Package: DaparToolshed 0.99.36

Samuel Wieczorek

DaparToolshed: Tools for the Differential Analysis of Proteins Abundance with R

The package DaparToolshed is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. It is an update of our previous package DAPAR and contains more functions to analyze the data and uses MultAssayExperiment and SummarizedExperiment data structures. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package).

Authors:Samuel Wieczorek [cre, aut], Thomas Burger [aut], Enora Fremy [ctb], Manon Gaudin [ctb]

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manual.pdf |manual.html✨
card.svg |card.png
DaparToolshed/json (API)
NEWS

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

Bug tracker:https://github.com/edyp-lab/dapartoolshed/issues

Pkgdown/docs site:https://edyp-lab.github.io

Datasets:

On BioConductor:DaparToolshed-0.99.36(bioc 3.24)

proteomicsnormalizationpreprocessingmassspectrometryqualitycontroldataimportprostar2

5.84 score 1 stars 33 scripts 195 exports 96 dependencies

Last updated from:dd69c315c6. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE257
linux-devel-x86_64OK1107
source / vignettesOK991
linux-release-x86_64OK1110
macos-release-arm64OK790
macos-oldrel-arm64OK925
windows-develOK535
windows-releaseOK498
windows-oldrelOK512
wasm-releaseOK214

Exports:Add_Aggregated_rowDataAdd_Item_to_DatasetAdd2HistoryAdjMatFiltersaggQmetacellaggregateFeatures4ProstaraggregateMethodsaggregateRedistributionallPeptidesanalysisanalysis<-applyAnovasOnProteinsBuildAdjacencyMatrixBuildColumnToProteinDatasetbuildGraphBuildMetacellcheckConditionscheckDesignChildrenclassic1wayAnovaCleanRowDatacompareNormalizationD_HCcompute_t_testsConnectedCompConnectedComp<-ConvertListToHtmlCountPepcreateQFeaturescustom_metacell_colorsdesign_qfdesign_qf<-diffAnaComputeAdjustedPValuesdiffAnaComputeFDRdiffAnaVolcanoplot_rChartsDifferentialAnalysisDifferentialAnalysis<-displayCCvisNetExtendPaletteExtractUniquePeptidesfilenamefilename<-filterFeaturesOneSEfindMECBlockformatPHResultsfudge2LRTFunctionFilterGetColorsForConditionsgetDesignLevelGetDetailedNbPeptidesGetDetailedNbPeptidesUsedGetHistoryGetIndices_BasedOnConditionsGetIndices_FunFilteringGetIndices_WholeLineGetIndices_WholeMatrixgetListNbValuesInLinesGetMetacellTagsGetMetadataSlotGetNbPeptidesUsedGetNbTagsgetNumberOfEmptyLinesgetPepProtCCgetProteinsStatsgetQuantile4ImpGetSoftAvailablesGetUniqueTagsglobalAdjPvalGlobalQuantileAlignmentGraphPepProthc_logFC_DensityPlothc_mvTypePlot2heatmapForMissingValueshistPValue_HCHypothesisTestHypothesisTest<-idcolidcol<-imputePA2InitializeHistoryinnerAggregateIterinnerMeaninnerMedianinnerMedianpolishinnerRobustsummaryinnerSumisDifferentialisOfTypeisSubsetKeep_Items_from_Datasetlast_assayLH0LH0_lmLH1LH1_lmlimmaCompleteTestlistSheetsLOESSmainAssaymakeContrastmakeDesignmakeDesign1makeDesign2makeDesign3matchMetacellMeanCenteringmetacell_aggMetacell_DIA_NNMetacell_genericMetacell_maxquantMetacell_prolinemetacellDefMetacellFilteringScopemetacellHisto_HCmetacellPerLinesHisto_HCmetacellPerLinesHistoPerCondition_HCmetacombinemvImagen_assays_in_qfNAIsZeronames_metacellnames_metacell<-nEmptyLinesnonzeronormalizeFunctionnormalizeMethodsOWAnovaparamshistoryparamshistory<-ParentparentProtIdparentProtId<-pepaTestPipelinespkgsRequireplotCompareAssaysplotJitterplotJitter_rChartspostHocTestpushpvalueQFeaturesFromSEqMetacellqMetacell<-qMetacellFilteringScopeqMetacellOnConditionsqMetacellWholeLineqMetacellWholeMatrixQuantileCenteringreadExcelreIntroduceMECReplaceSpecialCharsRunAggregationsamLRTsearchMetacellTagsselect_topnseparateAdjPvalSet_POV_MEC_tagsSet_POV_MEC_tags2SetHistorysharedPeptidesspecPeptidessplitAdjacencyMatsubAdjMat_sharedPeptidessubAdjMat_specificPeptidessubAdjMat_topnPeptidesSumByColumnsSymFilteringOperatorstestAnovaModelstestDesigntopnFunctionstopnPeptidestranslatedRandomBetatypeDatasettypeDataset<-UpdateMetacellAfterImputationversionversion<-vsnwrapperCalibrationPlotwrapperClassic1wayAnovawrapperDaparImputeMIwrapperImputeDetQuantwrapperImputeFixedValuewrapperImputeKNNwrapperImputeMLEwrapperImputePAwrapperImputePA2wrapperImputeSLSAwrapperMVImagewrapperPiratwrite_Assay_To_ExcelWrite_RowDataWrite_SamplesData_to_Excelwrite2excelwriteExcelWriteHistory

Dependencies:abindAnnotationFilteraskpassbase64encBiobaseBiocBaseUtilsBiocGenericsbslibcachemcliclueclustercpp11crosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomefsgenericsGenomicRangesggplot2gluegraphgtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeMsCoreUtilsMultiAssayExperimentopensslopenxlsxotelpillarpkgconfigplotlyplyrpreprocessCorepromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryamlzip

Peptide workflow with DaparToolshed

Manon Gaudin, Samuel Wieczorek, Thomas Burger

Rendered fromDaparToolshed.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2026-04-09
Started: 2025-08-08

Readme and manuals

Help Manual

Help pageTopics
Adds an instance of 'SummarizedExperiment' to a 'QFeatures' objectAdd_Item_to_Dataset
Add row to historyAdd2History
Filter a peptide assay on the basis of its adjacency matrix.adjacency-matrix-filter AdjMatFilters allPeptides sharedPeptides specPeptides subAdjMat_sharedPeptides subAdjMat_specificPeptides subAdjMat_topnPeptides topnFunctions topnPeptides
iteratively applies OWAnova() on the features of an MSnSet objectapplyAnovasOnProteins
Function matrix of appartenance groupBuildAdjacencyMatrix
Display a CCbuildGraph
Metacell functionBuildMetacell
Check if the design is validcheckConditions
Check if the design is validcheckDesign
Names of all children of a nodeChildren
Function to perform a One-way Anova statistical test on a MsnBase datasetclassic1wayAnova
Clean row dataCleanRowData
Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'plotly'compareNormalizationD_HC
Compute a t-testcompute_t_tests
Convert a list to unnumbered HTML listConvertListToHtml
Creates an object of class 'QFeatures' from text file.createQFeatures
Aggregate an assay's quantitative featuresAdd_Aggregated_rowData aggQmetacell aggregateFeatures4Prostar aggregateFeatures4Prostar,QFeatures-method aggregateFeatures4Prostar,SummarizedExperiment-method aggregateMethods BuildColumnToProteinDataset CountPep DaparToolshed-aggregate ExtractUniquePeptides GetDetailedNbPeptides GetDetailedNbPeptidesUsed GetNbPeptidesUsed getProteinsStats GraphPepProt innerAggregateIter innerMean innerMedian innerMedianpolish innerRobustsummary innerSum metacell_agg RunAggregation select_topn
Aggregate an assay's quantitative features with shared peptide redistributionaggregateRedistribution aggregateRedistribution,QFeatures-method aggregateRedistribution,SummarizedExperiment-method DaparToolshed-aggregateRedistribution
Computes the adjusted p-valuesdiffAnaComputeAdjustedPValues
Computes the FDR corresponding to the p-values of the differential analysisdiffAnaComputeFDR
Volcanoplot of the differential analysisdiffAnaVolcanoplot_rCharts
Display a CCdisplayCCvisNet
Extends a base-palette of the package RColorBrewer to n colors.ExtendPalette
Extracts the FC and the FWER ajusted p-values and format them in a data.frameformatHSDResults
Format Limma resultsformatLimmaResult
Extract logFC and raw pvalues from multiple post-hoc models summariesformatPHResults
Extracts the FC and the raw p-values and format them in a data.frameformatPHTResults
Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statisticfudge2LRT
Builds a complete color palette for the conditions given in argumentGetColorsForConditions
Get design levelgetDesignLevel
Wrapper for the 'paramshistory' function.GetHistory
Search lines which respects request on one or more conditions.GetIndices_BasedOnConditions
Delete the lines in the matrix of intensities and the metadata table given their indices.GetIndices_FunFiltering
