{ "_id": "6aca8cd7fe5cc25786e8b4b1", "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": "https://github.com/bioc/isobar", "RemoteRef": "HEAD", "RemoteSha": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 17:41:48 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "isobar_1.59.0.tar.gz", "_fileid": "https://r2.ropensci.org/d6b52c108d5f6589ae220b35bc8729a7373ce12a263d1ff1d050ec33c88306d5", "_filesize": 3122603, "_sha256": "d6b52c108d5f6589ae220b35bc8729a7373ce12a263d1ff1d050ec33c88306d5", "_expires": "2027-01-18T19:07:00.000Z", "_created": "2026-10-10T17:41:48.000Z", "_published": "2026-10-10T19:07:03.045Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38072469538", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114273638803, "time": 174, "config": "bioc-checks", "r": "4.6.1", "check": "FAILURE", "artifact": "" }, { "job": 114273638811, "time": 407, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11678215334" }, { "job": 114273638848, "time": 344, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11677801022" }, { "job": 114273638859, "time": 197, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11679134327" }, { "job": 114273638875, "time": 224, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11679549002" }, { "job": 114272623995, "time": 306, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11676944618" }, { "job": 114273638790, "time": 147, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11676809996" }, { "job": 114273638854, "time": 200, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11677780844" }, { "job": 114273638834, "time": 256, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11677406896" }, { "job": 114273638800, "time": 255, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11677566564" } ], "_upstream": "https://github.com/bioc/isobar", "_commit": { "id": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379761 }, "_maintainer": { "name": "Florian P Breitwieser", "email": "florian.bw@gmail.com", "login": "fbreitwieser", "description": "Babboon By: Henry Henderson | License: Creative Commons Attribution (CC BY 4.0)", "uuid": 516060 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10.0", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "distr", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "biomaRt", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "MSnbase", "role": "Suggests" }, { "package": "OrgMassSpecR", "role": "Suggests" }, { "package": "XML", "role": "Suggests" }, { "package": "RJSONIO", "role": "Suggests" }, { "package": "Hmisc", "role": "Suggests" }, { "package": "gplots", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "boot", "role": "Suggests" }, { "package": "DBI", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.59.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "immunooncology", "proteomics", "massspectrometry", "bioinformatics", "multiplecomparisons", "qualitycontrol" ], "_stars": 10, "_contributors": [ { "user": "fbreitwieser", "count": 28, "uuid": 516060 }, { "user": "alyst", "count": 16, "uuid": 348591 }, { "user": "jgriss", "count": 4, "uuid": 10997605 }, { "user": "ahainard", "count": 1, "uuid": 9199669 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 698, "source": "https://www.bioconductor.org/packages/stats/bioc/isobar" }, "_mentions": 4, "_devurl": "https://github.com/fbreitwieser/isobar", "_searchresults": 37, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/isobar.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/fbreitwieser/isobar", "_realowner": "bioc", "_cranurl": false, "_exports": [ "%inrange%", "adjust.ratio.pvalue", "as.data.frame.IBSpectra", "as.data.frame.ProteinGroup", "calc.delta.score", "calc.pep.delta.score", "calcCumulativeProbXGreaterThanY", "calcPeptidePosition", "calcProbXDiffNormals", "calcProbXGreaterThanY", "calculate.dNSAF", "calculate.emPAI", "calculate.mult.sample.pvalue", "calculate.ratio.pvalue", "calculate.sample.pvalue", "classLabels", "classLabels<-", "combn.matrix", "combn.protein.tbl", "connect.nodes", "correct.peptide.ratios", "correctIsotopeImpurities", "create.meta.reports", "create.reports", "distrprint", "do.log", "draw.boxplot", "draw.protein.group", "draw.proteingroup.row", "estimateRatio", "estimateRatioForPeptide", "estimateRatioForProtein", "estimateRatioNumeric", "exclude", "filterSpectraDeltaScore", "filterSpectraPhosphoRS", "fitCauchy", "fitGaussianMixture", "fitNorm", "fitNormalCauchyMixture", "fitTlsd", "fitWeightedNorm", "get_n_proteins", "get.log", "get.pep.group", "getMultUnifDensity", "getMultUnifPValues", "getPeptideModifContext", "getPhosphoRSProbabilities", "getProteinInfoFromBioDb", "getProteinInfoFromBiomart", "getProteinInfoFromEntrez", "getProteinInfoFromNextProt", "getProteinInfoFromTheInternet", "getProteinInfoFromUniprot", "getPtmInfoFromNextprot", "getPtmInfoFromPhosphoSitePlus", "groupMemberPeptides", "GROUPSPECIFIC", "human.protein.names", "ibSpectra.as.concise.data.frame", "IBSpectraTypes", "indistinguishableProteins", "initialize.env", "is.logged", "isotopeImpurities", "isotopeImpurities<-", "load.properties", "load.tex.properties", "lowIntensity", "lowIntensity<-", "maplot", "maplot.protein", "modif.site.count", "modif.sites", "modifs", "my.protein.info", "n.observable.peptides", "naRegion", "naRegion<-", "noiseFunction", "NoiseModel", "normalize", "number.ranges", "observable.peptides", "observedKnownSites", "parameter", "parameter<-", "paste0", "peptide.count", "peptideInfo", "peptideNProtein", "peptideRatios", "peptideRatiosNotQuant", "peptides", "peptideSpecificity", "plot.NoiseModel", "plotRatio", "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", "protein.ac", "protein.g", "proteinDescription", "proteinGeneName", "proteinGroup", "ProteinGroup", "proteinGroup.as.concise.data.frame", "proteinGroup<-", "proteinGroupTable", "proteinID", "proteinInfo", "proteinInfo<-", "proteinInfoIsOnSpliceVariants", "proteinNameAndDescription", "proteinRatios", "protGgdata", "raplot", "ratiosReshapeWide", "read.mzid", "readIBSpectra", "readPhosphoRSOutput", "readProteinGroup", "readProteinGroup2", "reporter.protein", "reporterData", "reporterData<-", "reporterIntensities", "reporterIntensities<-", "reporterIntensityPlot", "reporterMasses", "reporterMasses<-", "reporterMassPrecision", "reporterProteins", "REPORTERSPECIFIC", "reporterTagMasses", "reporterTagNames", "sanitize", "sequence.coverage", "shared.ratios", "shared.ratios.sign", "SPECIFICITIES", "spectra.count", "spectra.count2", "spectrumSel", "spectrumTitles", "spectrumToPeptide", "stddev", "subsetIBSpectra", "subtractAdditiveNoise", "summarize.ratios", "summary.ProteinGroup", "testPdflatex", "testPerl", "tikz.proteingroup", "Tlsd", "transform_pepmodif", "twodistr.plot", "UNSPECIFIC", "variance", "weightedMean", "weightedVariance", "write.tex.commands", "write.xls.report", "writeData", "writeHscoreData", "writeIBSpectra", "writePhosphoRSInput" ], "_datasets": [ { "name": "ib_phospho", "title": "Isobar Data packages", "object": "ib_phospho", "file": "ib_phospho.rda", "class": [ "iTRAQ4plexSpectra" ], "fields": [], "table": false, "tojson": false }, { "name": "ibspiked_set1", "title": "Isobar Data packages", "object": "ibspiked_set1", "file": "ibspiked_set1.rda", "class": [ "iTRAQ4plexSpectra" ], "fields": [], "table": false, "tojson": false }, { "name": "ibspiked_set2", "title": "Isobar Data packages", "object": "ibspiked_set2", "file": "ibspiked_set2.rda", "class": [ "iTRAQ4plexSpectra" ], "fields": [], "table": false, "tojson": false }, { "name": "noise.model.hcd", "title": "Isobar Data packages", "object": "noise.model.hcd", "file": "noise.model.hcd.rda", "class": [ "ExponentialNoiseModel" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "isobar-package", "title": "Analysis and quantitation of isobarically tagged MSMS proteomics data", "topics": [ "isobar-package", "isobar" ] }, { "page": "calc.delta.score", "title": "Calculate Delta Score from Ion Score", "topics": [ "calc.delta.score", "calc.pep.delta.score", "filterSpectraDeltaScore" ] }, { "page": "calc.startpos", "title": "Recalculate peptide start positions based on protein sequence", "topics": [ "calcPeptidePosition" ] }, { "page": "calculate-pvalues", "title": "Calculate and Adjust Ratio