{ "_id": "6a1be4771d7bb097a0a1963e", "Package": "isobar", "Title": "Analysis and quantitation of isobarically tagged MSMS proteomics\ndata", "Description": "isobar provides methods for preprocessing, normalization,\nand report generation for the analysis of quantitative mass\nspectrometry proteomics data labeled with isobaric tags, such\nas iTRAQ and TMT. Features modules for integrating and\nvalidating PTM-centric datasets (isobar-PTM). More information\non http://www.ms-isobar.org.", "Version": "1.59.0", "Author": "Florian P Breitwieser and Jacques\nColinge , with contributions from\nAlexey Stukalov , Xavier Robin\n and Florent Gluck\n", "Maintainer": "Florian P Breitwieser ", "biocViews": "ImmunoOncology, Proteomics, MassSpectrometry,\nBioinformatics, MultipleComparisons, QualityControl", "LazyLoad": "yes", "License": "LGPL-2", "URL": "https://github.com/fbreitwieser/isobar", "BugReports": "https://github.com/fbreitwieser/isobar/issues", "Collate": "utils.R ProteinGroup-class.R IBSpectra-class.R isobar-import.R\nIBSpectra-plots.R NoiseModel-class.R Tlsd-class.R\nratio-methods.R distr-methods.R sharedpep-methods.R\nreport-utils-xls.R report-utils-tex.R report-utils.R\nmetareport-utils.R ptm-methods.R MSnSet-methods.R zzz.R", "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:36:01 UTC", "RemoteUrl": 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"page": "getPhosphoRSProbabilities", "title": "Generate input files for PhosphoRS, call it, and get modification site probabilities", "topics": [ "filterSpectraPhosphoRS", "getPhosphoRSProbabilities", "readPhosphoRSOutput", "writePhosphoRSInput" ] }, { "page": "getPtmInfo", "title": "Get PTM site information for idenfied proteins from public databases.", "topics": [ "getPtmInfoFromNextprot", "getPtmInfoFromPhosphoSitePlus" ] }, { "page": "groupMemberPeptides", "title": "Peptide info for protein group members", "topics": [ "groupMemberPeptides" ] }, { "page": "human.protein.names", "title": "Info on proteins", "topics": [ "human.protein.names", "my.protein.info" ] }, { "page": "IBSpectra-class", "title": "IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data", "topics": [ "as.data.frame,IBSpectra-method", "as.data.frame.IBSpectra", "class:IBSpectra", "classLabels", "classLabels,IBSpectra-method", "classLabels<-", "classLabels<-,IBSpectra-method", 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ratio calculation", "topics": [ "estimateRatio", "estimateRatio,IBSpectra,ANY,character,character,character,missing-method", "estimateRatio,IBSpectra,ANY,character,character,character,NULL-method", "estimateRatio,IBSpectra,ANY,character,character,missing,character-method", "estimateRatio,IBSpectra,ANY,character,character,missing,data.frame-method", "estimateRatio,IBSpectra,ANY,character,character,missing,matrix-method", "estimateRatio,IBSpectra,ANY,character,character,NULL,character-method", "estimateRatio,IBSpectra,ANY,character,character,NULL,data.frame-method", "estimateRatio,IBSpectra,ANY,character,character,NULL,matrix-method", "estimateRatio,IBSpectra,ANY,missing,missing,character,missing-method", "estimateRatio,IBSpectra,ANY,missing,missing,missing,character-method", "estimateRatioForPeptide", "estimateRatioForProtein", "estimateRatioNumeric", "estimateRatioNumeric,numeric,numeric,missing-method", "estimateRatioNumeric,numeric,numeric,NoiseModel-method", "estimateRatioNumeric,numeric,numeric,NULL-method", "getMultUnifDensity", "getMultUnifPValues", "isobar-analysis" ] }, { "page": "isobar-import", "title": "Loading data into IBSpectra objects using readIBSpectra", "topics": [ "isobar-import", "read.mzid", "readIBSpectra", "readIBSpectra,character,character,character-method", "readIBSpectra,character,character,missing-method", "readIBSpectra,character,character-method", "readIBSpectra,character,data.frame,character-method", "readIBSpectra,character,data.frame,missing-method" ] }, { "page": "isobar-plots", "title": "IBSpectra