Spectra

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see Spectra.

Spectra Infrastructure for Mass Spectrometry Data

Bioconductor version: 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 iD ORCID: 0000-0002-1520-2268 , Johannes Rainer [aut] ORCID iD ORCID: 0000-0002-6977-7147 , Sebastian Gibb [aut] ORCID iD ORCID: 0000-0001-7406-4443 , Philippine Louail [aut] ORCID iD ORCID: 0009-0007-5429-6846 , Jan Stanstrup [ctb] ORCID iD ORCID: 0000-0003-0541-7369 , Nir Shahaf [ctb], Mar Garcia-Aloy [ctb] ORCID iD ORCID: 0000-0002-1330-6610 , Guillaume Deflandre [ctb] ORCID iD 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")

Creating new `MsBackend` class HTML R Script

Description and usage of Spectra object HTML R Script

Large-scale data handling and processing with Spectra 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 1.18.2

In Bioconductor since BioC 3.12 (R-4.0) (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

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.

Source Package Spectra_1.18.2.tar.gz

Windows Binary (x86_64) Spectra_1.18.2.zip

macOS Binary (x86_64) Spectra_1.18.2.tgz

macOS Binary (arm64) Spectra_1.18.2.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 3.21 Source Archive