and Sample p-values.", "topics": [ "adjust.ratio.pvalue", "calculate.mult.sample.pvalue", "calculate.ratio.pvalue", "calculate.sample.pvalue" ] }, { "page": "calculate.dNSAF", "title": "dNSAF approximate abundance calculations.", "topics": [ "calculate.dNSAF" ] }, { "page": "calculate.emPAI", "title": "emPAI approximate abundance calculations.", "topics": [ "calculate.emPAI", "n.observable.peptides", "observable.peptides" ] }, { "page": "correct.peptide.ratios", "title": "Correct peptide ratios with protein ratios from a separate experiment.", "topics": [ "correct.peptide.ratios" ] }, { "page": "distr-methods", "title": "Functions for distribution calculations", "topics": [ "AbscontDistribution-class", "calcCumulativeProbXGreaterThanY", "calcProbXDiffNormals", "calcProbXGreaterThanY", "Distribution-class", "distrprint", "Parameter-class", "twodistr.plot", "UnivariateDistribution-class" ] }, { "page": "fit-distr", "title": "Fit weighted and unweighted Cauchy and Normal distributions", "topics": [ "fitCauchy", "fitGaussianMixture", "fitNorm", "fitNormalCauchyMixture", "fitTlsd", "fitWeightedNorm" ] }, { "page": "getPeptideModifContext", "title": "Get context of modification", "topics": [ "getPeptideModifContext" ] }, { "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", "coerce,IBSpectra,data.frame-method", "IBSpectra", "IBSpectra-class", "ibSpectra.as.concise.data.frame", "IBSpectraTypes", "initialize,IBSpectra-method", "isotopeImpurities", "isotopeImpurities,IBSpectra-method", "isotopeImpurities<-", "isotopeImpurities<-,IBSpectra-method", "iTRAQ4plexSpectra", "iTRAQ4plexSpectra-class", "iTRAQ8plexSpectra", "iTRAQ8plexSpectra-class", "iTRAQSpectra", "iTRAQSpectra-class", "proteinGroup", "proteinGroup,IBSpectra-method", "proteinGroup<-", "proteinGroup<-,IBSpectra-method", "reporterData", "reporterData,IBSpectra-method", "reporterData<-", "reporterData<-,IBSpectra-method", "reporterIntensities", "reporterIntensities,IBSpectra-method", "reporterIntensities<-", "reporterIntensities<-,IBSpectra-method", "reporterMasses", "reporterMasses,IBSpectra-method", "reporterMasses<-", "reporterMasses<-,IBSpectra-method", "reporterTagMasses", "reporterTagMasses,IBSpectra-method", "reporterTagNames", "reporterTagNames,IBSpectra-method", "show,IBSpectra-method", "spectrumSel", "spectrumSel,IBSpectra,character,missing-method", "spectrumSel,IBSpectra,data.frame,missing-method", "spectrumSel,IBSpectra,matrix,missing-method", "spectrumSel,IBSpectra,missing,character-method", "spectrumSel,IBSpectra,missing,missing-method", "spectrumTitles", "spectrumTitles,IBSpectra-method", "TMT10plexSpectra", "TMT10plexSpectra-class", "TMT2plexSpectra", "TMT2plexSpectra-class", "TMT6plexSpectra", "TMT6plexSpectra-class", "TMT6plexSpectra2", "TMT6plexSpectra2-class", "TMTSpectra", "TMTSpectra-class", "VARMETADATA", "writeData", "writeData,IBSpectra-method" ] }, { "page": "isobar-log", "title": "Log functions for IBSpectra objects", "topics": [ "do.log", "do.log,IBSpectra,character-method", "get.log", "get.log,IBSpectra,character-method", "is.logged", "is.logged,IBSpectra,character-method" ] }, { "page": "utils", "title": "Isobar util functions", "topics": [ "%inrange%", "paste0" ] }, { "page": "isobar-analysis", "title": "IBSpectra analysis: Protein and peptide 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", "title": "Write identifications into a format suitable for Hscore.", "topics": [ "writeHscoreData" ] }, { "page": "writeIBSpectra", "title": "Write IBSpectra file as CSV in a format readable by readIBSpectra.", "topics": [ "writeIBSpectra" ] } ], "_readme": "https://github.com/bioc/isobar/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "biomaRt", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "dbplyr", "distr", "dplyr", "farver", "fastmap", "filelock", "generics", "ggplot2", "glue", "gtable", "hms", "httr", "httr2", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lifecycle", "magrittr", "MASS", "memoise", "mime", "openssl", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "progress", "purrr", "R6", "RColorBrewer", "Rcpp", "rlang", "RSQLite", "S4Vectors", "S7", "scales", "Seqinfo", "sfsmisc", "startupmsg", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "xml2", "XVector" ], "_vignettes": [ { "source": "isobar-devel.Rnw", "filename": "isobar-devel.pdf", "title": "isobar for developers", "engine": "utils::Sweave", "headings": [ "Introduction", "Classes", "Session Information" ], "created": "2013-11-01 20:22:06", "modified": "2013-11-01 20:22:06", "commits": 1 }, { "source": "isobar-ptm.Rnw", "filename": "isobar-ptm.pdf", "title": "isobar for quantification of PTM datasets", "engine": "utils::Sweave", "headings": [ "Introduction", "Modification Site Localization", "Peptide Ratio Calculation", "Harvesting public PTM databases" ], "created": "2013-11-01 20:22:06", "modified": "2013-11-01 20:22:06", "commits": 1 }, { "source": "isobar.Rnw", "filename": "isobar.pdf", "title": "isobar package for iTRAQ and TMT protein quantification", "engine": "utils::Sweave", "headings": [ "Introduction", "Loading data", "Data Analysis", "Data Analysis", "Report generation", "File formats", "properties.R for report generation", "Dependencies", "Session Information" ], "created": "2013-11-01 20:22:06", "modified": "2018-08-30 17:50:57", "commits": 5 }, { "source": "isobar-usecases.Rnw", "filename": "isobar-usecases.pdf", "title": "Usecases for isobar package", "engine": "utils::Sweave", "headings": [ "​" ], "created": "2014-11-29 20:44:54", "modified": "2014-11-29 20:44:54", "commits": 1 } ], "_score": 7.249442961442583, "_indexed": true, "_nocasepkg": "isobar", "_universes": [ "bioc", "fbreitwieser" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.59.0", "date": "2026-10-10T17:46:57.000Z", "distro": "resolute", "commit": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "fileid": "https://r2.ropensci.org/ecfa0c5ee55ffb8208f5c1cce499079565385de34e25137d28f259d6edafc31f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072469538" }, { "r": "4.6.1", "os": "linux", "version": "1.59.0", "date": "2026-10-10T17:45:48.000Z", "distro": "resolute", "commit": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "fileid": "https://r2.ropensci.org/ffcfae07d7fe318048bea4e8a6078c112c751baac05e7c2491c8bbb031800dd1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072469538" }, { "r": "4.5.3", "os": "mac", "version": "1.59.0", "date": "2026-10-10T19:04:27.000Z", "commit": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "fileid": "https://r2.ropensci.org/221848a613f1dc5b742191f0d481b5925e9d5f166e9dbb2f6957efa11128d79b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072469538" }, { "r": "4.6.1", "os": "mac", "version": "1.59.0", "date": "2026-10-10T19:04:40.000Z", "commit": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "fileid": "https://r2.ropensci.org/4e40e9b8228bd573b867d43a0bb7748c6990c827092ca9c6302b3b3ff3ddc343", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072469538" }, { "r": "4.6.0", "os": "wasm", "version": "1.59.0", "date": "2026-10-10T17:44:57.000Z", "commit": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "fileid": "https://r2.ropensci.org/7a037b59e0a6bb1cdb7d5295ebc3a84c49bdc2510122d0e6076d5ffb89408f47", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072469538" }, { "r": "4.7.0", "os": "win", "version": "1.59.0", "date": "2026-10-10T17:43:56.000Z", "commit": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "fileid": "https://r2.ropensci.org/a7804096a3f7872879e481fb2c189181b971ef875a71afca165bad3a405c04cd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072469538" }, { "r": "4.5.3", "os": "win", "version": "1.59.0", "date": "2026-10-10T17:43:57.000Z", "commit": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "fileid": "https://r2.ropensci.org/b9a0d9b3ec9051b1c4cb9177985a80b700eb9e2e6d6a287e13e22d048e88720a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072469538" }, { "r": "4.6.1", "os": "win", "version": "1.59.0", "date": "2026-10-10T17:43:52.000Z", "commit": "0bd497a10f5dca0191d26dddec3de8d2d5cb6044", "fileid": "https://r2.ropensci.org/a48f949d55d3c2bce5b171c5efb524db3379ac0f8a08cba8357be65b52ce96b5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072469538" } ] }