SpectraQL
This is the development version of SpectraQL; for the stable release version, see SpectraQL.
MassQL support for Spectra
Bioconductor version: Development (3.24)
The Mass Spec Query Language (MassQL) is a domain-specific language enabling to express a query and retrieve mass spectrometry (MS) data in a more natural and understandable way for MS users. It is inspired by SQL and is by design programming language agnostic. The SpectraQL package adds support for the MassQL query language to R, in particular to MS data represented by Spectra objects. Users can thus apply MassQL expressions to analyze and retrieve specific data from Spectra objects.
Author: Johannes Rainer [aut, cre]
, Andrea Vicini [aut], Sebastian Gibb [ctb]
Maintainer: Johannes Rainer <Johannes.Rainer at eurac.edu>
citation("SpectraQL")):
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("SpectraQL")
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("SpectraQL")| Mass Spec Query Language Support to the Spectra Package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 1.7.1 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0), ProtGenerics(>= 1.25.1) |
| Imports | Spectra(>= 1.5.6), MsCoreUtils, methods |
| System Requirements | |
| URL | https://github.com/RforMassSpectrometry/SpectraQL |
| Bug Reports | https://github.com/RforMassSpectrometry/SpectraQL/issues |
See More
| Suggests | testthat, MsDataHub, roxygen2, rmarkdown, knitr, S4Vectors, BiocStyle, mzR |
| 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 | SpectraQL_1.7.1.tar.gz |
| Windows Binary (x86_64) | SpectraQL_1.7.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SpectraQL_1.7.1.tgz |
| macOS Binary (sonoma-arm64) | SpectraQL_1.7.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpectraQL |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpectraQL |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpectraQL/ |
| Package Short Url | https://bioconductor.org/packages/SpectraQL/ |
| Package Downloads Report | Download Stats |