{ "_id": "6a17f019acfb0bcc41da697e", "Package": "DAPAR", "Type": "Package", "Title": "Tools for the Differential Analysis of Proteins Abundance with R", "Description": "The package DAPAR is a Bioconductor distributed R package\nwhich provides all the necessary functions to analyze\nquantitative data from label-free proteomics experiments.\nContrarily to most other similar R packages, it is endowed with\nrich and user-friendly graphical interfaces, so that no\nprogramming skill is required (see `Prostar` package).", "Version": "1.45.0", "Date": "2026-04-13", "Authors@R": "c(person(given = \"Samuel\", family = \"Wieczorek\",\nemail = \"samuel.wieczorek@cea.fr\", role = c(\"cre\", \"aut\")),\nperson(given = \"Florence\", family =\"Combes\",\nemail = \"florence.combes@cea.fr\", role = \"aut\"),\nperson(given = \"Thomas\", family =\"Burger\",\nemail = \"thomas.burger@cea.fr\", role = \"aut\"),\nperson(given = \"Vasile-Cosmin\", family =\"Lazar\",\nemail = \"vcosminlazar@gmail.com\", role = \"ctb\"),\nperson(given = \"Enora\", family =\"Fremy\",\nemail = \"enora.fremy@cea.fr\", role = \"ctb\"),\nperson(given = \"Helene\", family =\"Borges\",\nemail = \"helene.borges@cea.fr\", role = \"ctb\"),\nperson(given = \"Manon\", family = \"Gaudin\",\nemail = \"manon.gaudin@cea.fr\", role = c(\"ctb\")))", "License": "Artistic-2.0", "VignetteBuilder": "knitr", "biocViews": "Proteomics, Normalization, Preprocessing, MassSpectrometry,\nQualityControl, GO, DataImport", "NeedsCompilation": "no", "RoxygenNote": "7.3.3", "Packaged": { "Date": "2026-05-28 06:40:32 UTC", "User": "root" }, "Encoding": "UTF-8", "URL": "http://www.prostar-proteomics.org/", "BugReports": "https://github.com/edyp-lab/DAPAR/issues", "Collate": "agregation.R anova_analysis.R bioAnalysis.R clustering.R\ndataset_Validity.R compute.t.tests.R DiffAnalysis.R\nget_pep_prot_cc.R metacell.R inOutFiles.R limmaAnalysis.R\nlogText.R missingValuesFilter.R\nmissingValuesImputation_PeptideLevel.R\nmissingValuesImputation_ProteinLevel.R normalize.R pepa.R\nplots_boxplot.R plots_compare_Norm.R plots_corr_matrix.R\nplots_density.R plots_density_CV.R plots_heatmaps.R plots_pca.R\nplots_violin.R utils.R volcanoPlot.R palette.R hypothesisTest.R\nmetacell_Plots.R zzz.R", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:41:57 UTC", "RemoteUrl": "https://github.com/bioc/DAPAR", "RemoteRef": "HEAD", "RemoteSha": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "Author": "Samuel Wieczorek [cre, aut],\nFlorence Combes [aut],\nThomas Burger [aut],\nVasile-Cosmin Lazar [ctb],\nEnora Fremy [ctb],\nHelene Borges [ctb],\nManon Gaudin [ctb]", "Maintainer": "Samuel Wieczorek ", "MD5sum": "c70ff5b7e568d67e76c35b6853e71330", "_user": "bioc", "_type": "src", "_file": "DAPAR_1.45.0.tar.gz", "_fileid": "d9dc565b69a273a1020cd0ba7a00b407d62921e537fb819d549d9a5a1a149bdc", "_filesize": 563351, "_sha256": "d9dc565b69a273a1020cd0ba7a00b407d62921e537fb819d549d9a5a1a149bdc", "_created": "2026-05-28T06:40:32.000Z", "_published": "2026-05-28T07:34:49.109Z", "_jobs": [ { "job": 78237681562, "time": 286, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7259394414" }, { "job": 78237681580, "time": 569, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7259463067" }, { "job": 78237681625, "time": 652, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7259483906" }, { "job": 78237681642, "time": 393, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7260188924" }, { "job": 78237681620, "time": 345, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7260171285" }, { "job": 78236819338, "time": 423, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259324953" }, { "job": 78237681573, "time": 252, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7259385705" }, { "job": 78237681612, "time": 542, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7259456714" }, { "job": 78237681621, "time": 493, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7259444331" }, { "job": 78237681607, "time": 523, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7259451512" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558863920", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/DAPAR", "_commit": { "id": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380117 }, "_maintainer": { "name": "Samuel Wieczorek", "email": "samuel.wieczorek@cea.fr", "login": "samwieczorek", "description": "", "uuid": 2912670 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "Biobase", "role": "Imports" }, { "package": "MSnbase", "role": "Imports" }, { "package": "DAPARdata", "version": ">= 