{
  "_id": "6a274d4624555f66ed530564",
  "Package": "wrProteo",
  "Version": "2.0.2",
  "Title": "Proteomics Data Analysis Functions",
  "Authors@R": "person(\"Wolfgang\", \"Raffelsberger\", email = \"w.raffelsberger@gmail.com\", role = c(\"aut\", \"cre\"))",
  "Author": "Wolfgang Raffelsberger [aut, cre]",
  "Maintainer": "Wolfgang Raffelsberger <w.raffelsberger@gmail.com>",
  "Description": "Data analysis of proteomics experiments by mass\nspectrometry is supported by this collection of functions\nmostly dedicated to the analysis of (bottom-up) quantitative\n(XIC) data. Fasta-formatted proteomes (eg from UniProt\nConsortium <doi:10.1093/nar/gky1049>) can be read with\nautomatic parsing and multiple annotation types (like species\norigin, abbreviated gene names, etc) extracted. Initial results\nfrom multiple software for protein (and peptide) quantitation\ncan be imported (to a common format): MaxQuant (Tyanova et al\n2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020\n<doi:10.1038/s41592-019-0638-x>), Fragpipe (da Veiga et al 2020\n<doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021\n<doi:10.1101/2021.07.02.450686>), MassChroq (Valot et al 2011\n<doi:10.1002/pmic.201100120>), OpenMS (Strauss et al 2021\n<doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021\n<doi:10.3390/proteomes9010015>), Proline (Bouyssie et al 2020\n<doi:10.1093/bioinformatics/btaa118>), AlphaPept (preprint\nStrauss et al <doi:10.1101/2021.07.23.453379>) and Wombat-P\n(Bouyssie et al 2023 <doi:10.1021/acs.jproteome.3c00636>.\nMeta-data provided by initial analysis software and/or in sdrf\nformat can be integrated to the analysis. Quantitative\nproteomics measurements frequently contain multiple NA values,\ndue to physical absence of given peptides in some samples,\nlimitations in sensitivity or other reasons. Help is provided\nto inspect the data graphically to investigate the nature of\nNA-values via their respective replicate measurements and to\nhelp/confirm the choice of NA-replacement algorithms. Meta-data\nin sdrf-format (Perez-Riverol et al 2020\n<doi:10.1021/acs.jproteome.0c00376>) or similar tabular formats\ncan be imported and included. Missing values can be inspected\nand imputed based on the concept of NA-neighbours or other\nmethods. Dedicated filtering and statistical testing using the\nframework of package 'limma' <doi:10.18129/B9.bioc.limma> can\nbe run, enhanced by multiple rounds of NA-replacements to\nprovide robustness towards rare stochastic events.\nMulti-species samples, as frequently used in benchmark-tests\n(eg Navarro et al 2016 <doi:10.1038/nbt.3685>, Ramus et al 2016\n<doi:10.1016/j.jprot.2015.11.011>), can be run with special\noptions considering such sub-groups during normalization and\ntesting. Subsequently, ROC curves (Hand and Till 2001\n<doi:10.1023/A:1010920819831>) can be constructed to compare\nmultiple analysis approaches. As detailed example the data-set\nfrom Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>)\nquantified by MaxQuant, ProteomeDiscoverer, and Proline is\nprovided with a detailed analysis of heterologous spike-in\nproteins.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-08 23:12:42 UTC",
    "User": "root"
  },
  "Repository": "https://wraff.r-universe.dev",
  "Date/Publication": "2026-04-29 14:35:29 UTC",
  "RemoteUrl": "https://github.com/cran/wrProteo",
  "RemoteRef": "HEAD",
  "RemoteSha": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
  "MD5sum": "c391277e7ca4b32ac0b6a5974b2c5f33",
  "_user": "wraff",
  "_type": "src",
  "_file": "wrProteo_2.0.2.tar.gz",
  "_fileid": "4a2fd6a5187f6a5c2b86ac38a1e8730ae1de9ded8b3c083d9f75fce1867204c7",
  "_filesize": 8027280,
  "_sha256": "4a2fd6a5187f6a5c2b86ac38a1e8730ae1de9ded8b3c083d9f75fce1867204c7",
  "_created": "2026-06-08T23:12:42.000Z",
