MsBackendRawFileReader

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see MsBackendRawFileReader.

Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files

DOI: 10.18129/B9.bioc.MsBackendRawFileReader

Bioconductor version: 3.14

implements a MsBackend for the Spectra package using Thermo Fisher Scientific's NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package (Kockmann T. et al. (2020) ) Methods defined in this package are supposed to extend the Spectra Bioconductor package.

Author: Christian Panse [aut, cre] , Tobias Kockmann [aut]

Maintainer: Christian Panse <cp at fgcz.ethz.ch>

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

Installation

To install this package, start R (version "4.1") and enter:


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

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("MsBackendRawFileReader")

On Using and Extending the `MsBackendRawFileReader` Backend. HTML R Script

Reference Manual PDF

NEWS Text

INSTALL Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews MassSpectrometry, Metabolomics, Proteomics, Software

Version 1.0.0

In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)

License GPL-3

Depends R (>= 4.1), methods, Spectra(>= 1.2)

Imports MsCoreUtils, S4Vectors, IRanges, rawrr(>= 1.1.14), utils, BiocParallel

System Requirements mono-runtime 4.x or higher (including System.Data library) on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows.

URL https://github.com/fgcz/MsBackendRawFileReader

Bug Reports https://github.com/fgcz/MsBackendRawFileReader/issues

Suggests BiocStyle(>= 2.5), ExperimentHub, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare(>= 1.5), testthat

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Package Archives

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

Source Package MsBackendRawFileReader_1.0.0.tar.gz

Windows Binary MsBackendRawFileReader_1.0.0.zip (32- & 64-bit)

macOS 10.13 (High Sierra) MsBackendRawFileReader_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/MsBackendRawFileReader

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MsBackendRawFileReader

Bioc Package Browser https://code.bioconductor.org/browse/MsBackendRawFileReader/

Package Short Url https://bioconductor.org/packages/MsBackendRawFileReader/

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Old Source Packages for BioC 3.14 Source Archive