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

# 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:

subR25pept - SubR25pept dataset
subR25prot - SubR25prot dataset

On BioConductor:DaparToolshed-0.99.36(bioc 3.24)

proteomics normalization preprocessing massspectrometry qualitycontrol dataimport prostar2

6.14 score 2 stars 36 scripts 195 exports 96 dependencies

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

Target	Result	Time
bioc-checks	NOTE	241
linux-devel-x86_64	OK	1057
source / vignettes	OK	977
linux-release-x86_64	OK	1138
macos-release-arm64	OK	739
macos-oldrel-arm64	OK	837
windows-devel	OK	438
windows-release	OK	479
windows-oldrel	OK	430
wasm-release	OK	220

Exports:Add_Aggregated_rowData Add_Item_to_Dataset Add2History AdjMatFilters aggQmetacell aggregateFeatures4Prostar aggregateMethods aggregateRedistribution allPeptides analysis analysis<-applyAnovasOnProteins BuildAdjacencyMatrix BuildColumnToProteinDataset buildGraph BuildMetacell checkConditions checkDesign Children classic1wayAnova CleanRowData compareNormalizationD_HC compute_t_tests ConnectedComp ConnectedComp<-ConvertListToHtml CountPep createQFeatures custom_metacell_colors design_qf design_qf<-diffAnaComputeAdjustedPValues diffAnaComputeFDR diffAnaVolcanoplot_rCharts DifferentialAnalysis DifferentialAnalysis<-displayCCvisNet ExtendPalette ExtractUniquePeptides filename filename<-filterFeaturesOneSE findMECBlock formatPHResults fudge2LRT FunctionFilter GetColorsForConditions getDesignLevel GetDetailedNbPeptides GetDetailedNbPeptidesUsed GetHistory GetIndices_BasedOnConditions GetIndices_FunFiltering GetIndices_WholeLine GetIndices_WholeMatrix getListNbValuesInLines GetMetacellTags GetMetadataSlot GetNbPeptidesUsed GetNbTags getNumberOfEmptyLines getPepProtCC getProteinsStats getQuantile4Imp GetSoftAvailables GetUniqueTags globalAdjPval GlobalQuantileAlignment GraphPepProt hc_logFC_DensityPlot hc_mvTypePlot2 heatmapForMissingValues histPValue_HC HypothesisTest HypothesisTest<-idcol idcol<-imputePA2 InitializeHistory innerAggregateIter innerMean innerMedian innerMedianpolish innerRobustsummary innerSum isDifferential isOfType isSubset Keep_Items_from_Dataset last_assay LH0 LH0_lm LH1 LH1_lm limmaCompleteTest listSheets LOESS mainAssay makeContrast makeDesign makeDesign1 makeDesign2 makeDesign3 matchMetacell MeanCentering metacell_agg Metacell_DIA_NN Metacell_generic Metacell_maxquant Metacell_proline metacellDef MetacellFilteringScope metacellHisto_HC metacellPerLinesHisto_HC metacellPerLinesHistoPerCondition_HC metacombine mvImage n_assays_in_qf NAIsZero names_metacell names_metacell<-nEmptyLines nonzero normalizeFunction normalizeMethods OWAnova paramshistory paramshistory<-Parent parentProtId parentProtId<-pepaTest Pipelines pkgsRequire plotCompareAssays plotJitter plotJitter_rCharts postHocTest pushpvalue QFeaturesFromSE qMetacell qMetacell<-qMetacellFilteringScope qMetacellOnConditions qMetacellWholeLine qMetacellWholeMatrix QuantileCentering readExcel reIntroduceMEC ReplaceSpecialChars RunAggregation samLRT searchMetacellTags select_topn separateAdjPval Set_POV_MEC_tags Set_POV_MEC_tags2 SetHistory sharedPeptides specPeptides splitAdjacencyMat subAdjMat_sharedPeptides subAdjMat_specificPeptides subAdjMat_topnPeptides SumByColumns SymFilteringOperators testAnovaModels testDesign topnFunctions topnPeptides translatedRandomBeta typeDataset typeDataset<-UpdateMetacellAfterImputation version version<-vsn wrapperCalibrationPlot wrapperClassic1wayAnova wrapperDaparImputeMI wrapperImputeDetQuant wrapperImputeFixedValue wrapperImputeKNN wrapperImputeMLE wrapperImputePA wrapperImputePA2 wrapperImputeSLSA wrapperMVImage wrapperPirat write_Assay_To_Excel Write_RowData Write_SamplesData_to_Excel write2excel writeExcel WriteHistory

Dependencies:abind AnnotationFilter askpass base64enc Biobase BiocBaseUtils BiocGenerics bslib cachem cli clue cluster cpp11 crosstalk curl data.table DelayedArray digest dplyr evaluate farver fastmap fontawesome fs generics GenomicRanges ggplot2 glue graph gtable highr htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime MsCoreUtils MultiAssayExperiment openssl openxlsx otel pillar pkgconfig plotly plyr preprocessCore promises ProtGenerics purrr QFeatures R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XVector yaml zip