plots", "topics": [ "isobar-plots", "maplot", "maplot,IBSpectra,character,character-method", "maplot,IBSpectra,missing,missing-method", "maplot,missing,numeric,numeric-method", "maplot2", "maplot2,ANY,character,character-method", "maplot2,list,character,character-method", "plotRatio", "plotRatio,IBSpectra,character,character,character-method", "protGgdata", "protGgdata,ANY,character,character-method", "raplot", "raplot,IBSpectra-method", "reporterIntensityPlot", "reporterIntensityPlot,IBSpectra-method", "reporterIntensityPlot-methods", "reporterMassPrecision", "reporterMassPrecision,IBSpectra,logical-method", "reporterMassPrecision,IBSpectra,missing-method" ] }, { "page": "isobar-preprocessing", "title": "IBSpectra preprocessing", "topics": [ "correctIsotopeImpurities", "correctIsotopeImpurities,IBSpectra-method", "exclude", "exclude,IBSpectra,character-method", "isobar-preprocessing", "normalize", "subtractAdditiveNoise", "subtractAdditiveNoise,IBSpectra-method" ] }, { "page": "isobar-reports", "title": "Isobar reports", "topics": [ "connect.nodes", "create.meta.reports", "create.reports", "draw.boxplot", "draw.protein.group", "draw.proteingroup.row", "get_n_proteins", "initialize.env", "isobar-reports", "load.properties", "load.tex.properties", "modifs", "print_classlabels_tbl", "print_groupsize", "print_longtablehdr", "print_longtablehdr_peptide", "print_protein_grp_info", "print_protein_grp_tbl", "print_protein_notquant_tbl", "print_protein_quant_tbl", "print_sign_proteins_tbl", "property", "testPdflatex", "testPerl", "tikz.proteingroup", "transform_pepmodif", "write.tex.commands", "write.xls.report" ] }, { "page": "isobar-data", "title": "Isobar Data packages", "topics": [ "ibspiked_set1", "ibspiked_set2", "ib_phospho", "noise.model.hcd" ] }, { "page": "maplot.protein", "title": "Ratio intensity plot for individual proteins", "topics": [ "maplot.protein" ] }, { "page": "NoiseModel-class", "title": "NoiseModel objects", "topics": [ "class:NoiseModel", "ExponentialNoANoiseModel-class", "ExponentialNoiseModel-class", "GeneralNoiseModel-class", "initialize,NoiseModel-method", "InverseNoANoiseModel-class", "InverseNoiseModel-class", "lowIntensity", "lowIntensity,NoiseModel-method", "lowIntensity<-", "lowIntensity<-,NoiseModel-method", "naRegion", "naRegion,NoiseModel-method", "naRegion<-", "naRegion<-,NoiseModel-method", "noiseFunction", "noiseFunction,NoiseModel-method", "NoiseModel", "NoiseModel,IBSpectra-method", "NoiseModel-class", "parameter", "parameter,NoiseModel-method", "parameter<-", "parameter<-,NoiseModel-method", "plot.NoiseModel", "show,NoiseModel-method", "stddev", "stddev,NoiseModel-method", "variance", "variance,NoiseModel,numeric,missing-method", "variance,NoiseModel,numeric,numeric-method" ] }, { "page": "number.ranges", "title": "Helper function to transform number lists to ranges", "topics": [ "number.ranges" ] }, { "page": "observedKnownSites", "title": "Observed modification sites.", "topics": [ "modif.site.count", "modif.sites", "observedKnownSites" ] }, { "page": "peptide.count", "title": "Peptide counts, spectral counts and sequence coverage for ProteinGroup objects.", "topics": [ "peptide.count", "sequence.coverage", "spectra.count" ] }, { "page": "ratio-summ", "title": "Calculating and Summarizing Protein and Peptide Ratios", "topics": [ "combn.matrix", "combn.protein.tbl", "peptideRatios", "peptideRatiosNotQuant", "proteinRatios", "summarize.ratios", "weightedMean", "weightedMean,numeric,numeric-method", "weightedVariance", "weightedVariance,numeric,numeric,missing-method", "weightedVariance,numeric,numeric,numeric-method" ] }, { "page": "ProteinGroup-class", "title": "ProteinGroup