1.30.0", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "clusterProfiler", "role": "Suggests" }, { "package": "graph", "role": "Suggests" }, { "package": "diptest", "role": "Suggests" }, { "package": "cluster", "role": "Suggests" }, { "package": "vioplot", "role": "Suggests" }, { "package": "visNetwork", "role": "Suggests" }, { "package": "vsn", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "FactoMineR", "role": "Suggests" }, { "package": "factoextra", "role": "Suggests" }, { "package": "dendextend", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" }, { "package": "doParallel", "role": "Suggests" }, { "package": "Mfuzz", "role": "Suggests" }, { "package": "apcluster", "role": "Suggests" }, { "package": "forcats", "role": "Suggests" }, { "package": "readxl", "role": "Suggests" }, { "package": "openxlsx", "role": "Suggests" }, { "package": "multcomp", "role": "Suggests" }, { "package": "purrr", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "norm", "role": "Suggests" }, { "package": "scales", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "cp4p", "role": "Suggests" }, { "package": "imp4p", "version": ">= 1.1", "role": "Suggests" }, { "package": "lme4", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "preprocessCore", "role": "Suggests" }, { "package": "stringr", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "impute", "role": "Suggests" }, { "package": "gplots", "role": "Suggests" }, { "package": "grDevices", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "graphics", "role": "Suggests" }, { "package": "stats", "role": "Suggests" }, { "package": "methods", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "org.Sc.sgd.db", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-16", "n": 2 }, { "week": "2026-17", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "proteomics", "normalization", "preprocessing", "massspectrometry", "qualitycontrol", "go", "dataimport", "prostar1" ], "_stars": 2, "_contributors": [ { "user": "samwieczorek", "count": 505, "uuid": 2912670 }, { "user": "helbor", "count": 27, "uuid": 22997995 }, { "user": "enorafremy", "count": 21, "uuid": 57791608 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "combesf", "count": 10, "uuid": 29479051 }, { "user": "jwokaty", "count": 9, "uuid": 1744257 }, { "user": "dtenenba", "count": 8, "uuid": 2286826 }, { "user": "hpages", "count": 4, "uuid": 8810451 }, { "user": "thomasburger", "count": 4, "uuid": 5259649 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 }, { "user": "samuelwieczorek", "count": 1, "uuid": 71639216 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 512, "source": "https://www.bioconductor.org/packages/stats/bioc/DAPAR" }, "_mentions": 5, "_devurl": "https://github.com/edyp-lab/dapar", "_searchresults": 21, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DAPAR.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_homeurl": "https://github.com/edyp-lab/dapar", "_realowner": "bioc", "_cranurl": false, "_exports": [ "aggregateIter", "aggregateIterParallel", "aggregateMean", "AggregateMetacell", "aggregateSum", "aggregateTopn", "applyAnovasOnProteins", "averageIntensities", "barplotEnrichGO_HC", "barplotGroupGO_HC", "boxPlotD_HC", "BuildAdjacencyMatrix", "BuildColumnToProteinDataset", "buildGraph", "BuildMetaCell", "Check_Dataset_Validity", "Check_NbValues_In_Columns", "check.conditions", "check.design", "checkClusterability", "Children", "classic1wayAnova", "compareNormalizationD_HC", "compute_t_tests", "compute.selection.table", "corrMatrixD_HC", "CountPep", "createMSnset", "createMSnset2", "CVDistD_HC", "deleteLinesFromIndices", "densityPlotD_HC", "diffAnaComputeAdjustedPValues", "diffAnaComputeFDR", "diffAnaGetSignificant", "diffAnaSave", "diffAnaVolcanoplot", "diffAnaVolcanoplot_rCharts", "display.CC.visNet", "enrich_GO", "ExtendPalette", "finalizeAggregation", "findMECBlock", "formatPHResults", "fudge2LRT", "Get_AllComparisons", "get.pep.prot.cc", "GetCC", "GetColorsForConditions", "getDesignLevel", "GetDetailedNbPeptides", "GetDetailedNbPeptidesUsed", "GetIndices_BasedOnConditions", "GetIndices_MetacellFiltering", "GetIndices_WholeLine", "GetIndices_WholeMatrix", "getIndicesConditions", "getIndicesOfLinesToRemove", "GetKeyId", "getListNbValuesInLines", "GetMatAdj", "GetMetacell", "GetMetacellTags", "GetNbPeptidesUsed", "GetNbTags", "getNumberOf", "getNumberOfEmptyLines", "getPourcentageOfMV", "getProcessingInfo", "getProteinsStats", "getQuantile4Imp", "GetSoftAvailables", "getTextForAggregation", "getTextForAnaDiff", "getTextForFiltering", "getTextForGOAnalysis", "getTextForHypothesisTest", "getTextForNewDataset", "getTextForNormalization", "getTextForpeptideImputation", "getTextForproteinImputation", "GetTypeofData", "GetUniqueTags", "globalAdjPval", "GlobalQuantileAlignment", "GOAnalysisSave", "GraphPepProt", "group_GO", "hc_logFC_DensityPlot", "hc_mvTypePlot2", "heatmapD", "heatmapForMissingValues", "histPValue_HC", "impute.pa2", "inner.aggregate.iter", "inner.aggregate.topn", "inner.mean", "inner.sum", "is.subset", "LH0", "LH0.lm", "LH1", "LH1.lm", "limmaCompleteTest", "listSheets", "LOESS", "make.contrast", "make.design", "make.design.1", "make.design