Spectra
This is thereleased version of Spectra; for the devel version, seeSpectra.
Spectra Infrastructure for Mass Spectrometry Data
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | Infrastructure,MassSpectrometry,Metabolomics,Proteomics,Software |
| Version | 1.20.0 |
| 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 |
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 | Chromatograms,CompoundDb,MetaboAnnotation,MsExperiment,MsQuality,PSMatch,SpectraQL,SpectriPy,xcms |
| Suggests Me | koinar,MetNet,MsDataHub,MSnbase,RaMS |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | Spectra_1.20.0.tar.gz |
| Windows Binary (x86_64) | Spectra_1.20.0.zip (64-bit only) |
| macOS Binary (x86_64) | Spectra_1.20.0.tgz |
| macOS Binary (arm64) | Spectra_1.20.0.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 |
| Old Source Packages for BioC 3.22 | Source Archive |