MsBackendSql

SQL-based Mass Spectrometry Data Backend

Bioconductor version: Release (3.17)

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	1.0.1
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.2.0), Spectra(>= 1.9.12)
Imports	BiocParallel, S4Vectors, methods, ProtGenerics, DBI, MsCoreUtils, IRanges, data.table, progress
Linking To
Suggests	testthat, knitr (>= 1.1.0), roxygen2, BiocStyle(>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR
System Requirements
Enhances
URL	https://github.com/RforMassSpectrometry/MsBackendSql
Bug Reports	https://github.com/RforMassSpectrometry/MsBackendSql/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MsBackendSql_1.0.1.tar.gz
Windows Binary	MsBackendSql_1.0.1.zip
macOS Binary (x86_64)	MsBackendSql_1.0.1.tgz
macOS Binary (arm64)	MsBackendSql_1.0.1.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
Old Source Packages for BioC 3.17	Source Archive