.2", "make.design.3", "match.metacell", "MeanCentering", "Metacell_DIA_NN", "Metacell_generic", "Metacell_maxquant", "Metacell_proline", "metacell.def", "MetaCellFiltering", "MetacellFilteringScope", "metacellHisto_HC", "metacellPerLinesHisto_HC", "metacellPerLinesHistoPerCondition_HC", "metacombine", "mvImage", "nonzero", "normalizeMethods.dapar", "NumericalFiltering", "NumericalgetIndicesOfLinesToRemove", "OWAnova", "Parent", "pepa.test", "pkgs.require", "plotJitter", "plotJitter_rCharts", "plotPCA_Eigen", "plotPCA_Eigen_hc", "plotPCA_Ind", "plotPCA_Var", "postHocTest", "proportionConRev_HC", "QuantileCentering", "rbindMSnset", "readExcel", "reIntroduceMEC", "removeLines", "samLRT", "saveParameters", "scatterplotEnrichGO_HC", "search.metacell.tags", "separateAdjPval", "Set_POV_MEC_tags", "SetCC", "SetMatAdj", "splitAdjacencyMat", "StringBasedFiltering", "StringBasedFiltering2", "SumByColumns", "SymFilteringOperators", "test.design", "testAnovaModels", "translatedRandomBeta", "univ_AnnotDbPkg", "UpdateMetacellAfterImputation", "violinPlotD", "visualizeClusters", "vsn", "wrapper.compareNormalizationD_HC", "wrapper.corrMatrixD_HC", "wrapper.CVDistD_HC", "wrapper.dapar.impute.mi", "wrapper.heatmapD", "wrapper.impute.detQuant", "wrapper.impute.fixedValue", "wrapper.impute.KNN", "wrapper.impute.mle", "wrapper.impute.pa", "wrapper.impute.pa2", "wrapper.impute.slsa", "wrapper.mvImage", "wrapper.normalizeD", "wrapper.pca", "wrapperCalibrationPlot", "wrapperClassic1wayAnova", "wrapperRunClustering", "write.excel", "writeMSnsetToCSV", "writeMSnsetToExcel" ], "_help": [ { "page": "aggregateIter", "title": "xxxx", "topics": [ "aggregateIter" ] }, { "page": "aggregateIterParallel", "title": "xxxx", "topics": [ "aggregateIterParallel" ] }, { "page": "aggregateMean", "title": "Compute the intensity of proteins as the mean of the intensities of their peptides.", "topics": [ "aggregateMean" ] }, { "page": "AggregateMetacell", "title": "Symbolic product of matrices", "topics": [ "AggregateMetacell" ] }, { "page": "aggregateSum", "title": "Compute the intensity of proteins with the sum of the intensities of their peptides.", "topics": [ "aggregateSum" ] }, { "page": "aggregateTopn", "title": "Compute the intensity of proteins as the sum of the intensities of their n best peptides.", "topics": [ "aggregateTopn" ] }, { "page": "applyAnovasOnProteins", "title": "iteratively applies OWAnova() on the features of an MSnSet object", "topics": [ "applyAnovasOnProteins" ] }, { "page": "averageIntensities", "title": "Average protein/peptide abundances for each condition studied", "topics": [ "averageIntensities" ] }, { "page": "barplotEnrichGO_HC", "title": "A barplot that shows the result of a GO enrichment, using the package 'plotly'", "topics": [ "barplotEnrichGO_HC" ] }, { "page": "barplotGroupGO_HC", "title": "A barplot which shows the result of a GO classification, using the package 'plotly'", "topics": [ "barplotGroupGO_HC" ] }, { "page": "boxPlotD_HC", "title": "Builds a boxplot from a dataframe using the package 'plotly'", "topics": [ "boxPlotD_HC" ] }, { "page": "BuildAdjacencyMatrix", "title": "Function matrix of appartenance group", "topics": [ "BuildAdjacencyMatrix" ] }, { "page": "BuildColumnToProteinDataset", "title": "creates a column for the protein dataset after agregation by using the previous peptide dataset.", "topics": [ "BuildColumnToProteinDataset" ] }, { "page": "buildGraph", "title": "Display a CC", "topics": [ "buildGraph" ] }, { "page": "BuildMetaCell", "title": "Builds cells metadata", "topics": [ "BuildMetaCell" ] }, { "page": "Check_Dataset_Validity", "title": "xxx", "topics": [ "Check_Dataset_Validity" ] }, { "page": "Check_NbValues_In_Columns", "title": "xxx", "topics": [ "Check_NbValues_In_Columns" ] }, { "page": "check.conditions", "title": "Check if the design is valid", "topics": [ "check.conditions" ] }, { "page": "check.design", "title": "Check if the design is valid", "topics": [ "check.design" ] }, { "page": "checkClusterability", "title": "xxx", "topics": [ "checkClusterability" ] }, { "page": "Children", "title": "Names of all chidren of a node", "topics": [ "Children" ] }, { "page": "classic1wayAnova", "title": "Function to perform a One-way Anova statistical test on a MsnBase dataset", "topics": [ "classic1wayAnova" ] }, { "page": "compareNormalizationD_HC", "title": "Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'plotly'", "topics": [ "compareNormalizationD_HC" ] }, { "page": "compute_t_tests", "title": "xxxxxx", "topics": [ "compute_t_tests" ] }, { "page": "compute.selection.table", "title": "Applies an FDR threshold on a table of adjusted p-values and summarizes the results", "topics": [ "compute.selection.table" ] }, { "page": "corrMatrixD_HC", "title": "Displays a correlation matrix of the quantitative data of the 'Biobase::exprs()' table.", "topics": [ "corrMatrixD_HC" ] }, { "page": "CountPep", "title": "Compute the number of peptides used to aggregate proteins", "topics": [ "CountPep" ] }, { "page": "createMSnset", "title": "Creates an object of class 'MSnSet' from text file", "topics": [ "createMSnset" ] }, { "page": "createMSnset2", "title": "Creates an object of class 'MSnSet' from text file", "topics": [ "createMSnset2" ] }, { "page": "CVDistD_HC", "title": "Distribution of CV of entities", "topics": [ "CVDistD_HC" ] }, { "page": "deleteLinesFromIndices", "title": "Delete the lines in the matrix of intensities and the metadata table given their indice.", "topics": [ "deleteLinesFromIndices" ] }, { "page": "densityPlotD_HC", "title": "Builds a densityplot from a dataframe", "topics": [ "densityPlotD_HC" ] }, { "page": "diffAnaComputeAdjustedPValues", "title": "Computes the adjusted p-values", "topics": [ "diffAnaComputeAdjustedPValues" ] }, { "page": "diffAnaComputeFDR", "title": "Computes the FDR corresponding to the p-values of the differential analysis using", "topics": [ "diffAnaComputeFDR" ] }, { "page": "diffAnaGetSignificant", "title": "Returns a MSnSet object with only proteins significant after differential analysis.", "topics": [ "diffAnaGetSignificant" ] }, { "page": "diffAnaSave", "title": "Returns a 'MSnSet' object with the results of the differential analysis performed with 'limma' package.", "topics": [ "diffAnaSave" ] }, { "page": "diffAnaVolcanoplot", "title": "Volcanoplot of the differential analysis", "topics": [ "diffAnaVolcanoplot" ] }, { "page": "diffAnaVolcanoplot_rCharts", "title": "Volcanoplot of the differential analysis", "topics": [ "diffAnaVolcanoplot_rCharts" ] }, { "page": "display.CC.visNet", "title": "Display a CC", "topics": [ "display.CC.visNet" ] }, { "page": "enrich_GO", "title": "Calculates GO enrichment classes for a given list of proteins/genes ID. It results an enrichResult instance.", "topics": [ "enrich_GO" ] }, { "page": "ExtendPalette", "title": "Extends a base-palette of the package RColorBrewer to n colors.", "topics": [ "ExtendPalette" ] }, { "page": "finalizeAggregation", "title": "Finalizes the aggregation process", "topics": [ "finalizeAggregation" ] }, { "page": "findMECBlock", "title": "Finds the LAPALA into a 'MSnSet' object", "topics": [ "findMECBlock" ] }, { "page": "formatHSDResults", "title": "xxx", "topics": [ "formatHSDResults" ] }, { "page": "formatLimmaResult", "title": "xxxx", "topics": [ "formatLimmaResult" ] }, { "page": "formatPHResults", "title": "Extract logFC and raw pvalues from multiple post-hoc models summaries", "topics": [ "formatPHResults" ] }, { "page": "formatPHTResults", "title": "xxx", "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": "Get_AllComparisons", "title": "Returns list that contains a list of the statistical tests performed with DAPAR and recorded in an object of class 'MSnSet'.", "topics": [ "Get_AllComparisons" ] }, { "page": "get.pep.prot.cc", "title": "Build the list of connex composant of the adjacency matrix", "topics": [ "get.pep.prot.cc" ] }, { "page": "GetCC", "title": "Returns the contains of the slot processing of an object of class 'MSnSet'", "topics": [ "GetCC" ] }, { "page": "GetColorsForConditions", "title": "Builds a complete color palette for the conditions given in argument", "topics": [ "GetColorsForConditions" ] }, { "page": "getDesignLevel", "title": "xxx", "topics": [ "getDesignLevel" ] }, { "page": "GetDetailedNbPeptides", "title": "Computes the detailed number of peptides for each protein", "topics": [ "GetDetailedNbPeptides" ] }, { "page": "GetDetailedNbPeptidesUsed", "title": "Computes the detailed number of peptides used for aggregating each protein", "topics": [ "GetDetailedNbPeptidesUsed" ] }, { "page": "GetIndices_BasedOnConditions", "title": "Search lines which respects request on one or more conditions.", "topics": [ "GetIndices_BasedOnConditions" ] }, { "page": "GetIndices_MetacellFiltering", "title": "Delete the lines in the matrix of intensities and the metadata table given their indice.", "topics": [ "GetIndices_MetacellFiltering" ] }, { "page": "GetIndices_WholeLine", "title": "Search lines which respects query on all their elements.", "topics": [ "GetIndices_WholeLine" ] }, { "page": "GetIndices_WholeMatrix", "title": "Search lines which respects request on one or more conditions.", "topics": [ "GetIndices_WholeMatrix" ] }, { "page": "getIndicesConditions", "title": "Gets the conditions indices.", "topics": [ "getIndicesConditions" ] }, { "page": "getIndicesOfLinesToRemove", "title": "Get the indices of the lines to delete, based on a prefix string", "topics": [ "getIndicesOfLinesToRemove" ] }, { "page": "GetKeyId", "title": "xxxx", "topics": [ "GetKeyId" ] }, { "page": "getListNbValuesInLines", "title": "Returns the possible number of values in lines in the data", "topics": [ "getListNbValuesInLines" ] }, { "page": "GetMatAdj", "title": "Returns the contains of the slot processing of an object of class 'MSnSet'", "topics": [ "GetMatAdj" ] }, { "page": "GetMetacell", "title": "xxxx", "topics": [ "GetMetacell" ] }, { "page": "GetMetacellTags", "title": "List of metacell tags", "topics": [ "GetMetacellTags" ] }, { "page": "GetNbPeptidesUsed", "title": "Computes the number of peptides used for aggregating each protein", "topics": [ "GetNbPeptidesUsed" ] }, { "page": "GetNbTags", "title": "Number of each metacell tags", "topics": [ "GetNbTags" ] }, { "page": "getNumberOf", "title": "Number of lines with prefix", "topics": [ "getNumberOf" ] }, { "page": "getNumberOfEmptyLines", "title": "Returns the number of empty lines in the data", "topics": [ "getNumberOfEmptyLines" ] }, { "page": "getPourcentageOfMV", "title": "Percentage of missing values", "topics": [ "getPourcentageOfMV" ] }, { "page": "getProcessingInfo", "title": "Returns the contains of the slot processing of an object of class 'MSnSet'", "topics": [ "getProcessingInfo" ] }, { "page": "getProteinsStats", "title": "Computes the number of proteins that are only defined by specific peptides, shared peptides or a mixture of two.", "topics": [ "getProteinsStats" ] }, { "page": "getQuantile4Imp", "title": "Quantile imputation value definition", "topics": [ "getQuantile4Imp" ] }, { "page": "GetSoftAvailables", "title": "The set of softwares available", "topics": [ "GetSoftAvailables" ] }, { "page": "getTextForAggregation", "title": "Build the text information for the Aggregation process", "topics": [ "getTextForAggregation" ] }, { "page": "getTextForAnaDiff", "title": "Build the text information for the Aggregation process", "topics": [ "getTextForAnaDiff" ] }, { "page": "getTextForFiltering", "title": "Build the text information for the filtering process", "topics": [ "getTextForFiltering" ] }, { "page": "getTextForGOAnalysis", "title": "Build the text information for the Aggregation process", "topics": [ "getTextForGOAnalysis" ] }, { "page": "getTextForHypothesisTest", "title": "Build the text information for the hypothesis test process", "topics": [ "getTextForHypothesisTest" ] }, { "page": "getTextForNewDataset", "title": "Build the text information for a new dataset", "topics": [ "getTextForNewDataset" ] }, { "page": "getTextForNormalization", "title": "Build the text information for the Normalization process", "topics": [ "getTextForNormalization" ] }, { "page": "getTextForpeptideImputation", "title": "Build the text information for the peptide Imputation process", "topics": [ "getTextForpeptideImputation" ] }, { "page": "getTextForproteinImputation", "title": "Build the text information for the protein Imputation process", "topics": [ "getTextForproteinImputation" ] }, { "page": "GetTypeofData", "title": "xxxx", "topics": [ "GetTypeofData" ] }, { "page": "GetUniqueTags", "title": "xxxx", "topics": [ "GetUniqueTags" ] }, { "page": "globalAdjPval", "title": "Computes the adjusted p-values on all the stacked contrasts using CP4P", "topics": [ "globalAdjPval" ] }, { "page": "GlobalQuantileAlignment", "title": "Normalisation GlobalQuantileAlignement", "topics": [ "GlobalQuantileAlignment" ] }, { "page": "GOAnalysisSave", "title": "Returns an 'MSnSet' object with the results of the GO analysis performed with the functions 'enrichGO' and/or 'groupGO' of the `clusterProfiler` package.", "topics": [ "GOAnalysisSave" ] }, { "page": "GraphPepProt", "title": "Function to create a histogram that shows the repartition of peptides w.r.t. the proteins", "topics": [ "GraphPepProt" ] }, { "page": "group_GO", "title": "Calculates the GO profile of a vector of genes/proteins at a given level of the Gene Ontology", "topics": [ "group_GO" ] }, { "page": "hc_logFC_DensityPlot", "title": "Density plots of logFC values", "topics": [ "hc_logFC_DensityPlot" ] }, { "page": "hc_mvTypePlot2", "title": "Distribution of Observed values with respect to intensity values", "topics": [ "hc_mvTypePlot2" ] }, { "page": "heatmapD", "title": "This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'Biobase::exprs()' table of an object of class 'MSnSet'", "topics": [ "heatmapD" ] }, { "page": "heatmapForMissingValues", "title": "xxx", "topics": [ "heatmapForMissingValues" ] }, { "page": "histPValue_HC", "title": "Plots a histogram ov p-values", "topics": [ "histPValue_HC" ] }, { "page": "impute.pa2", "title": "Missing values imputation from a 'MSnSet' object", "topics": [ "impute.pa2" ] }, { "page": "inner.aggregate.iter", "title": "xxxx", "topics": [ "inner.aggregate.iter" ] }, { "page": "inner.aggregate.topn", "title": "xxxx", "topics": [ "inner.aggregate.topn" ] }, { "page": "inner.mean", "title": "xxxx", "topics": [ "inner.mean" ] }, { "page": "inner.sum", "title": "xxxx", "topics": [ "inner.sum" ] }, { "page": "is.subset", "title": "xxx", "topics": [ "is.subset" ] }, { "page": "LH0", "title": "xxxxxx", "topics": [ "LH0" ] }, { "page": "LH0.lm", "title": "xxxxxx", "topics": [ "LH0.lm" ] }, { "page": "LH1", "title": "xxxxxx", "topics": [ "LH1" ] }, { "page": "LH1.lm", "title": "xxxxxx", "topics": [ "LH1.lm" ] }, { "page": "limmaCompleteTest", "title": "Computes a hierarchical differential analysis", "topics": [ "limmaCompleteTest" ] }, { "page": "listSheets", "title": "This function returns the list of the sheets names in a Excel file.", "topics": [ "listSheets" ] }, { "page": "LOESS", "title": "Normalisation LOESS", "topics": [ "LOESS" ] }, { "page": "make.contrast", "title": "Builds the contrast matrix", "topics": [ "make.contrast" ] }, { "page": "make.design", "title": "Builds the design matrix", "topics": [ "make.design" ] }, { "page": "make.design.1", "title": "Builds the design matrix for designs of level 1", "topics": [ "make.design.1" ] }, { "page": "make.design.2", "title": "Builds the design matrix for designs of level 2", "topics": [ "make.design.2" ] }, { "page": "make.design.3", "title": "Builds the design matrix for designs of level 3", "topics": [ "make.design.3" ] }, { "page": "match.metacell", "title": "Similar to the function 'is.na' but focused on the equality with the paramter 'type'.", "topics": [ "match.metacell" ] }, { "page": "MeanCentering", "title": "Normalisation MeanCentering", "topics": [ "MeanCentering" ] }, { "page": "Metacell_DIA_NN", "title": "Sets the metacell dataframe for datasets which are from Dia-NN software", "topics": [ "Metacell_DIA_NN" ] }, { "page": "Metacell_generic", "title": "Sets the metacell dataframe for dataset without information about the origin of identification", "topics": [ "Metacell_generic" ] }, { "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.def", "title": "Metadata vocabulary for entities", "topics": [ "metacell.def" ] }, { "page": "MetaCellFiltering", "title": "Filter lines in the matrix of intensities w.r.t. some criteria", "topics": [ "MetaCellFiltering" ] }, { "page": "MetacellFilteringScope", "title": "Lists the metacell scopes for filtering", "topics": [ "MetacellFilteringScope" ] }, { "page": "metacellHisto_HC", "title": "Histogram of missing values", "topics": [ "metacellHisto_HC" ] }, { "page": "metacellPerLinesHisto_HC", "title": "Bar plot of missing values per lines using plotly", "topics": [ "metacellPerLinesHisto_HC" ] }, { "page": "metacellPerLinesHistoPerCondition_HC", "title": "Bar plot of missing values per lines and per condition", "topics": [ "metacellPerLinesHistoPerCondition_HC" ] }, { "page": "metacombine", "title": "Combine peptide metadata to build protein metadata", "topics": [ "metacombine" ] }, { "page": "mvImage", "title": "Heatmap of missing values", "topics": [ "mvImage" ] }, { "page": "nonzero", "title": "Retrieve the indices of non-zero elements in sparse matrices", "topics": [ "nonzero" ] }, { "page": "normalizeMethods.dapar", "title": "List normalization methods with tracking option", "topics": [ "normalizeMethods.dapar" ] }, { "page": "NumericalFiltering", "title": "Removes lines in the dataset based on numerical conditions.", "topics": [ "NumericalFiltering" ] }, { "page": "NumericalgetIndicesOfLinesToRemove", "title": "Get the indices of the lines to delete, based on a prefix string", "topics": [ "NumericalgetIndicesOfLinesToRemove" ] }, { "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": "Parent", "title": "Parent name of a node", "topics": [ "Parent" ] }, { "page": "pepa.test", "title": "PEptide based Protein differential Abundance test", "topics": [ "pepa.test" ] }, { "page": "pkgs.require", "title": "Loads packages", "topics": [ "pkgs.require" ] }, { "page": "plotJitter", "title": "Jitter plot of CC", "topics": [ "plotJitter" ] }, { "page": "plotJitter_rCharts", "title": "Display a a jitter plot for CC", "topics": [ "plotJitter_rCharts" ] }, { "page": "plotPCA_Eigen", "title": "Plots the eigen values of PCA", "topics": [ "plotPCA_Eigen" ] }, { "page": "plotPCA_Eigen_hc", "title": "Plots the eigen values of PCA with the plotly library", "topics": [ "plotPCA_Eigen_hc" ] }, { "page": "plotPCA_Ind", "title": "Plots individuals of PCA", "topics": [ "plotPCA_Ind" ] }, { "page": "plotPCA_Var", "title": "Plots variables of PCA", "topics": [ "plotPCA_Var" ] }, { "page": "postHocTest", "title": "Post-hoc tests for classic 1-way ANOVA", "topics": [ "postHocTest" ] }, { "page": "proportionConRev_HC", "title": "Barplot of proportion of contaminants and reverse", "topics": [ "proportionConRev_HC" ] }, { "page": "QuantileCentering", "title": "Normalisation QuantileCentering", "topics": [ "QuantileCentering" ] }, { "page": "rbindMSnset", "title": "Similar to the function 'rbind' but applies on two subsets of the same 'MSnSet' object.", "topics": [ "rbindMSnset" ] }, { "page": "readExcel", "title": "This function reads a sheet of an Excel file and