{ "_id": "6a1ee73ab401979e734116ef", "Package": "DaparToolshed", "Type": "Package", "Title": "Tools for the Differential Analysis of Proteins Abundance with R", "Version": "0.99.36", "Date": "2026-05-07", "Authors@R": "c(\nperson(given = \"Samuel\", family = \"Wieczorek\",\nemail = \"samuel.wieczorek@cea.fr\", role = c(\"cre\", \"aut\"),\ncomment=c(ORCID=\"0000-0002-5016-1203\")),\nperson(given = \"Thomas\", family =\"Burger\",\nemail = \"thomas.burger@cea.fr\", role = c(\"aut\")),\nperson(given = \"Enora\", family =\"Fremy\",\nemail = \"enora.fremy@cea.fr\", role = c(\"ctb\")),\nperson(given = \"Manon\", family =\"Gaudin\",\nemail = \"manon.gaudin@cea.fr\", role = c(\"ctb\"))\n)", "Description": "The package DaparToolshed is a Bioconductor distributed R\npackage which provides all the necessary functions to analyze\nquantitative data from label-free proteomics experiments. It is\nan update of our previous package DAPAR and contains more\nfunctions to analyze the data and uses MultAssayExperiment and\nSummarizedExperiment data structures. Contrarily to most other\nsimilar R packages, it is endowed with rich and user-friendly\ngraphical interfaces, so that no programming skill is required\n(see `Prostar` package).", "URL": "https://github.com/edyp-lab/DaparToolshed,\nhttps://edyp-lab.github.io/DaparToolshed/", "BugReports": "https://github.com/edyp-lab/DaparToolshed/issues", "License": "Artistic-2.0", "biocViews": "Proteomics, Normalization, Preprocessing, MassSpectrometry,\nQualityControl, DataImport", "NeedsCompilation": "no", "Collate": "history_utils.R plots_volcano.R DiffAnalysis.R\nadjacencyMatrix.R plots_compare_assays.R\nmissingValuesImputation_ProteinLevel.R\nmissingValuesImputation_PeptideLevel.R hypothesisTest_plot.R\nanova_analysis.R compute.t.tests.R limmaAnalysis.R\nplots_normalization.R funcs_FunctionFiltering.R plot_metacell.R\nfuncs_normalize.R doc-data.R QFeatures_utils.R output2Excel.R\nDaparToolshed_Params_Addons.R metacell.R\nDaparToolshed_filter_Adjmat.R 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Same as compareNormalizationD but uses the library 'plotly'", "topics": [ "compareNormalizationD_HC" ] }, { "page": "compute_t_tests", "title": "Compute a t-test", "topics": [ "compute_t_tests" ] }, { "page": "ConvertListToHtml", "title": "Convert a list to unnumbered HTML list", "topics": [ "ConvertListToHtml" ] }, { "page": "import-export-QFeatures", "title": "Creates an object of class 'QFeatures' from text file.", "topics": [ "createQFeatures" ] }, { "page": "DaparToolshed-aggregate", "title": "Aggregate an assay's quantitative features", "topics": [ "Add_Aggregated_rowData", "aggQmetacell", "aggregateFeatures4Prostar", "aggregateFeatures4Prostar,QFeatures-method", "aggregateFeatures4Prostar,SummarizedExperiment-method", "aggregateMethods", "BuildColumnToProteinDataset", "CountPep", "DaparToolshed-aggregate", "ExtractUniquePeptides", "GetDetailedNbPeptides", "GetDetailedNbPeptidesUsed", "GetNbPeptidesUsed", "getProteinsStats", "GraphPepProt", "innerAggregateIter", "innerMean", 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"title": "Extends a base-palette of the package RColorBrewer to n colors.", "topics": [ "ExtendPalette" ] }, { "page": "formatHSDResults", "title": "Extracts the FC and the FWER ajusted p-values and format them in a data.frame", "topics": [ "formatHSDResults" ] }, { "page": "formatLimmaResult", "title": "Format Limma results", "topics": [ "formatLimmaResult" ] }, { "page": "formatPHResults", "title": "Extract