recipe bioconductor-rmassbank

Workflow to process tandem MS files and build MassBank records






Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

package bioconductor-rmassbank

(downloads) docker_bioconductor-rmassbank



depends bioconductor-biobase:


depends bioconductor-chemmineob:


depends bioconductor-chemminer:


depends bioconductor-msnbase:


depends bioconductor-mzr:


depends bioconductor-s4vectors:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends openbabel:

depends r-assertthat:

depends r-base:


depends r-data.table:

depends r-digest:

depends r-envipat:

depends r-httr:

depends r-logger:

depends r-r.utils:

depends r-rcdk:

depends r-rcpp:

depends r-rcurl:

depends r-readjdx:

depends r-rjson:

depends r-webchem:

depends r-xml:

depends r-yaml:



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-rmassbank

and update with::

   mamba update bioconductor-rmassbank

To create a new environment, run:

mamba create --name myenvname bioconductor-rmassbank

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

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