put the data into a data.frame.", "topics": [ "readExcel" ] }, { "page": "reIntroduceMEC", "title": "Put back LAPALA into a 'MSnSet' object", "topics": [ "reIntroduceMEC" ] }, { "page": "removeLines", "title": "Removes lines in the dataset based on a prefix string.", "topics": [ "removeLines" ] }, { "page": "samLRT", "title": "xxxxxx", "topics": [ "samLRT" ] }, { "page": "saveParameters", "title": "Saves the parameters of a tool in the pipeline of Prostar", "topics": [ "saveParameters" ] }, { "page": "scatterplotEnrichGO_HC", "title": "A dotplot that shows the result of a GO enrichment, using the package 'plotly'", "topics": [ "scatterplotEnrichGO_HC" ] }, { "page": "search.metacell.tags", "title": "Search pattern in metacell vocabulary", "topics": [ "search.metacell.tags" ] }, { "page": "separateAdjPval", "title": "Computes the adjusted p-values separately on contrast using CP4P", "topics": [ "separateAdjPval" ] }, { "page": "Set_POV_MEC_tags", "title": "Sets the MEC tag in the metacell", "topics": [ "Set_POV_MEC_tags" ] }, { "page": "SetCC", "title": "Returns the connected components", "topics": [ "SetCC" ] }, { "page": "SetMatAdj", "title": "Record the adjacency matrices in a slot of the dataset of class 'MSnSet'", "topics": [ "SetMatAdj" ] }, { "page": "splitAdjacencyMat", "title": "splits an adjacency matrix into specific and shared", "topics": [ "splitAdjacencyMat" ] }, { "page": "StringBasedFiltering", "title": "Removes lines in the dataset based on a prefix strings (contaminants, reverse or both).", "topics": [ "StringBasedFiltering" ] }, { "page": "StringBasedFiltering2", "title": "Removes lines in the dataset based on a prefix strings.", "topics": [ "StringBasedFiltering2" ] }, { "page": "SumByColumns", "title": "Normalisation SumByColumns", "topics": [ "SumByColumns" ] }, { "page": "SymFilteringOperators", "title": "xxx", "topics": [ "SymFilteringOperators" ] }, { "page": "test.design", "title": "Check if xxxxxx", "topics": [ "test.design" ] }, { "page": "testAnovaModels", "title": "Applies a statistical test on each element of a list of linear models", "topics": [ "testAnovaModels" ] }, { "page": "thresholdpval4fdr", "title": "xxx", "topics": [ "thresholdpval4fdr" ] }, { "page": "translatedRandomBeta", "title": "Generator of simulated values", "topics": [ "translatedRandomBeta" ] }, { "page": "univ_AnnotDbPkg", "title": "Returns the totality of ENTREZ ID (gene id) of an OrgDb annotation package. Careful : org.Pf.plasmo.db : no ENTREZID but ORF", "topics": [ "univ_AnnotDbPkg" ] }, { "page": "UpdateMetacellAfterImputation", "title": "Update the cells metadata tags after imputation", "topics": [ "UpdateMetacellAfterImputation" ] }, { "page": "violinPlotD", "title": "Builds a violinplot from a dataframe", "topics": [ "violinPlotD" ] }, { "page": "visualizeClusters", "title": "Visualize the clusters according to pvalue thresholds", "topics": [ "visualizeClusters" ] }, { "page": "vsn", "title": "Normalisation vsn", "topics": [ "vsn" ] }, { "page": "wrapper.compareNormalizationD_HC", "title": "Builds a plot from a dataframe", "topics": [ "wrapper.compareNormalizationD_HC" ] }, { "page": "wrapper.corrMatrixD_HC", "title": "Displays a correlation matrix of the quantitative data of the 'Biobase::exprs()' table", "topics": [ "wrapper.corrMatrixD_HC" ] }, { "page": "wrapper.CVDistD_HC", "title": "Distribution of CV of entities", "topics": [ "wrapper.CVDistD_HC" ] }, { "page": "wrapper.dapar.impute.mi", "title": "Missing values imputation using the LSimpute algorithm.", "topics": [ "wrapper.dapar.impute.mi" ] }, { "page": "wrapper.heatmapD", "title": "This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'Biobase::exprs()' table of an object of class 'MSnSet'", "topics": [ "wrapper.heatmapD" ] }, { "page": "wrapper.impute.detQuant", "title": "Wrapper of the function `impute.detQuant()` for objects of class 'MSnSet'", "topics": [ "wrapper.impute.detQuant" ] }, { "page": "wrapper.impute.fixedValue", "title": "Missing values imputation from a 'MSnSet' object", "topics": [ "wrapper.impute.fixedValue" ] }, { "page": "wrapper.impute.KNN", "title": "KNN missing values imputation from a 'MSnSet' object", "topics": [ "wrapper.impute.KNN" ] }, { "page": "wrapper.impute.mle", "title": "Imputation of peptides having no values in a biological condition.", "topics": [ "wrapper.impute.mle" ] }, { "page": "wrapper.impute.pa", "title": "Imputation of peptides having no values in a biological condition.", "topics": [ "wrapper.impute.pa" ] }, { "page": "wrapper.impute.pa2", "title": "Missing values imputation from a 'MSnSet' object", "topics": [ "wrapper.impute.pa2" ] }, { "page": "wrapper.impute.slsa", "title": "Imputation of peptides having no values in a biological condition.", "topics": [ "wrapper.impute.slsa" ] }, { "page": "wrapper.mvImage", "title": "Heatmap of missing values from a 