logFC and raw pvalues from multiple post-hoc models summaries", "topics": [ "formatPHResults" ] }, { "page": "formatPHTResults", "title": "Extracts the FC and the raw p-values and format them in a data.frame", "topics": [ "formatPHTResults" ] }, { "page": "fudge2LRT", "title": "Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic", "topics": [ "fudge2LRT" ] }, { "page": "GetColorsForConditions", "title": "Builds a complete color palette for the conditions given in argument", "topics": [ 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"page": "imputePA2", "title": "Missing values imputation from a 'MSnSet' object", "topics": [ "imputePA2" ] }, { "page": "InitializeHistory", "title": "Initialize the history", "topics": [ "InitializeHistory" ] }, { "page": "isDifferential", "title": "Identification of differentially abundant peptide/protein", "topics": [ "isDifferential" ] }, { "page": "isOfType", "title": "Similar to the function 'is.na()' but focused on the equality with the paramter 'type'.", "topics": [ "isOfType" ] }, { "page": "isSubset", "title": "Check is a given set is a subset of another one.", "topics": [ "isSubset" ] }, { "page": "Keep_Items_from_Dataset", "title": "Removes assay from a 'QFeatures' object", "topics": [ "Keep_Items_from_Dataset" ] }, { "page": "LH0", "title": "Compute the likelihood of the null hypothesis for the global model", "topics": [ "LH0" ] }, { "page": "LH0_lm", "title": "Compute the likelihoods of the null hypothesis for the \"local\" component-wise model", "topics": [ "LH0_lm" ] }, { "page": "LH1", "title": "Compute the likelihood of the alternative hypothesis for the global model", "topics": [ "LH1" ] }, { "page": "LH1_lm", "title": "Compute the likelihoods of the alternative hypothesis for the \"local\" component-wise model", "topics": [ "LH1_lm" ] }, { "page": "limmaCompleteTest", "title": "Computes a hierarchical differential analysis", "topics": [ "limmaCompleteTest" ] }, { "page": "makeContrast", "title": "Builds the contrast matrix", "topics": [ "makeContrast" ] }, { "page": "makeDesign", "title": "Builds the design matrix", "topics": [ "makeDesign" ] }, { "page": "makeDesign1", "title": "Builds the design matrix for designs of level 1", "topics": [ "makeDesign1" ] }, { "page": "makeDesign2", "title": "Builds the design matrix for designs of level 2", "topics": [ "makeDesign2" ] }, { "page": "makeDesign3", "title": "Builds the design matrix for designs of level 3", "topics": [ "makeDesign3" ] }, { "page": "matchMetacell", "title": "Similar to the function 'is.na()' but focused on the equality with the paramter 'type'.", "topics": [ "matchMetacell" ] }, { "page": "Metacell_DIA_NN", "title": "Sets the metacell dataframe for datasets which are from Dia-NN software", "topics": [ "Metacell_DIA_NN" ] }, { "page": "Metacell_maxquant", "title": "Sets the metacell dataframe", "topics": [ "Metacell_maxquant" ] }, { "page": "Metacell_proline", "title": "Sets the metacell dataframe for datasets which are from Proline software", "topics": [ "Metacell_proline" ] }, { "page": "metacell-plots", "title": "Bar plot of missing values per lines using plotly", "topics": [ "hc_mvTypePlot2", "metacell-plots", "metacellHisto_HC", "metacellPerLinesHistoPerCondition_HC", "metacellPerLinesHisto_HC", "mvImage", "wrapperMVImage" ] }, { "page": "MetacellFilteringScope", "title": "Lists the metacell scopes for filtering", "topics": [ "MetacellFilteringScope" ] }, { "page": "mv_imputation_protein", "title": "Finds