recipe bioconductor-msbackendmassbank

Mass Spectrometry Data Backend for MassBank record Files






Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.

package bioconductor-msbackendmassbank

(downloads) docker_bioconductor-msbackendmassbank



depends bioconductor-biocparallel:


depends bioconductor-iranges:


depends bioconductor-mscoreutils:


depends bioconductor-protgenerics:


depends bioconductor-s4vectors:


depends bioconductor-spectra:


depends r-base:


depends r-dbi:



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-msbackendmassbank

and update with::

   mamba update bioconductor-msbackendmassbank

To create a new environment, run:

mamba create --name myenvname bioconductor-msbackendmassbank

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-msbackendmassbank/tags`_ for valid values for ``<tag>``)

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