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Bioconductor - Spectra

Spectra

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

Spectra Infrastructure for Mass Spectrometry Data

Bioconductor version: Release (3.21)

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

Author: RforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut] ORCID: 0000-0002-1520-2268 , Johannes Rainer [aut] ORCID: 0000-0002-6977-7147 , Sebastian Gibb [aut] ORCID: 0000-0001-7406-4443 , Philippine Louail [aut] ORCID: 0009-0007-5429-6846 , Jan Stanstrup [ctb] ORCID: 0000-0003-0541-7369 , Nir Shahaf [ctb], Mar Garcia-Aloy [ctb] ORCID: 0000-0002-1330-6610 , Guillaume Deflandre [ctb] ORCID: 0009-0008-1257-2416

Maintainer: RforMassSpectrometry Package Maintainer <maintainer at rformassspectrometry.org>

Citation (from within R, enter citation("Spectra")): Installation

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


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

BiocManager::install("Spectra")

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("Spectra")

Details biocViews Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software Version 1.18.2 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License Artistic-2.0 Depends R (>= 4.1.0), S4Vectors, BiocParallel Imports ProtGenerics(>= 1.39.2), methods, IRanges, MsCoreUtils(>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils System Requirements URL https://github.com/RforMassSpectrometry/Spectra Bug Reports https://github.com/RforMassSpectrometry/Spectra/issues See More Suggests testthat, knitr (>= 1.1.0), msdata(>= 0.19.3), roxygen2, BiocStyle(>= 2.5.19), mzR(>= 2.19.6), rhdf5(>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick Linking To Enhances Depends On Me hdxmsqc, MetCirc, MsBackendMassbank, MsBackendMetaboLights, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql Imports Me CompoundDb, MetaboAnnotation, MsExperiment, MsQuality, PSMatch, SpectraQL, xcms Suggests Me koinar, MetNet, MsDataHub, MSnbase, RaMS Links To Me Build Report Build Report Package Archives

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

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