the LAPALA", "topics": [ "findMECBlock", "getQuantile4Imp", "mv_imputation_protein", "reIntroduceMEC", "wrapperImputeDetQuant", "wrapperImputeFixedValue", "wrapperImputeKNN", "wrapperImputePA", "wrapperImputeSLSA" ] }, { "page": "NAIsZero", "title": "Set NA values to 0", "topics": [ "NAIsZero" ] }, { "page": "nEmptyLines", "title": "Number of empty lines in the data", "topics": [ "nEmptyLines" ] }, { "page": "nonzero", "title": "Retrieve the indices of non-zero elements in sparse matrices", "topics": [ "nonzero" ] }, { "page": "normalization_methods", "title": "Normalisation", "topics": [ "GlobalQuantileAlignment", "LOESS", "MeanCentering", "normalization_methods", "normalizeMethods", "QuantileCentering", "SumByColumns", "vsn" ] }, { "page": "normalizeFunction", "title": "Normalisation for QFeatures", "topics": [ "normalizeFunction" ] }, { "page": "output_2_Excel", "title": "This function exports a data.frame to a Excel file.", "topics": [ "listSheets", "output_2_Excel", "readExcel", "writeExcel", "WriteHistory", "write_Assay_To_Excel", "Write_RowData", "Write_SamplesData_to_Excel" ] }, { "page": "OWAnova", "title": "Applies aov() on a vector of protein abundances using the design derived from the sample names (simple aov wrapper)", "topics": [ "OWAnova" ] }, { "page": "QFeatures-accessors", "title": "List of metacell tags", "topics": [ "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<-" ] }, { "page": "Parent", "title": "Parent name of a node", "topics": [ "Parent" ] }, { "page": "pepaTest", "title": "PEptide based Protein differential Abundance test", "topics": [ "pepaTest" ] }, { "page": "Pipelines", "title": "List of available pipelines in the package", "topics": [ "Pipelines" ] }, { "page": "pkgsRequire", "title": "Loads packages", "topics": [ "pkgsRequire" ] }, { "page": "compare-assays", "title": "Compare two assays", "topics": [ "plotCompareAssays" ] }, { "page": "plotJitter", "title": "Jitter plot of CC", "topics": [ "plotJitter" ] }, { "page": "plotJitter_rCharts", "title": "Display a a jitter plot for CC", "topics": [ "plotJitter_rCharts" ] }, { "page": "postHocTest", "title": "Post-hoc tests for classic 1-way ANOVA", "topics": [ "postHocTest" ] }, { "page": "pushpvalue", "title": "Push p-values based on metacell tags", "topics": [ "pushpvalue" ] }, { "page": "q_metacell", "title": "Quantitative metadata vocabulary for entities", "topics": [ "custom_metacell_colors", "metacellDef", "Metacell_generic", "metacombine", "q_metacell", "searchMetacellTags", "Set_POV_MEC_tags", "Set_POV_MEC_tags2", "UpdateMetacellAfterImputation", "UpdateMetacellAfterImputation,SummarizedExperiment-method" ] }, { "page": "QFeatures-excel", "title": "Exports a 'QFeatures' object to a Excel file.", "topics": [ "addColors", "QFeatures-excel", "write2excel", "write2excel,QFeatures-method", "write2excel,SummarizedExperiment-method", "write2excelSE" ] }, { "page": "QFeatures-filtering-oneSE", "title": "Filter features of one SE based on their rowData", "topics": [ "DaparToolsehd,", "filterFeaturesOneSE", "filterFeaturesOneSE,", "filterFeaturesOneSE,QFeatures-method", "FunctionFilter", "FunctionFilter,", "FunctionFilter-class", "QFeatures-filtering-oneSE", "VariableFilter" ] }, { "page": "QFeatures-utils", "title": "Utility funcitons to dela with QFeatures objects.", "topics": [ "last_assay", "n_assays_in_qf", "QFeatures-utils", "QFeaturesFromSE" ] }, { "page": "ReplaceSpecialChars", "title": "Standardize