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✨
DESCRIPTION |NEWS
card.svg |card.png
rawDiag/json (API)

# 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)

massspectrometry proteomics metabolomics infrastructure software shinyapps fast mass-spectrometry multiplatform orbitrap visualization

6.27 score 37 stars 25 scripts 16 exports 64 dependencies

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

Target	Result	Time
bioc-checks	WARNING	170
linux-devel-x86_64	ERROR	226
source / vignettes	OK	329
linux-release-x86_64	ERROR	217
macos-release-arm64	ERROR	138
macos-oldrel-arm64	ERROR	122
windows-devel	ERROR	161
windows-release	ERROR	176
windows-oldrel	ERROR	135
wasm-release	OK	180

Exports:buildRawDiagShinyApp checkRawrr is.rawDiag plotChargeState plotCycleLoad plotCycleTime plotInjectionTime plotLockMassCorrection plotMassDistribution plotMzDistribution plotPrecursorHeatmap plotScanTime plotTicBasepeak rawDiagServer rawDiagUI readRaw

Dependencies:base64enc BH BiocManager BiocParallel bslib cachem cli codetools commonmark cpp11 digest dplyr farver fastmap fontawesome formatR fs futile.logger futile.options generics ggplot2 glue gtable hexbin htmltools httpuv isoband jquerylib jsonlite labeling lambda.r later lattice lifecycle magrittr memoise mime otel pillar pkgconfig plyr promises R6 rappdirs rawrr RColorBrewer Rcpp reshape2 rlang S7 sass scales shiny snow sourcetools stringi stringr tibble tidyselect utf8 vctrs viridisLite withr xtable

Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful

Rendered fromrawDiag.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Master Scan Number	.calculatioMasterScan
Calculate MS Cycle Time	.cycleTime
Fill NA values with last previous value	.fillNAgaps
Build the rawDiag shiny application	buildRawDiagShinyApp
Checks Bioconductor installation instructions	checkRawrr
Is an Object an rawDiag Object?	is.rawDiag
Charge State Overview Plot	PlotChargeState plotChargeState
Cycle Load Plot	PlotCycleLoad plotCycleLoad
Plot Cycle Time	PlotCycleTime plotCycleTime
Plot Injection Time	PlotInjectionTime plotInjectionTime
Lock Mass Correction Plot	PlotLockMassCorrection plotLockMassCorrection
Mass Distribution Plot	PlotMassDistribution plotMassDistribution
mZ Distribution Plot of Ms2 Scans	PlotMzDistribution plotMzDistribution
Precursor Mass versus StartTime MS2 based hexagons	PlotPrecursorHeatmap plotPrecursorHeatmap
Scan Event Plot	PlotScanTime plotScanTime
Total Ion Count and Base Peak Plot	PlotTicBasepeak plotTicBasepeak
rawDiag shiny module	rawDiagServer
rawDiag shiny module UI	rawDiagUI
Reads selected raw file trailer information for rawDiag plot functions	rawDiag readRaw