Spectra
Spectra Infrastructure for Mass Spectrometry Data
Bioconductor version: 3.23 · Package version: 1.22.2
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Spectra")Details
| Maintainer | RforMassSpectrometry Package Maintainer <maintainer@rformassspectrometry.org> |
| Author | RforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut] (ORCID: <https://orcid.org/0000-0002-1520-2268>), Johannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>), Sebastian Gibb [aut] (ORCID: <https://orcid.org/0000-0001-7406-4443>), Philippine Louail [aut] (ORCID: <https://orcid.org/0009-0007-5429-6846>), Jan Stanstrup [ctb] (ORCID: <https://orcid.org/0000-0003-0541-7369>), Nir Shahaf [ctb], Mar Garcia-Aloy [ctb] (ORCID: <https://orcid.org/0000-0002-1330-6610>), Guillaume Deflandre [ctb] (ORCID: <https://orcid.org/0009-0008-1257-2416>), Ahlam Mentag [ctb] (ORCID: <https://orcid.org/0009-0008-5438-7067>) |
| License | Artistic-2.0 |
| URL | https://github.com/RforMassSpectrometry/Spectra |
| Bug Reports | https://github.com/RforMassSpectrometry/Spectra/issues |
| Downloads rank | 3955 |
| Source branch | RELEASE_3_23 |
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
Documentation
- Creating new MsBackend classes
- Description and usage of Spectra objects
- Large-scale data handling and processing with Spectra
Download
Dependencies
Depends: R (>= 4.1.0), S4Vectors, BiocParallel
Imports: ProtGenerics (>= 1.39.2), methods, IRanges, MsCoreUtils (>= 1.23.6), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils, data.table
Suggests: testthat, knitr (>= 1.1.0), MsDataHub, roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick
Reverse dependencies
Depends On Me (8): hdxmsqc, MetCirc, MsBackendMassbank, MsBackendMetaboLights, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql
Imports Me (10): Chromatograms, CompoundDb, lcmsPlot, MetaboAnnotation, MsExperiment, MsQuality, PSMatch, SpectraQL, SpectriPy, xcms