recipe bioconductor-msbackendmetabolights

Retrieve Mass Spectrometry Data from MetaboLights

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/MsBackendMetaboLights.html

License:

Artistic-2.0

Recipe:

/bioconductor-msbackendmetabolights/meta.yaml

MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.

package bioconductor-msbackendmetabolights

versions:

1.0.0-0

depends bioconductor-biocfilecache:

>=2.14.0,<2.15.0

depends bioconductor-protgenerics:

>=1.38.0,<1.39.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-spectra:

>=1.16.0,<1.17.0

depends r-base:

>=4.4,<4.5.0a0

depends r-curl:

requirements:

additional platforms:

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-msbackendmetabolights

and update with::

   mamba update bioconductor-msbackendmetabolights

To create a new environment, run:

mamba create --name myenvname bioconductor-msbackendmetabolights

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-msbackendmetabolights:<tag>

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

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Link to this page

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