recipe bioconductor-rmassbank

Workflow to process tandem MS files and build MassBank records

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-rmassbank/meta.yaml

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

versions:
3.12.0-03.10.0-03.8.0-13.8.0-03.4.0-23.4.0-13.4.0-03.2.0-03.0.0-1

3.12.0-03.10.0-03.8.0-13.8.0-03.4.0-23.4.0-13.4.0-03.2.0-03.0.0-13.0.0-02.13.0-02.12.0-12.10.1-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-chemmineob:

>=1.40.0,<1.41.0

depends bioconductor-chemmineob:

>=1.40.0,<1.41.0a0

depends bioconductor-chemminer:

>=3.54.0,<3.55.0

depends bioconductor-chemminer:

>=3.54.0,<3.55.0a0

depends bioconductor-msnbase:

>=2.28.0,<2.29.0

depends bioconductor-msnbase:

>=2.28.1,<2.29.0a0

depends bioconductor-mzr:

>=2.36.0,<2.37.0

depends bioconductor-mzr:

>=2.36.0,<2.37.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends openbabel:

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-digest:

depends r-envipat:

depends r-glue:

depends r-httr:

depends r-logger:

depends r-r.utils:

depends r-rcdk:

depends r-rcpp:

depends r-readjdx:

depends r-rjson:

depends r-webchem:

depends r-xml:

depends r-yaml:

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-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 quay.io/biocontainers/bioconductor-rmassbank:<tag>

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

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