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MsBackendSql

SQL-based Mass Spectrometry Data Backend


Bioconductor version: Release (3.18)

SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.

Author: Johannes Rainer [aut, cre] , Chong Tang [ctb], Laurent Gatto [ctb]

Maintainer: Johannes Rainer <Johannes.Rainer at eurac.edu>

Citation (from within R, enter citation("MsBackendSql")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MsBackendSql")

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("MsBackendSql")
Storing Mass Spectrometry Data in SQL Databases HTML R Script
Reference Manual PDF

Details

biocViews DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License Artistic-2.0
Depends R (>= 4.2.0), Spectra(>= 1.9.12)
Imports BiocParallel, S4Vectors, methods, ProtGenerics, DBI, MsCoreUtils, IRanges, data.table, progress, BiocGenerics
System Requirements
URL https://github.com/RforMassSpectrometry/MsBackendSql
Bug Reports https://github.com/RforMassSpectrometry/MsBackendSql/issues
See More
Suggests testthat, knitr (>= 1.1.0), roxygen2, BiocStyle(>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MsBackendSql_1.2.0.tar.gz
Windows Binary MsBackendSql_1.2.0.zip
macOS Binary (x86_64) MsBackendSql_1.2.0.tgz
macOS Binary (arm64) MsBackendSql_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MsBackendSql
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MsBackendSql
Bioc Package Browser https://code.bioconductor.org/browse/MsBackendSql/
Package Short Url https://bioconductor.org/packages/MsBackendSql/
Package Downloads Report Download Stats