Package Recipe 'bioconductor-rmassbank'

recipe bioconductor-rmassbank

Workflow to process tandem MS files and build MassBank records

Homepage:: https://bioconductor.org/packages/3.20/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¶

Versions:

3.20.0-0, 3.16.0-0, 3.12.0-0, 3.10.0-0, 3.8.0-1, 3.8.0-0, 3.4.0-2, 3.4.0-1, 3.4.0-0,

3.20.0-0, 3.16.0-0, 3.12.0-0, 3.10.0-0, 3.8.0-1, 3.8.0-0, 3.4.0-2, 3.4.0-1, 3.4.0-0, 3.2.0-0, 3.0.0-1, 3.0.0-0, 2.13.0-0, 2.12.0-1, 2.10.1-0

Depends:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biobase >=2.70.0,<2.71.0a0
on bioconductor-chemminer >=3.62.0,<3.63.0
on bioconductor-chemminer >=3.62.0,<3.63.0a0
on bioconductor-msnbase >=2.36.0,<2.37.0
on bioconductor-msnbase >=2.36.0,<2.37.0a0
on bioconductor-mzr >=2.44.0,<2.45.0
on bioconductor-mzr >=2.44.0,<2.45.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on openbabel
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-digest
on r-dplyr
on r-envipat
on r-glue
on r-httr
on r-httr2
on r-logger
on r-purrr
on r-r.utils
on r-rcdk
on r-rcpp
on r-readjdx
on r-readr
on r-rjson
on r-tibble
on r-tidyselect
on r-webchem
on r-xml
on r-yaml

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-rmassbank

to add into an existing workspace instead, run:

pixi add bioconductor-rmassbank

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-rmassbank

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rmassbank

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-rmassbank/README.html)