Spectra
This is the development version of Spectra; for the stable release version, see Spectra.
Spectra Infrastructure for Mass Spectrometry Data
Bioconductor version: Development (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:
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")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 1.17.4 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0), S4Vectors, BiocParallel |
| Imports | ProtGenerics(>= 1.39.1), 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 | CompoundDb, MetaboAnnotation, MsExperiment, MsQuality, SpectraQL, xcms |
| Suggests Me | koinar, MetNet, MsDataHub, MSnbase, PSMatch, RaMS |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Spectra_1.17.4.tar.gz |
| Windows Binary (x86_64) | Spectra_1.17.4.zip |
| macOS Binary (x86_64) | Spectra_1.17.4.tgz |
| macOS Binary (arm64) | Spectra_1.17.4.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 |