recipe bioconductor-clumsid

Clustering of MS2 Spectra for Metabolite Identification

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/CluMSID.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-clumsid/meta.yaml

CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.

package bioconductor-clumsid

versions:

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0, 

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-msnbase:

>=2.28.0,<2.29.0

depends bioconductor-mzr:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-dbscan:

depends r-ggally:

depends r-ggplot2:

depends r-gplots:

depends r-network:

depends r-plotly:

depends r-rcolorbrewer:

depends r-sna:

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-clumsid

and update with::

   mamba update bioconductor-clumsid

To create a new environment, run:

mamba create --name myenvname bioconductor-clumsid

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-clumsid:<tag>

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

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