objects", "topics": [ "as.data.frame,ProteinGroup-method", "as.data.frame.ProteinGroup", "class:ProteinGroup", "coerce,data.frame,ProteinGroup-method", "get.pep.group", "indistinguishableProteins", "indistinguishableProteins,ProteinGroup,ANY,ANY-method", "indistinguishableProteins,ProteinGroup,character,missing-method", "indistinguishableProteins,ProteinGroup,missing,character-method", "indistinguishableProteins,ProteinGroup,missing,missing-method", "indistinguishableProteins,ProteinGroup-method", "peptideInfo", "peptideInfo,ProteinGroup-method", "peptideInfo-methods", "peptideNProtein", "peptideNProtein,ProteinGroup-method", "peptides", "peptides,ProteinGroup,character-method", "peptides,ProteinGroup,missing-method", "peptideSpecificity", "peptideSpecificity,ProteinGroup-method", "protein.ac", "protein.ac,ProteinGroup,character-method", "protein.ac,ProteinGroup,missing-method", "protein.g", "protein.g,ProteinGroup,character,character-method", "protein.g,ProteinGroup,character-method", "ProteinGroup", "ProteinGroup,data.frame,missing-method", "ProteinGroup,data.frame,NULL-method", "ProteinGroup,data.frame,ProteinGroup-method", "ProteinGroup-class", "proteinGroup.as.concise.data.frame", "proteinGroupTable", "proteinGroupTable,ProteinGroup-method", "readProteinGroup", "readProteinGroup2", "reporterProteins", "reporterProteins,ProteinGroup-method", "show,ProteinGroup-method", "spectrumToPeptide", "spectrumToPeptide,ProteinGroup-method", "summary.ProteinGroup" ] }, { "page": "proteinInfo-methods", "title": "Methods for Function proteinInfo", "topics": [ "getProteinInfoFromBioDb", "getProteinInfoFromBiomart", "getProteinInfoFromEntrez", "getProteinInfoFromNextProt", "getProteinInfoFromTheInternet", "getProteinInfoFromUniprot", "proteinInfo", "proteinInfo,ProteinGroup,character,missing-method", "proteinInfo,ProteinGroup,missing,character-method", "proteinInfo,ProteinGroup,missing,missing-method", "proteinInfo,ProteinGroup-method", "proteinInfo-methods", "proteinInfo<-", "proteinInfo<-,ProteinGroup-method", "proteinInfoIsOnSpliceVariants" ] }, { "page": "proteinNameAndDescription", "title": "Get protein gene names and description from protein info of protein group.", "topics": [ "proteinDescription", "proteinGeneName", "proteinID", "proteinNameAndDescription" ] }, { "page": "ratiosReshapeWide", "title": "Reshape output of proteinRatios into wide format", "topics": [ "ratiosReshapeWide" ] }, { "page": "reporter.protein-methods", "title": "Get reporter protein group identifier for protein group identifier", "topics": [ "reporter.protein", "reporter.protein,ProteinGroup,character-method", "reporter.protein-methods" ] }, { "page": "sanitize", "title": "Helper function for LaTeX export", "topics": [ "sanitize" ] }, { "page": "shared.ratios", "title": "Shared ratio calculation", "topics": [ "shared.ratios" ] }, { "page": "shared.ratios.sign", "title": "Plot and get significantly shared ratios.", "topics": [ "shared.ratios.sign" ] }, { "page": "specificities", "title": "Peptide specificities", "topics": [ "group-specific", "GROUPSPECIFIC", "reporter-specific", "REPORTERSPECIFIC", "SPECIFICITIES", "specificities", "UNSPECIFIC", "unspecific" ] }, { "page": "spectra.count2", "title": "Spectral count for peptides and proteins in ProteinGroup objects.", "topics": [ "spectra.count2" ] }, { "page": "subsetIBSpectra", "title": "Subset IBSpectra objects", "topics": [ "subsetIBSpectra" ] }, { "page": "Tlsd-class", "title": "Class '\"Tlsd\"'", "topics": [ "Tlsd", "Tlsd-class" ] }, { "page": "TlsParameter-class", "title": "Class '\"TlsParameter\"'", "topics": [ "TlsParameter-class" ] }, { "page": "writeHscoreData", 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