Spectra

DOI: 10.18129/B9.bioc.Spectra  

Spectra Infrastructure for Mass Spectrometry Data

Bioconductor version: Release (3.17)

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] , Johannes Rainer [aut] , Sebastian Gibb [aut] , Jan Stanstrup [ctb]

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

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	Creating new `MsBackend` class
HTML	R Script	Description and usage of Spectra object
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.10.3
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), S4Vectors, BiocParallel, ProtGenerics(>= 1.29.1)
Imports	methods, IRanges, MsCoreUtils(>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics
LinkingTo
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)
SystemRequirements
Enhances
URL	https://github.com/RforMassSpectrometry/Spectra
BugReports	https://github.com/RforMassSpectrometry/Spectra/issues
Depends On Me	MetCirc, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql
Imports Me	CompoundDb, MetaboAnnotation, MobilityTransformR, MsExperiment, MsQuality
Suggests Me	MetNet, MsDataHub, PSMatch, xcms
Links To Me
Build Report

Package Archives

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

Source Package	Spectra_1.10.3.tar.gz
Windows Binary	Spectra_1.10.3.zip
macOS Binary (x86_64)	Spectra_1.10.3.tgz
macOS Binary (arm64)	Spectra_1.10.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Spectra
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Spectra
Bioc Package Browser	https://code.bioconductor.org/browse/Spectra/
Package Short Url	https://bioconductor.org/packages/Spectra/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive