rawDiag

This is the development version of rawDiag; for the stable release version, see rawDiag.

Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful


Bioconductor version: Development (3.21)

Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.

Author: Christian Panse [aut, cre] (ORCID: ), Christian Trachsel [aut], Tobias Kockmann [aut]

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("rawDiag")

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("rawDiag")
Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful HTML R Script
Reference Manual PDF

Details

biocViews Infrastructure, MassSpectrometry, Metabolomics, Proteomics, ShinyApps, Software
Version 1.3.0
In Bioconductor since BioC 3.19 (R-4.4) (0.5 years)
License GPL-3
Depends R (>= 4.4)
Imports dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools, BiocManager, BiocParallel, rawrr(>= 1.13.3), rlang, reshape2, scales, shiny (>= 1.5), stats, utils
System Requirements mono 4.x or higher on OSX / Linux, .NET 4.x or higher on Windows, 'msbuild' and 'nuget' available in the path
URL https://github.com/fgcz/rawDiag/
Bug Reports https://github.com/fgcz/rawDiag/issues
See More
Suggests BiocStyle(>= 2.28), ExperimentHub, tartare, knitr, testthat
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Package Archives

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

Source Package rawDiag_1.3.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/rawDiag
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rawDiag
Bioc Package Browser https://code.bioconductor.org/browse/rawDiag/
Package Short Url https://bioconductor.org/packages/rawDiag/
Package Downloads Report Download Stats