recipe bioconductor-cliquems

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

Homepage:

https://bioconductor.org/packages/3.18/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:

1.16.0-0,  1.13.0-0,  1.12.0-1,  1.12.0-0,  1.8.0-2,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1, 

1.16.0-0,  1.13.0-0,  1.12.0-1,  1.12.0-0,  1.8.0-2,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0

depends bioconductor-msnbase:

>=2.28.0,<2.29.0

depends bioconductor-msnbase:

>=2.28.1,<2.29.0a0

depends bioconductor-xcms:

>=4.0.0,<4.1.0

depends bioconductor-xcms:

>=4.0.0,<4.1.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-bh:

depends r-igraph:

depends r-matrixstats:

depends r-qlcmatrix:

depends r-rcpp:

>=0.12.15

depends r-rcpparmadillo:

requirements:

Installation

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-cliquems

and update with::

   mamba update bioconductor-cliquems

To create a new environment, run:

mamba create --name myenvname bioconductor-cliquems

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

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

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