recipe bioconductor-metaboannotation

Utilities for Annotation of Metabolomics Data

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-metaboannotation/meta.yaml

High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.

package bioconductor-metaboannotation

versions:

1.6.1-0,  1.4.1-0,  1.2.0-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-compounddb:

>=1.6.0,<1.7.0

depends bioconductor-metabocoreutils:

>=1.10.0,<1.11.0

depends bioconductor-mscoreutils:

>=1.14.0,<1.15.0

depends bioconductor-protgenerics:

>=1.34.0,<1.35.0

depends bioconductor-qfeatures:

>=1.12.0,<1.13.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-spectra:

>=1.12.0,<1.13.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

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-metaboannotation

and update with::

   mamba update bioconductor-metaboannotation

To create a new environment, run:

mamba create --name myenvname bioconductor-metaboannotation

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-metaboannotation:<tag>

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

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