recipe bioconductor-mzr

parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/mzR.html

License:

Artistic-2.0

Recipe:

/bioconductor-mzr/meta.yaml

Links:

biotools: mzr

mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

package bioconductor-mzr

versions:

2.34.1-0,  2.32.0-1,  2.32.0-0,  2.28.0-2,  2.28.0-1,  2.28.0-0,  2.26.0-0,  2.24.1-0,  2.24.0-0, 

2.34.1-0,  2.32.0-1,  2.32.0-0,  2.28.0-2,  2.28.0-1,  2.28.0-0,  2.26.0-0,  2.24.1-0,  2.24.0-0,  2.22.0-0,  2.20.0-0,  2.18.0-1,  2.16.2-1,  2.16.2-0,  2.16.0-0,  2.12.0-1,  2.10.0-0,  2.6.3-1,  2.6.3-0,  2.4.1-1

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-protgenerics:

>=1.32.0,<1.33.0

depends bioconductor-rhdf5lib:

>=1.22.0,<1.23.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-ncdf4:

depends r-rcpp:

>=0.10.1

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-mzr

and update with::

   mamba update bioconductor-mzr

To create a new environment, run:

mamba create --name myenvname bioconductor-mzr

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-mzr:<tag>

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

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