  "_published": "2026-06-08T23:16:22.931Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 80215734839,
      "time": 173,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7494719321"
    },
    {
      "job": 80215734835,
      "time": 165,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7494717425"
    },
    {
      "job": 80215734834,
      "time": 116,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7494705514"
    },
    {
      "job": 80215734836,
      "time": 117,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7494705680"
    },
    {
      "job": 80215131305,
      "time": 288,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7494677838"
    },
    {
      "job": 80215734833,
      "time": 157,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7494715305"
    },
    {
      "job": 80215734838,
      "time": 95,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7494700309"
    },
    {
      "job": 80215734861,
      "time": 133,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7494709875"
    },
    {
      "job": 80215734849,
      "time": 149,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7494713484"
    }
  ],
  "_buildurl": "https://github.com/r-universe/wraff/actions/runs/27172718927",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/wrProteo",
  "_commit": {
    "id": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
    "author": "Wolfgang Raffelsberger <w.raffelsberger@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.0.2\n",
    "time": 1777473329
  },
  "_maintainer": {
    "name": "Wolfgang Raffelsberger",
    "email": "w.raffelsberger@gmail.com",
    "login": "wraff",
    "description": "",
    "uuid": 53934347
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "wrMisc",
      "version": ">= 2.0.1",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Suggests"
    },
    {
      "package": "fdrtool",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "RColorBrewer",
      "role": "Suggests"
    },
    {
      "package": "readxl",
      "role": "Suggests"
    },
    {
      "package": "ROTS",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "R.utils",
      "role": "Suggests"
    },
    {
      "package": "sm",
      "role": "Suggests"
    },
    {
      "package": "wrGraph",
      "version": ">= 1.3.12",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-34",
      "n": 1
    },
    {
      "week": "2026-11",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.13.3",
      "date": "2025-08-22"
    },
    {
      "name": "2.0.0.2",
      "date": "2026-03-11"
    },
    {
      "name": "2.0.2",
      "date": "2026-04-29"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "wraff",
      "count": 26,
      "uuid": 53934347
    }
  ],
  "_userbio": {
    "uuid": 53934347,
    "type": "user",
    "name": "Wolfgang Raffelsberger"
  },
  "_downloads": {
    "count": 1157,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/wrProteo"
  },
  "_searchresults": 15,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/wrProteo.html",
    "manual.pdf"
  ],
  "_realowner": "wraff",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2020-01-08"
    },
    {
      "version": "1.1.1",
      "date": "2020-04-29"
    },
    {
      "version": "1.1.2",
      "date": "2020-07-15"
    },
    {
      "version": "1.1.3",
      "date": "2020-07-18"
    },
    {
      "version": "1.1.4",
      "date": "2020-10-07"
    },
    {
      "version": "1.2.0",
      "date": "2020-10-18"
    },
    {
      "version": "1.3.0",
      "date": "2020-11-27"
    },
    {
      "version": "1.4.0",
      "date": "2021-03-10"
    },
    {
      "version": "1.4.1",
      "date": "2021-04-15"
    },
    {
      "version": "1.4.2",
      "date": "2021-07-05"
    },
    {
      "version": "1.4.3",
      "date": "2021-07-13"
    },
    {
      "version": "1.5.0",
