Package: SpectriPy 1.3.0

Johannes Rainer

SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python

The SpectriPy package allows integration of Python-based MS analysis code with the Spectra package. Spectra objects can be converted into Python MS data structures. In addition, SpectriPy integrates and wraps the similarity scoring and processing/filtering functions from the Python matchms package into R.

Authors:Michael Witting [aut], Johannes Rainer [aut, cre], Carolin Huber [aut], Helge Hecht [ctb], Marilyn De Graeve [aut], Wout Bittremieux [aut], Thomas Naake [aut], Victor Chrone [ctb], Matthias Anagho-Mattanovich [ctb], Pierre Marchal [ctb], Philippine Louail [ctb]

SpectriPy_1.3.0.tar.gz
SpectriPy_1.3.0.zip(r-4.7)SpectriPy_1.3.0.zip(r-4.6)SpectriPy_1.3.0.zip(r-4.5)
SpectriPy_1.3.0.tgz(r-4.6-any)SpectriPy_1.3.0.tgz(r-4.5-any)
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SpectriPy_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpectriPy/json (API)

# Install 'SpectriPy' in R:
install.packages('SpectriPy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rformassspectrometry/spectripy/issues

On BioConductor:SpectriPy-1.3.0(bioc 3.24)SpectriPy-1.2.1(bioc 3.23)

infrastructuremetabolomicsmassspectrometryproteomicsmass-spectrometrypythonquarto

7.79 score 13 stars 28 scripts 24 exports 42 dependencies

Last updated from:c61370bce4. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING234
linux-devel-x86_64NOTE540
source / vignettesOK369
linux-release-x86_64NOTE528
macos-release-arm64NOTE443
macos-oldrel-arm64NOTE348
windows-develNOTE836
windows-releaseNOTE779
windows-oldrelNOTE795
wasm-releaseOK183

Exports:compareSpectriPyCosineGreedyCosineHungariandefaultSpectraVariableMappingfilterSpectriPyModifiedCosineModifiedCosineGreedyModifiedCosineHungarianMsBackendPyNeutralLossesCosinenormalize_intensitiespyspec_copy_on_replacepyspec_to_rspecreindexremove_peaks_around_precursor_mzrspec_to_pyspecselect_by_intensityselect_by_mzsetBackendsetSpectraVariableMappingspectraData<-spectraNames<-spectraVariableMappingspectraVariableMapping<-

Dependencies:BHBiocGenericsBiocParallelcliclueclustercodetoolscpp11data.tableformatRfsfutile.loggerfutile.optionsgenericsgluehereIRangesjsonlitelambda.rlatticelifecyclemagrittrMASSMatrixMetaboCoreUtilsMsCoreUtilspngProtGenericsrappdirsRcppRcppTOMLreticulaterlangrprojrootS4VectorssnakecasesnowSpectrastringistringrvctrswithr

Enabling integration of Python libraries and R packages for combined mass spectrometry data analysis
Introduction | System requirements | Installation | Translating data structures between R and Python | Library loading and system setup | Converting MS data from R to Python | Converting MS data from Python to R | Using a dedicated MS data backend for MS data in Python | Replacing data and ensuring data consistency | Conversion of spectra variables | Combined MS data analysis | Summary | Appendix | General comments | Session information
Rendered fromSpectriPy.qmdusingquarto::html

Last update: 2026-04-21
Started: 2025-02-25

Detailed information on installation and configuration
Introduction | Installation | Configure reticulate with host system Python environment (optional) | SpectriPy pre-requisites and installation instructions | Installing Bioconductor | Installing SpectriPy | Check installation completed | Appendix | Installation instructions for first-time R users | Installing R and RStudio | How to Download and Install R | Windows | Mac | Linux | Using R | RStudio | Opening R | Startup and Python configuration | Fixing package installation or loading problems | Session information
Rendered fromdetailed-installation-configuration.qmdusingquarto::html

Last update: 2025-10-13
Started: 2025-02-25

Readme and manuals

Help Manual

Help pageTopics
Spectra similarity calculations using Python's matchms librarycompareSpectriPy compareSpectriPy,Spectra,missing,CosineGreedy-method compareSpectriPy,Spectra,Spectra,CosineGreedy-method CosineGreedy CosineHungarian ModifiedCosine ModifiedCosineGreedy ModifiedCosineHungarian NeutralLossesCosine
Converting between R and Python MS data structuresconversion defaultSpectraVariableMapping pyspec_to_rspec rspec_to_pyspec r_to_py.Spectra setSpectraVariableMapping spectraVariableMapping,character-method spectraVariableMapping,missing-method
Filter Spectra using Python's matchms libraryfilterSpectriPy filterSpectriPy,Spectra,filter_param-method normalize_intensities remove_peaks_around_precursor_mz select_by_intensity select_by_mz
A MS data backend for MS data stored in Python$,MsBackendPy-method $<-,MsBackendPy-method backendInitialize,MsBackendPy-method intensity<-,MsBackendPy-method length,MsBackendPy-method MsBackendPy mz<-,MsBackendPy-method peaksData,MsBackendPy-method peaksData<-,MsBackendPy-method reindex setBackend,Spectra,MsBackendPy-method spectraData,MsBackendPy-method spectraData<-,MsBackendPy-method spectraNames<-,MsBackendPy-method spectraVariableMapping,MsBackendPy-method spectraVariableMapping<-,MsBackendPy-method spectraVariables,MsBackendPy-method
Copy Python MS data structure on MS data replacement operationspyspec_copy_on_replace