Package: rawDiag 1.9.0

Christian Panse

rawDiag: Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful

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.

Authors:Christian Panse [aut, cre], Christian Trachsel [aut], Tobias Kockmann [aut]

rawDiag_1.9.0.tar.gz
rawDiag_1.9.0.zip(r-4.7)rawDiag_1.9.0.zip(r-4.6)rawDiag_1.9.0.zip(r-4.5)
rawDiag_1.9.0.tgz(r-4.6-any)rawDiag_1.9.0.tgz(r-4.5-any)
rawDiag_1.9.0.tar.gz(r-4.7-any)rawDiag_1.9.0.tar.gz(r-4.6-any)
rawDiag_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rawDiag/json (API)
NEWS

# Install 'rawDiag' in R:
install.packages('rawDiag', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fgcz/rawdiag/issues

On BioConductor:rawDiag-1.9.0(bioc 3.24)rawDiag-1.8.0(bioc 3.23)

massspectrometryproteomicsmetabolomicsinfrastructuresoftwareshinyappsfastmass-spectrometrymultiplatformorbitrapvisualization

6.23 score 37 stars 23 scripts 252 downloads 16 exports 64 dependencies

Last updated from:d2d26ca4b3. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING179
linux-devel-x86_64ERROR189
source / vignettesOK244
linux-release-x86_64ERROR258
macos-release-arm64ERROR139
macos-oldrel-arm64ERROR137
windows-develERROR160
windows-releaseERROR184
windows-oldrelERROR120
wasm-releaseOK158

Exports:buildRawDiagShinyAppcheckRawrris.rawDiagplotChargeStateplotCycleLoadplotCycleTimeplotInjectionTimeplotLockMassCorrectionplotMassDistributionplotMzDistributionplotPrecursorHeatmapplotScanTimeplotTicBasepeakrawDiagServerrawDiagUIreadRaw

Dependencies:base64encBHBiocManagerBiocParallelbslibcachemclicodetoolscommonmarkcpp11digestdplyrfarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsggplot2gluegtablehexbinhtmltoolshttpuvisobandjquerylibjsonlitelabelinglambda.rlaterlatticelifecyclemagrittrmemoisemimeotelpillarpkgconfigplyrpromisesR6rappdirsrawrrRColorBrewerRcppreshape2rlangS7sassscalesshinysnowsourcetoolsstringistringrtibbletidyselectutf8vctrsviridisLitewithrxtable

Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful

Christian Trachsel, Christian Panse, Tobias Kockmann

Rendered fromrawDiag.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-11-08
Started: 2023-12-05

Readme and manuals

Help Manual

Help pageTopics
Calculate Master Scan Number.calculatioMasterScan
Calculate MS Cycle Time.cycleTime
Fill NA values with last previous value.fillNAgaps
Build the rawDiag shiny applicationbuildRawDiagShinyApp
Checks Bioconductor installation instructionscheckRawrr
Is an Object an rawDiag Object?is.rawDiag
Charge State Overview PlotPlotChargeState plotChargeState
Cycle Load PlotPlotCycleLoad plotCycleLoad
Plot Cycle TimePlotCycleTime plotCycleTime
Plot Injection TimePlotInjectionTime plotInjectionTime
Lock Mass Correction PlotPlotLockMassCorrection plotLockMassCorrection
Mass Distribution PlotPlotMassDistribution plotMassDistribution
mZ Distribution Plot of Ms2 ScansPlotMzDistribution plotMzDistribution
Precursor Mass versus StartTime MS2 based hexagonsPlotPrecursorHeatmap plotPrecursorHeatmap
Scan Event PlotPlotScanTime plotScanTime
Total Ion Count and Base Peak PlotPlotTicBasepeak plotTicBasepeak
rawDiag shiny modulerawDiagServer
rawDiag shiny module UIrawDiagUI
Reads selected raw file trailer information for rawDiag plot functionsrawDiag readRaw