      "date": "2022-01-10"
    },
    {
      "version": "1.6.0",
      "date": "2022-03-01"
    },
    {
      "version": "1.7.0.1",
      "date": "2022-11-24"
    },
    {
      "version": "1.7.1",
      "date": "2023-01-27"
    },
    {
      "version": "1.8.0",
      "date": "2023-03-23"
    },
    {
      "version": "1.9.0",
      "date": "2023-04-20"
    },
    {
      "version": "1.10.0",
      "date": "2023-06-16"
    },
    {
      "version": "1.10.1",
      "date": "2023-08-18"
    },
    {
      "version": "1.11.0.1",
      "date": "2024-02-14"
    },
    {
      "version": "1.12.0",
      "date": "2024-07-26"
    },
    {
      "version": "1.13.0",
      "date": "2024-11-18"
    },
    {
      "version": "1.13.1",
      "date": "2025-04-01"
    },
    {
      "version": "1.13.3",
      "date": "2025-08-22"
    },
    {
      "version": "2.0.0.2",
      "date": "2026-03-11"
    },
    {
      "version": "2.0.2",
      "date": "2026-04-29"
    }
  ],
  "_exports": [
    ".atomicMasses",
    ".checkKnitrProt",
    ".checkSetupGroups",
    ".commonSpecies",
    ".extrSpecPref",
    ".imputeNA",
    ".parseFastaHeader",
    ".plotQuantDistr",
    "AAmass",
    "AucROC",
    "cleanListCoNames",
    "combineMultFilterNAimput",
    "convAASeq2mass",
    "corColumnOrder",
    "countNoOfCommonPeptides",
    "exportAsWombatP",
    "exportSdrfDraft",
    "extractTestingResults",
    "extrSpeciesAnnot",
    "foldChangeArrow2",
    "fuseProteomicsProjects",
    "getUPS1acc",
    "inspectSpeciesIndic",
    "isolNAneighb",
    "massDeFormula",
    "matrixNAinspect",
    "matrixNAneighbourImpute",
    "plotROC",
    "razorNoFilter",
    "readAlphaPeptFile",
    "readDiaNNFile",
    "readDiaNNPeptides",
    "readFasta2",
    "readFragpipeFile",
    "readIonbotPeptides",
    "readMassChroQFile",
    "readMaxQuantFile",
    "readMaxQuantPeptides",
    "readOpenMSFile",
    "readProlineFile",
    "readProtDiscovererPeptides",
    "readProtDiscovFile",
    "readProteomeDiscovererFile",
    "readProteomeDiscovererPeptides",
    "readSampleMetaData",
    "readSdrf",
    "readUCSCtable",
    "readUniProtExport",
    "readWombatNormFile",
    "removeSampleInList",
    "replMissingProtNames",
    "shortSoftwName",
    "summarizeForROC",
    "test2grp",
    "testRobustToNAimputation",
    "VolcanoPlotW2",
    "writeFasta2"
  ],
  "_help": [
    {
      "page": "dot-atomicMasses",
      "title": "Molecular mass for Elements",
      "topics": [
        ".atomicMasses"
      ]
    },
    {
      "page": "dot-checkKnitrProt",
      "title": "Checking presence of knitr and rmarkdown",
      "topics": [
        ".checkKnitrProt"
      ]
    },
    {
      "page": "dot-checkSetupGroups",
      "title": "Additional/final Check And Adjustments To Sample-order After readSampleMetaData()",
      "topics": [
        ".checkSetupGroups"
      ]
    },
    {
      "page": "dot-commonSpecies",
      "title": "Get Matrix With UniProt Abbreviations For Selected Species As Well As Simple Names",
      "topics": [
        ".commonSpecies"
      ]
    },
    {
      "page": "dot-extrSpecPref",
      "title": "Extract Additional Information To Construct The Colum 'SpecType', Allows Adding Information From Fasta",
      "topics": [
        ".extrSpecPref"
      ]
    },
    {
      "page": "dot-imputeNA",
      "title": "Basic NA-imputaton (main)",
      "topics": [
        ".imputeNA"
      ]
    },
    {
      "page": "dot-parseFastaHeader",
      "title": "Parse Fasta Header",
      "topics": [
        ".parseFastaHeader"
      ]
    },
    {
      "page": "dot-plotQuantDistr",
      "title": "Generic Plotting Of Density Distribution For Quantitation Import-functions",
      "topics": [
        ".plotQuantDistr"
      ]
    },
    {
      "page": "AAmass",
      "title": "Molecular mass for amino-acids",