'MSnSet' object", "topics": [ "wrapper.mvImage" ] }, { "page": "wrapper.normalizeD", "title": "Normalisation", "topics": [ "wrapper.normalizeD" ] }, { "page": "wrapper.pca", "title": "Compute the PCA", "topics": [ "wrapper.pca" ] }, { "page": "wrapperCalibrationPlot", "title": "Performs a calibration plot on an 'MSnSet' object, calling the 'cp4p' package functions.", "topics": [ "wrapperCalibrationPlot" ] }, { "page": "wrapperClassic1wayAnova", "title": "Wrapper for One-way Anova statistical test", "topics": [ "wrapperClassic1wayAnova" ] }, { "page": "wrapperRunClustering", "title": "clustering pipeline of protein/peptide abundance profiles.", "topics": [ "wrapperRunClustering" ] }, { "page": "write.excel", "title": "This function exports a data.frame to a Excel file.", "topics": [ "write.excel" ] }, { "page": "writeMSnsetToCSV", "title": "Exports a MSnset dataset into a zip archive containing three zipped CSV files.", "topics": [ "writeMSnsetToCSV" ] }, { "page": "writeMSnsetToExcel", "title": "This function exports a 'MSnSet' object to a Excel file.", "topics": [ "writeMSnsetToExcel" ] } ], "_rundeps": [ "abind", "affy", "affyio", "AnnotationFilter", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "biocmake", "BiocManager", "BiocParallel", "bslib", "cachem", "cli", "clue", "cluster", "codetools", "cpp11", "crosstalk", "curl", "DAPARdata", "data.table", "DelayedArray", "digest", "dir.expiry", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "igraph", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "magrittr", "MALDIquant", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "MetaboCoreUtils", "mime", "MsCoreUtils", "MSnbase", "MultiAssayExperiment", "mzID", "mzR", "ncdf4", "openssl", "otel", "pcaMethods", "pillar", "pkgconfig", "plotly", "plyr", "preprocessCore", "promises", "ProtGenerics", "PSMatch", "PTMods", "purrr", "QFeatures", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "Rhdf5lib", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "Spectra", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "vsn", "withr", "xfun", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "DAPAR.Rmd", "filename": "DAPAR.html", "title": "DAPAR user manual", "author": "Samuel Wieczorek, Thomas Burger", "engine": "knitr::rmarkdown", "headings": [ "Introduction" ], "created": "2026-04-15 13:54:11", "modified": "2026-04-15 13:54:11", "commits": 1 } ], "_score": 6.317854489331469, "_indexed": true, "_nocasepkg": "dapar", "_universes": [ "bioc", "samwieczorek", "edyp-lab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.45.0", "date": "2026-05-28T06:45:42.000Z", "distro": "noble", "commit": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "fileid": "d08e38448db2767a70f6732c4701c136314b79b0d5e82b6b7bb8fdbbb09be63d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558863920" }, { "r": "4.6.0", "os": "linux", "version": "1.45.0", "date": "2026-05-28T06:46:42.000Z", "distro": "noble", "commit": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "fileid": "2334fcf0336f749c12684972a7436767cce59c4b2d9b106205b4124e996fc618", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558863920" }, { "r": "4.5.3", "os": "mac", "version": "1.45.0", "date": "2026-05-28T07:30:15.000Z", "commit": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "fileid": "4d1f83d3a189b26ed420f3f18f64103ebe2c65c6443258c5136fcc51c94f3099", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558863920" }, { "r": "4.6.0", "os": "mac", "version": "1.45.0", "date": "2026-05-28T07:29:44.000Z", "commit": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "fileid": "ac77621c97bdf30c5f5739ad6abbba6bbafb6cb71ff101e01932b26b7f9aef89", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558863920" }, { "r": "4.6.0", "os": "wasm", "version": "1.45.0", "date": "2026-05-28T06:45:32.000Z", "commit": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "fileid": "aee851b6f8284de41faa5271e70b2776a774e079309ec815783cd26ae6db6558", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558863920" }, { "r": "4.7.0", "os": "win", "version": "1.45.0", "date": "2026-05-28T06:44:14.000Z", "commit": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "fileid": "d6c5a86ef7ef0cbc60c3cd8a2db905aee2e7e7a4470cb5916287f1b47c46ff22", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558863920" }, { "r": "4.5.3", "os": "win", "version": "1.45.0", "date": "2026-05-28T06:44:19.000Z", "commit": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "fileid": "50c4012accd33be5c38770f356a0685be86ee5ac533fe767953f00333720d7f3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558863920" }, { "r": "4.6.0", "os": "win", "version": "1.45.0", "date": "2026-05-28T06:43:53.000Z", "commit": "5c3a2c95665bb2f37c8369d80ecba26f06513c57", "fileid": "4562146c0e44eb03e43becd018fb9c9449b32fb87f9f1616780478e5d02631d9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558863920" } ] }