SpectriPy

This is the released version of SpectriPy; for the devel version, see SpectriPy.

All versions

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

Bioconductor version: Release (3.23)

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")):

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 1.2.1, https://bioconductor.org/packages/SpectriPy.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("SpectriPy")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SpectriPy")

detailed-installation-configuration.html	HTML	R Script
SpectriPy.html	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.2.1
In Bioconductor since	BioC 3.22 (R-4.5) (1 year)
License	Artistic-2.0
Depends	R (>= 4.4.0), reticulate (>= 1.42.0)
Imports	Spectra (>= 1.19.9), IRanges, S4Vectors, MsCoreUtils, ProtGenerics, methods, data.table, snakecase
System Requirements	python (>= 3.12), pandoc, quarto
URL	https://github.com/RforMassSpectrometry/SpectriPy
Bug Reports	https://github.com/RforMassSpectrometry/SpectriPy/issues

Suggests	testthat, quarto, MsBackendMgf, MsDataHub, mzR, knitr, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SpectriPy_1.2.1.tar.gz
Windows Binary (x86_64)	SpectriPy_1.2.1.zip
macOS Binary (big-sur-x86_64)	SpectriPy_1.2.1.tgz
macOS Binary (sonoma-arm64)	SpectriPy_1.2.1.tgz
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
Old Source Packages for BioC 3.23	Source Archive