      "topics": [
        "AAmass"
      ]
    },
    {
      "page": "AucROC",
      "title": "AUC from ROC-curves",
      "topics": [
        "AucROC"
      ]
    },
    {
      "page": "cleanListCoNames",
      "title": "Selective batch cleaning of sample- (ie column-) names in list",
      "topics": [
        "cleanListCoNames"
      ]
    },
    {
      "page": "combineMultFilterNAimput",
      "title": "Combine Multiple Filters On NA-imputed Data",
      "topics": [
        "combineMultFilterNAimput"
      ]
    },
    {
      "page": "convAASeq2mass",
      "title": "Molecular mass for amino-acids",
      "topics": [
        "convAASeq2mass"
      ]
    },
    {
      "page": "corColumnOrder",
      "title": "Order Columns In List Of Matrixes, Data.frames And Vectors",
      "topics": [
        "corColumnOrder"
      ]
    },
    {
      "page": "countNoOfCommonPeptides",
      "title": "Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides. The in-silico digestion may be performed separately using the package cleaver. Note: input must be list (or multiple names lists) of proteins with their respective peptides (eg by in-silico digestion).",
      "topics": [
        "countNoOfCommonPeptides"
      ]
    },
    {
      "page": "exportAsWombatP",
      "title": "Export As Wombat-P Set Of Files",
      "topics": [
        "exportAsWombatP"
      ]
    },
    {
      "page": "exportSdrfDraft",
      "title": "Export Sample Meta-data from Quantification-Software as Sdrf-draft",
      "topics": [
        "exportSdrfDraft"
      ]
    },
    {
      "page": "extractTestingResults",
      "title": "Extract Results From Moderated t-tests",
      "topics": [
        "extractTestingResults"
      ]
    },
    {
      "page": "extrSpeciesAnnot",
      "title": "Extract species annotation",
      "topics": [
        "extrSpeciesAnnot"
      ]
    },
    {
      "page": "foldChangeArrow2",
      "title": "Add arrow for expected Fold-Change to VolcanoPlot or MA-plot",
      "topics": [
        "foldChangeArrow2"
      ]
    },
    {
      "page": "fuseProteomicsProjects",
      "title": "Combine Multiple Proteomics Data-Sets",
      "topics": [
        "fuseProteomicsProjects"
      ]
    },
    {
      "page": "getUPS1acc",
      "title": "UniProt Accession-Numbers And Names Of UPS1 Proteins",
      "topics": [
        "getUPS1acc"
      ]
    },
    {
      "page": "inspectSpeciesIndic",
      "title": "Inspect Species Indictaion Or Group of Proteins",
      "topics": [
        "inspectSpeciesIndic"
      ]
    },
    {
      "page": "isolNAneighb",
      "title": "Isolate NA-neighbours",
      "topics": [
        "isolNAneighb"
      ]
    },
    {
      "page": "massDeFormula",
      "title": "Molecular mass from chemical formula",
      "topics": [
        "massDeFormula"
      ]
    },
    {
      "page": "matrixNAinspect",
      "title": "Histogram of content of NAs in matrix",
      "topics": [
        "matrixNAinspect"
      ]
    },
    {
      "page": "matrixNAneighbourImpute",
      "title": "Imputation Of NA-Values Based On Non-NA Replicates",
      "topics": [
        "matrixNAneighbourImpute"
      ]
    },
    {
      "page": "plotROC",
      "title": "Plot ROC curves",
      "topics": [
        "plotROC"
      ]
    },
    {
      "page": "razorNoFilter",
      "title": "Filter based on either number of total peptides and specific peptides or number of razor petides",
      "topics": [
        "razorNoFilter"
      ]
    },
    {
      "page": "readAlphaPeptFile",
      "title": "Read (Normalized) Quantitation Data Files Produced By AlphaPept",
      "topics": [
        "readAlphaPeptFile"
      ]
    },
    {
      "page": "readDiaNNFile",
      "title": "Read Tabulated Files Exported by DIA-NN At Protein Level",
      "topics": [
        "readDiaNNFile"