names", "topics": [ "ReplaceSpecialChars" ] }, { "page": "samLRT", "title": "Computes a regularized version of the likelihood ratio statistic", "topics": [ "samLRT" ] }, { "page": "separateAdjPval", "title": "Computes the adjusted p-values separately on contrast using CP4P", "topics": [ "separateAdjPval" ] }, { "page": "SetHistory", "title": "Standardize names", "topics": [ "SetHistory" ] }, { "page": "splitAdjacencyMat", "title": "splits an adjacency matrix into specific and shared", "topics": [ "splitAdjacencyMat" ] }, { "page": "subR25pept", "title": "subR25pept dataset", "topics": [ "subR25pept" ] }, { "page": "subR25prot", "title": "subR25prot dataset", "topics": [ "subR25prot" ] }, { "page": "qMetacell-filter", "title": "Search lines which respects request on one or more conditions.", "topics": [ "qMetacell-filter", "qMetacellFilteringScope", "qMetacellOnConditions", "qMetacellWholeLine", "qMetacellWholeMatrix", "SymFilteringOperators" ] }, { "page": "testAnovaModels", "title": "Applies a statistical test on each element of a list of linear models", "topics": [ "testAnovaModels" ] }, { "page": "testDesign", "title": "Check the validity of the design", "topics": [ "testDesign" ] }, { "page": "thresholdpval4fdr", "title": "Applies p-value adjustment using cp4p on p-values below a given threshold", "topics": [ "thresholdpval4fdr" ] }, { "page": "translatedRandomBeta", "title": "Generator of simulated values", "topics": [ "translatedRandomBeta" ] }, { "page": "wrapperCalibrationPlot", "title": "Performs a calibration plot on an 'SummarizedExperiment' object, calling the 'cp4p' package functions.", "topics": [ "wrapperCalibrationPlot" ] }, { "page": "wrapperClassic1wayAnova", "title": "Wrapper for One-way Anova statistical test", "topics": [ "wrapperClassic1wayAnova" ] }, { "page": "wrapperDaparImputeMI", "title": "Missing values imputation using the LSimpute algorithm.", "topics": [ "wrapperDaparImputeMI" ] }, { "page": "wrapperImputeMLE", "title": "Imputation of peptides having no values in a biological condition.", "topics": [ "wrapperImputeMLE" ] }, { "page": "wrapperImputePA2", "title": "Missing values imputation from a 'SummarizedExperiment' object", "topics": [ "wrapperImputePA2" ] }, { "page": "wrapperPirat", "title": "Missing values imputation using Pirat", "topics": [ "wrapperPirat" ] } ], "_readme": "https://github.com/bioc/DaparToolshed/raw/HEAD/README.md", "_rundeps": [ "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", 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information", "References" ], "created": "2025-08-08 08:48:46", "modified": "2026-04-09 06:02:14", "commits": 16 } ], "_score": 5.840733234611807, "_indexed": true, "_nocasepkg": "dapartoolshed", "_universes": [ "bioc", "samwieczorek", "edyp-lab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.36", "date": "2026-05-19T19:21:56.000Z", "distro": "noble", "commit": "dd69c315c69f443771cf70f41b7d57e3f11f259a", "fileid": "e27d4f617d844dc8846a38880c28a98809e98291a0aeb74966bb29cdb5e2c091", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26118777676" }, { "r": "4.6.0", "os": "linux", "version": "0.99.36", "date": "2026-05-19T19:22:04.000Z", "distro": "noble", "commit": "dd69c315c69f443771cf70f41b7d57e3f11f259a", "fileid": "662bad87b63ae59c6a13c4c87935a06affde920a13b67c11f502b4bbb093f515", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26118777676" }, { "r": "4.5.3", "os": "mac", 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