Search lines which respects query on all their elements.GetIndices_WholeLine
Search lines which respects request on one or more conditions.GetIndices_WholeMatrix
Returns the possible number of values in lines in the datagetListNbValuesInLines
Number of each metacell tagsGetNbTags
Returns the number of empty lines in the datagetNumberOfEmptyLines
Build the list of connex composant of the adjacency matrixgetPepProtCC
The set of available softwares to convert fromGetSoftAvailables
Computes the adjusted p-values on all the stacked contrasts using CP4PglobalAdjPval
Density plots of logFC valueshc_logFC_DensityPlot
Display a heatmap for data with missing valuesheatmapForMissingValues
Plots a histogram of p-valueshistPValue_HC
Missing values imputation from a 'MSnSet' objectimputePA2
Initialize the historyInitializeHistory
Identification of differentially abundant peptide/proteinisDifferential
Similar to the function 'is.na()' but focused on the equality with the paramter 'type'.isOfType
Check is a given set is a subset of another one.isSubset
Removes assay from a 'QFeatures' objectKeep_Items_from_Dataset
Compute the likelihood of the null hypothesis for the global modelLH0
Compute the likelihoods of the null hypothesis for the "local" component-wise modelLH0_lm
Compute the likelihood of the alternative hypothesis for the global modelLH1
Compute the likelihoods of the alternative hypothesis for the "local" component-wise modelLH1_lm
Computes a hierarchical differential analysislimmaCompleteTest
Builds the contrast matrixmakeContrast
Builds the design matrixmakeDesign
Builds the design matrix for designs of level 1makeDesign1
Builds the design matrix for designs of level 2makeDesign2
Builds the design matrix for designs of level 3makeDesign3
Similar to the function 'is.na()' but focused on the equality with the paramter 'type'.matchMetacell
Sets the metacell dataframe for datasets which are from Dia-NN softwareMetacell_DIA_NN
Sets the metacell dataframeMetacell_maxquant
Sets the metacell dataframe for datasets which are from Proline softwareMetacell_proline
Bar plot of missing values per lines using plotlyhc_mvTypePlot2 metacell-plots metacellHisto_HC metacellPerLinesHistoPerCondition_HC metacellPerLinesHisto_HC mvImage wrapperMVImage
Lists the metacell scopes for filteringMetacellFilteringScope
Finds the LAPALAfindMECBlock getQuantile4Imp mv_imputation_protein reIntroduceMEC wrapperImputeDetQuant wrapperImputeFixedValue wrapperImputeKNN wrapperImputePA wrapperImputeSLSA
Set NA values to 0NAIsZero
Number of empty lines in the datanEmptyLines
Retrieve the indices of non-zero elements in sparse matricesnonzero
NormalisationGlobalQuantileAlignment LOESS MeanCentering normalization_methods normalizeMethods QuantileCentering SumByColumns vsn
Normalisation for QFeaturesnormalizeFunction
This function exports a data.frame to a Excel file.listSheets output_2_Excel readExcel writeExcel WriteHistory write_Assay_To_Excel Write_RowData Write_SamplesData_to_Excel
Applies aov() on a vector of protein abundances using the design derived from the sample names (simple aov wrapper)OWAnova
