SpectraStash
This is the development version of SpectraStash; to use it, please install the devel version of Bioconductor.
Serialize and restore Spectra objects in interoperable file formats
Bioconductor version: Development (3.24)
The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The SpectraStash package implements the serialization methods from the MsStash package for Spectra objects and its MsBackend classes. A variety of different file formats and types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package are supported. The file type can be defined and configured through a second argument `param` of the save/read methods.
Author: Johannes Rainer [aut, cre]
, Philippine Louail [aut]
, Laurent Gatto [ctb]
, Gabriele Tomè [ctb] (ORCID:
, fnd: MetaRbolomics4Galaxy project (CUP: D53C25001030003) co-funded by the Autonomous Province of Bolzano under the Joint Projects South Tyrol–Germany 2025 program.)
Maintainer: Johannes Rainer <Johannes.Rainer at eurac.edu>
citation("SpectraStash")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("SpectraStash")
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("SpectraStash")| Safely Store MS Data Object in a Portable Stash | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.6.0), MsStash |
| Imports | methods, Spectra(>= 1.23.2), utils, S4Vectors, alabaster.base, jsonlite, BiocParallel |
| System Requirements | |
| URL | https://github.com/RforMassSpectrometry/SpectraStash |
| Bug Reports | https://github.com/RforMassSpectrometry/SpectraStash/issues |
See More
| Suggests | BiocStyle, MsDataHub, testthat, mzR, fs, knitr, pkgload, callr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpectraStash_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SpectraStash |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpectraStash |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpectraStash/ |
| Package Short Url | https://bioconductor.org/packages/SpectraStash/ |
| Package Downloads Report | Download Stats |