SpectriPy

This is the development version of SpectriPy; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.22)

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.

Author: Michael Witting [aut] ORCID: 0000-0002-1462-4426 , Johannes Rainer [aut, cre] ORCID: 0000-0002-6977-7147 , Carolin Huber [aut] ORCID: 0000-0002-9355-8948 , Helge Hecht [ctb] ORCID: 0000-0001-6744-996X , Marilyn De Graeve [aut] ORCID: 0000-0001-6916-401X , Wout Bittremieux [aut] ORCID: 0000-0002-3105-1359 , Thomas Naake [aut] ORCID: 0000-0001-7917-5580 , Victor Chrone [ctb] ORCID: 0009-0007-2121-4066 , Matthias Anagho-Mattanovich [ctb] ORCID: 0000-0001-7561-7898 , Pierre Marchal [ctb] ORCID: 0009-0006-6567-6257 , Philippine Louail [ctb] ORCID: 0009-0007-5429-6846

Maintainer: Johannes Rainer <Johannes.Rainer at eurac.edu>

Citation (from within R, enter citation("SpectriPy")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SpectriPy")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	0.99.4
In Bioconductor since	BioC 3.22 (R-4.5)
License	Artistic-2.0
Depends	R (>= 4.1.0), reticulate
Imports	Spectra(>= 1.17.7), IRanges, S4Vectors, MsCoreUtils, ProtGenerics, methods
System Requirements	python (>= 3.10), pandoc, quarto
URL	https://github.com/RforMassSpectrometry/SpectriPy
Bug Reports	https://github.com/RforMassSpectrometry/SpectriPy/issues

Suggests	testthat, quarto, MsBackendMgf, msdata, mzR, knitr, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/SpectriPy
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpectriPy
Package Short Url	https://bioconductor.org/packages/SpectriPy/
Package Downloads Report	Download Stats