List of metacell tagsanalysis analysis,QFeatures-method analysis,SummarizedExperiment-method analysis<- ConnectedComp ConnectedComp,QFeatures-method ConnectedComp,SummarizedExperiment-method ConnectedComp<- design_qf design_qf,QFeatures-method design_qf<- DifferentialAnalysis DifferentialAnalysis,QFeatures-method DifferentialAnalysis,SummarizedExperiment-method DifferentialAnalysis<- filename filename,QFeatures-method filename<- GetMetacellTags GetMetacellTags,data.frame-method GetMetacellTags,QFeatures-method GetMetacellTags,SummarizedExperiment-method GetMetadataSlot GetRowdataSlot GetUniqueTags GetUniqueTags,QFeatures-method GetUniqueTags,SummarizedExperiment-method HypothesisTest HypothesisTest,QFeatures-method HypothesisTest,SummarizedExperiment-method HypothesisTest<- idcol idcol,QFeatures-method idcol,SummarizedExperiment-method idcol<- mainAssay names_metacell names_metacell,QFeatures-method names_metacell,SummarizedExperiment-method names_metacell<- paramshistory paramshistory,QFeatures-method paramshistory,SummarizedExperiment-method paramshistory<- parentProtId parentProtId,QFeatures-method parentProtId,SummarizedExperiment-method parentProtId<- QFeatures-accessors qMetacell qMetacell,QFeatures-method qMetacell,SummarizedExperiment-method qMetacell<- typeDataset typeDataset,QFeatures-method typeDataset,SummarizedExperiment-method typeDataset<- version version,QFeatures-method version<-
Parent name of a nodeParent
PEptide based Protein differential Abundance testpepaTest
List of available pipelines in the packagePipelines
Loads packagespkgsRequire
Compare two assaysplotCompareAssays
Jitter plot of CCplotJitter
Display a a jitter plot for CCplotJitter_rCharts
Post-hoc tests for classic 1-way ANOVApostHocTest
Push p-values based on metacell tagspushpvalue
Quantitative metadata vocabulary for entitiescustom_metacell_colors metacellDef Metacell_generic metacombine q_metacell searchMetacellTags Set_POV_MEC_tags Set_POV_MEC_tags2 UpdateMetacellAfterImputation UpdateMetacellAfterImputation,SummarizedExperiment-method
Exports a 'QFeatures' object to a Excel file.addColors QFeatures-excel write2excel write2excel,QFeatures-method write2excel,SummarizedExperiment-method write2excelSE
Filter features of one SE based on their rowDataDaparToolsehd, filterFeaturesOneSE filterFeaturesOneSE, filterFeaturesOneSE,QFeatures-method FunctionFilter FunctionFilter, FunctionFilter-class QFeatures-filtering-oneSE VariableFilter
Utility funcitons to dela with QFeatures objects.last_assay n_assays_in_qf QFeatures-utils QFeaturesFromSE
Standardize namesReplaceSpecialChars
Computes a regularized version of the likelihood ratio statisticsamLRT
Computes the adjusted p-values separately on contrast using CP4PseparateAdjPval
Standardize namesSetHistory
splits an adjacency matrix into specific and sharedsplitAdjacencyMat
subR25pept datasetsubR25pept
subR25prot datasetsubR25prot
Search lines which respects request on one or more conditions.qMetacell-filter qMetacellFilteringScope qMetacellOnConditions qMetacellWholeLine qMetacellWholeMatrix SymFilteringOperators
Applies a statistical test on each element of a list of linear modelstestAnovaModels
Check the validity of the designtestDesign
Applies p-value adjustment using cp4p on p-values below a given thresholdthresholdpval4fdr
Generator of simulated valuestranslatedRandomBeta
Performs a calibration plot on an 'SummarizedExperiment' object, calling the 'cp4p' package functions.wrapperCalibrationPlot
Wrapper for One-way Anova statistical testwrapperClassic1wayAnova
Missing values imputation using the LSimpute algorithm.wrapperDaparImputeMI
Imputation of peptides having no values in a biological condition.wrapperImputeMLE
Missing values imputation from a 'SummarizedExperiment' objectwrapperImputePA2
Missing values imputation using PiratwrapperPirat