mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-mzr
and update with:
conda update bioconductor-mzr
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-mzr.