SpectriPy

This is the development version of SpectriPy; for the stable release version, see SpectriPy.

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

Bioconductor version: Development (3.24)

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")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

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


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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.3.0
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

Package Archives

Follow 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 (64-bit only)
macOS Binary (big-sur-x86_64)	SpectriPy_1.3.0.tgz
macOS Binary (sonoma-arm64)	SpectriPy_1.3.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpectriPy
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpectriPy
Bioc Package Browser	https://code.bioconductor.org/browse/SpectriPy/
Package Short Url	https://bioconductor.org/packages/SpectriPy/
Package Downloads Report	Download Stats