Introduction | ChemoProtSet class | Setting Parameters | Importing Data | Data requirements | Intensities or Fold-Changes | Peptide Removal Process | Normalizing the Data | Fitting a Model | Plotting Results | Example | Shiny Application | References
Package: Doscheda 1.35.0
Bruno Contrino
Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline
Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.
Authors:
Doscheda_1.35.0.tar.gz
Doscheda_1.35.0.zip(r-4.7)Doscheda_1.35.0.zip(r-4.6)Doscheda_1.35.0.zip(r-4.5)
Doscheda_1.35.0.tgz(r-4.6-any)Doscheda_1.35.0.tgz(r-4.5-any)
Doscheda_1.35.0.tar.gz(r-4.7-any)Doscheda_1.35.0.tar.gz(r-4.6-any)
Doscheda_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Doscheda/json (API)
| # Install 'Doscheda' in R: |
| install.packages('Doscheda', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- doschedaData - Peptide Intensity data set for Doscheda
- processedExample - Processed Peptide Intensity data set for Doscheda
On BioConductor:Doscheda-1.35.0(bioc 3.24)Doscheda-1.34.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
proteomicsnormalizationpreprocessingmassspectrometryqualitycontroldataimportregression
Last updated from:ca63fa99cf. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 196 | ||
| linux-devel-x86_64 | NOTE | 336 | ||
| source / vignettes | OK | 284 | ||
| linux-release-x86_64 | NOTE | 345 | ||
| macos-release-arm64 | NOTE | 183 | ||
| macos-oldrel-arm64 | NOTE | 147 | ||
| windows-devel | NOTE | 216 | ||
| windows-release | NOTE | 207 | ||
| windows-oldrel | NOTE | 200 | ||
| wasm-release | OK | 183 |
Exports:boxplotcorrPlotdensityPlotdoschedaAppfitModelgetDatasetsgetFinalgetInputgetNormgetParametersmakeReportmeanSdPlotpcaPlotremovePeptidesreplicatePlotrunDoschedarunNormalisationsetDatasetParametersvolcanoPlot
Dependencies:abindaffyaffyioaskpassbackportsbase64encBiobaseBiocGenericsBiocManagerbootbroombslibcachemcalibratecarcarDatacellrangerclicodetoolscolorspacecommonmarkcorrgramcowplotcpp11crayoncrosstalkcurldata.tableDerivdiagramdigestdoBydplyrdrcDTellipseevaluatefarverfastmapfontawesomeforecastFormulafracdifffsfuturefuture.applygenericsggplot2globalsgluegridExtragtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelavalazyevallifecyclelimmalistenvlme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrmultcompmvtnormnlmenloptrnnetnumDerivopensslotelparallellypbkrtestpillarpkgconfigplotrixplyrpreprocessCoreprettyunitsprodlimprogressprogressrpromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadxlreformulasrematchreshape2rlangrmarkdownS7sandwichsassscalesshapeshinyshinydashboardsourcetoolsSparseMSQUAREMstatmodstringistringrsurvivalsysTH.datatibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitevsnwithrxfunxtableyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Default boxplot for objects of class ChemoProtSet | boxplot,ChemoProtSet-method |
| An S4 class to run the doscheda pipeline | ChemoProtSet-class DoschedaSet |
| Plot showing correlation between all channels across replicates | corrPlot corrPlot,ANY,ANY-method corrPlot,ChemoProtSet-method |
| Density plot for objects of class ChemoProtSet | densityPlot densityPlot,ANY,ANY-method densityPlot,ChemoProtSet-method |
| Doscheda: A package for Down Stream Chemo-Proteomics Data Analysis | doscheda-package doscheda |
| Run shiny application for DOSCHEDA | doschedaApp |
| Peptide Intensity data set for Doscheda | doschedaData |
| Method to fit a model to an object of class 'ChemoProtSet' | fitModel fitModel,ANY,ANY-method fitModel,ChemoProtSet-method |
| Accessor function for the datasets slot. | getDatasets getDatasets,ANY,ANY-method getDatasets,ChemoProtSet-method |
| Accessor function for the finalData slot. | getFinal getFinal,ANY,ANY-method getFinal,ChemoProtSet-method |
| Accessor function for the Input | getInput getInput,ANY,ANY-method getInput,ChemoProtSet-method |
| Accessor function for the normData | getNorm getNorm,ANY,ANY-method getNorm,ChemoProtSet-method |
| Accessor function for the parameters slot. | getParameters getParameters,ANY,ANY-method getParameters,ChemoProtSet-method |
| Create report from 'ChemProtSet' object | makeReport |
| MeanSd plot for objects of class ChemoProtSet | meanSdPlot meanSdPlot,ANY,ANY-method meanSdPlot,ChemoProtSet-method |
| PCA of the main data sets contained in a object of class ChemoProtSet | pcaPlot pcaPlot,ANY,ANY-method pcaPlot,ChemoProtSet-method |
| Default plot for objects of class ChemoProtSet | plot.ChemoProtSet |
| Processed Peptide Intensity data set for Doscheda | processedExample |
| Method to remove peptides from input data of an object of class 'ChemoProtSet' | removePeptides removePeptides,ANY,ANY-method removePeptides,ChemoProtSet-method |
| Plot replicates between concentrations | replicatePlot replicatePlot,ANY,ANY-method replicatePlot,ChemoProtSet-method |
| Wrapper Function to run the entire Doscheda pipeline | runDoscheda |
| Method to remove peptides from input data of an object of class 'ChemoProtSet' | runNormalisation runNormalisation,ANY,ANY-method runNormalisation,ChemoProtSet-method |
| Method for attaching and standardising data for objects of class 'ChemoProtSet' | setData setData,ANY,ANY-method setData,ChemoProtSet-method |
| Method to set parameters for a ChemoProtSet | setParameters setParameters,ANY,ANY-method setParameters,ChemoProtSet-method |
| Volcano plot for objects of class ChemoProtSet | volcanoPlot volcanoPlot,ANY,ANY-method volcanoPlot,ChemoProtSet-method |