      ]
    },
    {
      "page": "readDiaNNPeptides",
      "title": "Read Tabulated Files Exported by DiaNN At Peptide Level",
      "topics": [
        "readDiaNNPeptides"
      ]
    },
    {
      "page": "readFasta2",
      "title": "Read File Of Protein Sequences In Fasta Format",
      "topics": [
        "readFasta2"
      ]
    },
    {
      "page": "readFragpipeFile",
      "title": "Read Tabulated Files Exported by FragPipe At Protein Level",
      "topics": [
        "readFragpipeFile"
      ]
    },
    {
      "page": "readIonbotPeptides",
      "title": "Read Tabulated Files Exported by Ionbot At Peptide Level",
      "topics": [
        "readIonbotPeptides"
      ]
    },
    {
      "page": "readMassChroQFile",
      "title": "Read tabulated files imported from MassChroQ",
      "topics": [
        "readMassChroQFile"
      ]
    },
    {
      "page": "readMaxQuantFile",
      "title": "Read Quantitation Data-Files (proteinGroups.txt) Produced From MaxQuant At Protein Level",
      "topics": [
        "readMaxQuantFile"
      ]
    },
    {
      "page": "readMaxQuantPeptides",
      "title": "Read Peptide Identification and Quantitation Data-Files (peptides.txt) Produced By MaxQuant",
      "topics": [
        "readMaxQuantPeptides"
      ]
    },
    {
      "page": "readOpenMSFile",
      "title": "Read csv files exported by OpenMS",
      "topics": [
        "readOpenMSFile"
      ]
    },
    {
      "page": "readProlineFile",
      "title": "Read xlsx, csv or tsv Files Exported From Proline And MS-Angel",
      "topics": [
        "readProlineFile"
      ]
    },
    {
      "page": "readProtDiscovererPeptides",
      "title": "readProtDiscovererPeptides, deprecated",
      "topics": [
        "readProtDiscovererPeptides"
      ]
    },
    {
      "page": "readProtDiscovFile",
      "title": "Read Tabulated Files Exported By ProteomeDiscoverer At Protein Level, Deprecated",
      "topics": [
        "readProtDiscovFile"
      ]
    },
    {
      "page": "readProteomeDiscovererFile",
      "title": "Read Tabulated Files Exported By ProteomeDiscoverer At Protein Level",
      "topics": [
        "readProteomeDiscovererFile"
      ]
    },
    {
      "page": "readProteomeDiscovererPeptides",
      "title": "Read Tabulated Files Exported By ProteomeDiscoverer At Peptide Level",
      "topics": [
        "readProteomeDiscovererPeptides"
      ]
    },
    {
      "page": "readSampleMetaData",
      "title": "Read Sample Meta-data from Quantification-Software And/Or Sdrf And Align To Experimental Data",
      "topics": [
        "readSampleMetaData"
      ]
    },
    {
      "page": "readSdrf",
      "title": "Read proteomics meta-data as sdrf file",
      "topics": [
        "readSdrf"
      ]
    },
    {
      "page": "readUCSCtable",
      "title": "Read annotation files from UCSC",
      "topics": [
        "readUCSCtable"
      ]
    },
    {
      "page": "readUniProtExport",
      "title": "Read protein annotation as exported from UniProt batch-conversion",
      "topics": [
        "readUniProtExport"
      ]
    },
    {
      "page": "readWombatNormFile",
      "title": "Read (Normalized) Quantitation Data Files Produced By Wombat At Protein Level",
      "topics": [
        "readWombatNormFile"
      ]
    },
    {
      "page": "removeSampleInList",
      "title": "Remove Samples/Columns From List Of Matrixes",
      "topics": [
        "removeSampleInList"
      ]
    },
    {
      "page": "replMissingProtNames",
      "title": "Complement Missing EntryNames In Annotation",
      "topics": [
        "replMissingProtNames"
      ]
    },
    {
      "page": "shortSoftwName",
      "title": "Get Short Names of Proteomics Quantitation Software",
      "topics": [
        "shortSoftwName"
      ]
    },
    {
      "page": "summarizeForROC",
