recipe bioconductor-metabolomicsworkbenchr

Metabolomics Workbench in R






This package provides functions for interfacing with the Metabolomics Workbench RESTful API. Study, compound, protein and gene information can be searched for using the API. Methods to obtain study data in common Bioconductor formats such as SummarizedExperiment and MultiAssayExperiment are also included.

package bioconductor-metabolomicsworkbenchr

(downloads) docker_bioconductor-metabolomicsworkbenchr



depends bioconductor-multiassayexperiment:


depends bioconductor-struct:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-data.table:

depends r-httr:

depends r-jsonlite:



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-metabolomicsworkbenchr

and update with::

   mamba update bioconductor-metabolomicsworkbenchr

To create a new environment, run:

mamba create --name myenvname bioconductor-metabolomicsworkbenchr

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<tag>

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

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