SpectriPy
Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python
Bioconductor version: 3.24 · Package version: 1.3.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpectriPy")Details
| Maintainer | Johannes Rainer <Johannes.Rainer@eurac.edu> |
| Author | Michael Witting [aut] (ORCID: <https://orcid.org/0000-0002-1462-4426>), Johannes Rainer [aut, cre] (ORCID: <https://orcid.org/0000-0002-6977-7147>), Carolin Huber [aut] (ORCID: <https://orcid.org/0000-0002-9355-8948>), Helge Hecht [ctb] (ORCID: <https://orcid.org/0000-0001-6744-996X>), Marilyn De Graeve [aut] (ORCID: <https://orcid.org/0000-0001-6916-401X>), Wout Bittremieux [aut] (ORCID: <https://orcid.org/0000-0002-3105-1359>), Thomas Naake [aut] (ORCID: <https://orcid.org/0000-0001-7917-5580>), Victor Chrone [ctb] (ORCID: <https://orcid.org/0009-0007-2121-4066>), Matthias Anagho-Mattanovich [ctb] (ORCID: <https://orcid.org/0000-0001-7561-7898>), Pierre Marchal [ctb] (ORCID: <https://orcid.org/0009-0006-6567-6257>), Philippine Louail [ctb] (ORCID: <https://orcid.org/0009-0007-5429-6846>) |
| License | Artistic-2.0 |
| URL | https://github.com/RforMassSpectrometry/SpectriPy |
| Bug Reports | https://github.com/RforMassSpectrometry/SpectriPy/issues |
| System Requirements | python (>= 3.12), pandoc, quarto |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/SpectriPy/ |
Citation
From within R, enter citation("SpectriPy"):
Michael Witting, Johannes Rainer, Carolin Huber, Marilyn De Graeve, Wout Bittremieux, Thomas Naake. SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python. doi:10.18129/B9.bioc.SpectriPy, R package version 1.3.0, https://bioconductor.org/packages/SpectriPy.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Detailed information on installation and configuration
- Enabling integration of Python libraries and R packages for combined mass spectrometry data analysis
Download
Follow the installation instructions to use this package in your R session.
| Source package | SpectriPy_1.3.0.tar.gz |
| Windows binary (x86_64) | SpectriPy_1.3.0.zip |
| macOS binary (arm64) | SpectriPy_1.3.0.tgz |
| macOS binary (x86_64) | SpectriPy_1.3.0.tgz |
Dependencies
Depends: R (>= 4.4.0), reticulate (>= 1.42.0)
Imports: Spectra (>= 1.19.9), IRanges, S4Vectors, MsCoreUtils, ProtGenerics, methods, data.table, snakecase
Suggests: testthat, quarto, MsBackendMgf, MsDataHub, mzR, knitr, BiocStyle