Package: Doscheda 1.29.0
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_1.29.0.tar.gz
Doscheda_1.29.0.zip(r-4.5)Doscheda_1.29.0.zip(r-4.4)Doscheda_1.29.0.zip(r-4.3)
Doscheda_1.29.0.tgz(r-4.4-any)Doscheda_1.29.0.tgz(r-4.3-any)
Doscheda_1.29.0.tar.gz(r-4.5-noble)Doscheda_1.29.0.tar.gz(r-4.4-noble)
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Doscheda.pdf |Doscheda.html✨
Doscheda/json (API)
NEWS
| # Install 'Doscheda' in R: |
| install.packages('Doscheda', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- doschedaData - Peptide Intensity data set for Doscheda
- processedExample - Processed Peptide Intensity data set for Doscheda
On BioConductor:Doscheda-1.29.0(bioc 3.21)Doscheda-1.28.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
proteomicsnormalizationpreprocessingmassspectrometryqualitycontroldataimportregression
Last updated 2 months agofrom:305a40ad7d. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Dec 19 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Dec 19 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Dec 19 2024 |
Exports:boxplotcorrPlotdensityPlotdoschedaAppfitModelgetDatasetsgetFinalgetInputgetNormgetParametersmakeReportmeanSdPlotpcaPlotremovePeptidesreplicatePlotrunDoschedarunNormalisationsetDatasetParametersvolcanoPlot
Dependencies:abindaffyaffyioaskpassbackportsbase64encBiobaseBiocGenericsBiocManagerbootbroombslibcachemcalibratecarcarDatacellrangerclicodetoolscolorspacecommonmarkcorrgramcowplotcpp11crayoncrosstalkcurldata.tableDerivdiagramdigestdoBydplyrdrcDTevaluatefansifarverfastmapfontawesomeFormulafsfuturefuture.applygenericsggplot2globalsgluegridExtragtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelavalazyevallifecyclelimmalistenvlme4magrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnumDerivopensslparallellypbkrtestpillarpkgconfigplotrixplyrpreprocessCoreprettyunitsprodlimprogressprogressrpromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreadxlrematchreshape2rlangrmarkdownsandwichsassscalesshapeshinyshinydashboardsourcetoolsSparseMSQUAREMstatmodstringistringrsurvivalsysTH.datatibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxfunxtableyamlzlibbioczoo
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 |
