Spectra

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

Spectra Infrastructure for Mass Spectrometry Data

Bioconductor version: Release (3.23)

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 , Ahlam Mentag [ctb] ORCID: 0009-0008-5438-7067

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

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

Laurent Gatto, Johannes Rainer, Sebastian Gibb, Philippine Louail. Spectra: Spectra Infrastructure for Mass Spectrometry Data. doi:10.18129/B9.bioc.Spectra, R package version 1.22.2, https://bioconductor.org/packages/Spectra.

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("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")

Creating new `MsBackend` class	HTML	R Script
Large-scale data handling and processing with Spectra	HTML	R Script
Description and usage of Spectra object	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	1.22.2
In Bioconductor since	BioC 3.12 (R-4.0) (6 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), S4Vectors, BiocParallel
Imports	ProtGenerics (>= 1.39.2), methods, IRanges, MsCoreUtils (>= 1.23.6), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils, data.table
System Requirements
URL	https://github.com/RforMassSpectrometry/Spectra
Bug Reports	https://github.com/RforMassSpectrometry/Spectra/issues

Suggests	testthat, knitr (>= 1.1.0), MsDataHub, 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	Chromatograms, CompoundDb, lcmsPlot, MetaboAnnotation, MsExperiment, MsQuality, PSMatch, SpectraQL, SpectriPy, xcms
Suggests Me	fioRa, MetNet, MsDataHub, MSnbase, RaMS
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	Spectra_1.22.2.tar.gz
Windows Binary (x86_64)	Spectra_1.22.2.zip
macOS Binary (big-sur-x86_64)	Spectra_1.22.2.tgz
macOS Binary (sonoma-arm64)	Spectra_1.22.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Spectra
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Spectra
Package Short Url	https://bioconductor.org/packages/Spectra/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive