recipe bioconductor-cosmiq

cosmiq - COmbining Single Masses Into Quantities







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

(downloads) docker_bioconductor-cosmiq



depends bioconductor-faahko:


depends bioconductor-faahko:


depends bioconductor-massspecwavelet:


depends bioconductor-massspecwavelet:


depends bioconductor-xcms:


depends bioconductor-xcms:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-pracma:

depends r-rcpp:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-cosmiq

and update with::

   mamba update bioconductor-cosmiq

To create a new environment, run:

mamba create --name myenvname bioconductor-cosmiq

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

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

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