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Integrating Spectra with Python’s matchms package

Project Status: Active – The project has reached a stable, usable state and is being actively developed. R-CMD-check-bioc codecov license

The SpectriPy package allows integration of Python MS packages into a Spectra-based MS analysis in R. Python functionality is wrapped into R functions allowing a seamless integration of the functionality of Python’s matchms package into R. In addition, functions to convert between R’s Spectra objects and Python’s matchms spectrum objects are available to the advanced user or developer.

Pre-requisites and installation instructions

SpectriPy uses basilisk to ensure all required python packages are installed and available (in the correct version) on each system. basilisk installs a self-contained conda environment, thus, the SpectriPy package is independent of the system’s Python environment.

To install the package use

BiocManager::install("RforMassSpectrometry/SpectriPy")

Concepts and examples

See the package’s vignette.

Contributions

Contributions are highly welcome and should follow the contribution guidelines. Also, please check the coding style guidelines in the RforMassSpectrometry vignette.