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Spectra

Spectra Infrastructure for Mass Spectrometry Data


Bioconductor version: Release (3.18)

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] , Nir Shahaf [ctb]

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

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

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

Details

biocViews Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), S4Vectors, BiocParallel, ProtGenerics(>= 1.33.1)
Imports 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 MetCirc, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql
Imports Me CompoundDb, MetaboAnnotation, MobilityTransformR, MsExperiment, MsQuality, xcms
Suggests Me MetNet, MsDataHub, PSMatch
Links To Me
Build Report Build Report

Package Archives

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

Source Package Spectra_1.12.0.tar.gz
Windows Binary Spectra_1.12.0.zip (64-bit only)
macOS Binary (x86_64) Spectra_1.12.0.tgz
macOS Binary (arm64) Spectra_1.12.0.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