recipe bioconductor-cliquems

Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

Homepage

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

License

GPL (>= 2)

Recipe

/bioconductor-cliquems/meta.yaml

Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Bioinformatics, 35(20), 2019), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.

package bioconductor-cliquems

Versions

1.2.0-0

Depends

• bioconductor-msnbase >=2.14.0,<2.15.0

• 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-bh

• r-igraph

• r-matrixstats

• r-qlcmatrix

• r-rcpp >=0.12.15

• r-rcpparmadillo

Required By

Installation

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

conda install bioconductor-cliquems

and update with:

conda update bioconductor-cliquems

or use the docker container:

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

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

Link to this page

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