masses Into Quantities

Homepage

https://bioconductor.org/packages/3.11/bioc/html/cosmiq.html

License

GPL-3

Recipe

/bioconductor-cosmiq/meta.yaml

Links

biotools: cosmiq, doi: 10.5167/uzh-107947

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.

package bioconductor-cosmiq

Versions

1.22.0-0,  1.20.0-1,  1.18.0-1,  1.16.1-0,  1.16.0-0,  1.12.0-0

Depends

• bioconductor-faahko >=1.28.0,<1.29.0

• bioconductor-massspecwavelet >=1.54.0,<1.55.0

• bioconductor-xcms >=3.10.0,<3.11.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• libstdcxx-ng >=7.3.0

• r-base >=4.0,<4.1.0a0

• r-pracma

• r-rcpp

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-cosmiq

and update with:

conda update bioconductor-cosmiq

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-cosmiq:<tag>

(see bioconductor-cosmiq/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

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