Peptide workflow with DaparToolshed

Rendered fromDaparToolshed.Rmdusingknitr::rmarkdown

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

Help page	Topics
Adds an instance of 'SummarizedExperiment' to a 'QFeatures' object	Add_Item_to_Dataset
Add row to history	Add2History
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 object	applyAnovasOnProteins
Function matrix of appartenance group	BuildAdjacencyMatrix
Display a CC	buildGraph
Metacell function	BuildMetacell
Check if the design is valid	checkConditions
Check if the design is valid	checkDesign
Names of all children of a node	Children
Function to perform a One-way Anova statistical test on a MsnBase dataset	classic1wayAnova
Clean row data	CleanRowData
Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'plotly'	compareNormalizationD_HC
Compute a t-test	compute_t_tests
Convert a list to unnumbered HTML list	ConvertListToHtml
Creates an object of class 'QFeatures' from text file.	createQFeatures
Aggregate an assay's quantitative features	Add_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 redistribution	aggregateRedistribution aggregateRedistribution,QFeatures-method aggregateRedistribution,SummarizedExperiment-method DaparToolshed-aggregateRedistribution
Computes the adjusted p-values	diffAnaComputeAdjustedPValues
Computes the FDR corresponding to the p-values of the differential analysis	diffAnaComputeFDR
Volcanoplot of the differential analysis	diffAnaVolcanoplot_rCharts
Display a CC	displayCCvisNet
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.frame	formatHSDResults
Format Limma results	formatLimmaResult
Extract logFC and raw pvalues from multiple post-hoc models summaries	formatPHResults
Extracts the FC and the raw p-values and format them in a data.frame	formatPHTResults
Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic	fudge2LRT
Builds a complete color palette for the conditions given in argument	GetColorsForConditions
Get design level	getDesignLevel
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 data	getListNbValuesInLines
Number of each metacell tags	GetNbTags
Returns the number of empty lines in the data	getNumberOfEmptyLines
Build the list of connex composant of the adjacency matrix	getPepProtCC
The set of available softwares to convert from	GetSoftAvailables
Computes the adjusted p-values on all the stacked contrasts using CP4P	globalAdjPval
Density plots of logFC values	hc_logFC_DensityPlot
Display a heatmap for data with missing values	heatmapForMissingValues
Plots a histogram of p-values	histPValue_HC
Missing values imputation from a 'MSnSet' object	imputePA2
Initialize the history	InitializeHistory
Identification of differentially abundant peptide/protein	isDifferential
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' object	Keep_Items_from_Dataset
Compute the likelihood of the null hypothesis for the global model	LH0
Compute the likelihoods of the null hypothesis for the "local" component-wise model	LH0_lm
Compute the likelihood of the alternative hypothesis for the global model	LH1
Compute the likelihoods of the alternative hypothesis for the "local" component-wise model	LH1_lm
Computes a hierarchical differential analysis	limmaCompleteTest
Builds the contrast matrix	makeContrast
Builds the design matrix	makeDesign
Builds the design matrix for designs of level 1	makeDesign1
Builds the design matrix for designs of level 2	makeDesign2
Builds the design matrix for designs of level 3	makeDesign3
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 software	Metacell_DIA_NN
Sets the metacell dataframe	Metacell_maxquant
Sets the metacell dataframe for datasets which are from Proline software	Metacell_proline
Bar plot of missing values per lines using plotly	hc_mvTypePlot2 metacell-plots metacellHisto_HC metacellPerLinesHistoPerCondition_HC metacellPerLinesHisto_HC mvImage wrapperMVImage
Lists the metacell scopes for filtering	MetacellFilteringScope
Finds the LAPALA	findMECBlock getQuantile4Imp mv_imputation_protein reIntroduceMEC wrapperImputeDetQuant wrapperImputeFixedValue wrapperImputeKNN wrapperImputePA wrapperImputeSLSA
Set NA values to 0	NAIsZero
Number of empty lines in the data	nEmptyLines
Retrieve the indices of non-zero elements in sparse matrices	nonzero
Normalisation	GlobalQuantileAlignment LOESS MeanCentering normalization_methods normalizeMethods QuantileCentering SumByColumns vsn
Normalisation for QFeatures	normalizeFunction
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 tags	analysis 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 node	Parent
PEptide based Protein differential Abundance test	pepaTest
List of available pipelines in the package	Pipelines
Loads packages	pkgsRequire
Compare two assays	plotCompareAssays
Jitter plot of CC	plotJitter
Display a a jitter plot for CC	plotJitter_rCharts
Post-hoc tests for classic 1-way ANOVA	postHocTest
Push p-values based on metacell tags	pushpvalue
Quantitative metadata vocabulary for entities	custom_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 rowData	DaparToolsehd, 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 names	ReplaceSpecialChars
Computes a regularized version of the likelihood ratio statistic	samLRT
Computes the adjusted p-values separately on contrast using CP4P	separateAdjPval
Standardize names	SetHistory
splits an adjacency matrix into specific and shared	splitAdjacencyMat
subR25pept dataset	subR25pept
subR25prot dataset	subR25prot
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 models	testAnovaModels
Check the validity of the design	testDesign
Applies p-value adjustment using cp4p on p-values below a given threshold	thresholdpval4fdr
Generator of simulated values	translatedRandomBeta
Performs a calibration plot on an 'SummarizedExperiment' object, calling the 'cp4p' package functions.	wrapperCalibrationPlot
Wrapper for One-way Anova statistical test	wrapperClassic1wayAnova
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' object	wrapperImputePA2
Missing values imputation using Pirat	wrapperPirat

Package: DaparToolshed 0.99.36

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

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