      "title": "Summarize statistical test result for plotting ROC-curves",
      "topics": [
        "summarizeForROC"
      ]
    },
    {
      "page": "test2grp",
      "title": "t-test each line of 2 groups of data",
      "topics": [
        "test2grp"
      ]
    },
    {
      "page": "testRobustToNAimputation",
      "title": "Pairwise Testing Robust To NA-Imputation",
      "topics": [
        "testRobustToNAimputation"
      ]
    },
    {
      "page": "VolcanoPlotW2",
      "title": "Deprecialed Volcano-plot",
      "topics": [
        "VolcanoPlotW2"
      ]
    },
    {
      "page": "writeFasta2",
      "title": "Write Sequences In Fasta Format To File This function writes sequences from character vector or parsed matrix to file as fasta formatted file (close to UniProt) This function also allows comparing the main vector of sequences with a reference vector 'ref' to check if any of the sequences therein are truncated.",
      "topics": [
        "writeFasta2"
      ]
    }
  ],
  "_rundeps": [
    "evaluate",
    "highr",
    "knitr",
    "limma",
    "MASS",
    "statmod",
    "wrMisc",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "wrProteoVignetteUPS1.Rmd",
      "filename": "wrProteoVignetteUPS1.html",
      "title": "Analyzing Proteomics UPS1 Spike-in Experiments (Example Ramus 2016 Dataset)",
      "author": "Wolfgang Raffelsberger",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Experimental Setup For Benchmark Tests",
        "The Ramus Data-Set",
        "Meta-Data Describing The Experiment (sdrf)",
        "Key Elements And Additional Functions",
        "Protein Identification and Initial Quantification",
        "MaxQuant",
        "ProteomeDiscoverer",
        "Proline",
        "Further Preparation Of Data",
        "Basic Data Treatment",
        "Structure of Experiment",
        "Normalization",
        "Presence of NA-values",
        "NA-Imputation and Statistical Testing for Changes in Abundance",
        "Analysis Using All Proteins Identified (Matrix + UPS1)",
        "Pairwise Testing Summary",
        "Volcano Plots",
        "ROC for Multiple Pairs",
        "Grouping of ROC Curves to Display Representative Ones",
        "Plotting ROC Curves for the Best Cluster  (the '+++++')",
        "ROC Curves for 2nd Best Cluster  (the '++++')",
        "ROC Curves for the 3rd Best Cluster  (the '+++')",
        "ROC Curves for the 4th Best Cluster  (the '++')",
        "ROC Curves for the Weakest Cluster 1  (the '+')",
        "Analysis Focussing on UPS1 Spike-In Proteins Only",
        "Similarity by PCA  (UPS1 proteins only)",
        "PCA of UPS1 for ProteomeDiscoverer",
        "PCA of UPS1 for MaxQuant",
        "PCA of UPS1 for Proline",
        "CV of Replicates",
        "Testing All Individual UPS1 Proteins By Linear Regression",
        "Linear Regression for each UPS1 : ProteomeDiscoverer",
        "Linear Regression for each UPS1 : MaxQuant",
        "Linear Regression for each UPS1 : Proline",
        "Frequency Of Starting Levels For Regression",
        "Global Comparison Of Regression Models",
        "Summarize Linear Regression Results",
        "Grouping of UPS1 Proteins to Display Representative Proteins",
        "Representative UPS1-protein of the Best Group  (the '+++++')",
        "Representative UPS1-protein of the 2nd Best Group  (the '++++')",
        "Representative UPS1-protein of the 3rd Group  (the '+++')",
        "Representative UPS1-protein of the 4th Group  (the '++')",
        "Representative UPS1-protein of the 5th (And Last) Group  (the '+')",
        "Additional Comments",
        "Acknowledgements",
        "Session-Info"
      ],
      "created": "2020-10-18 20:50:02",
      "modified": "2026-04-29 14:35:29",
      "commits": 21
    },
    {
      "source": "wrProteoVignette1.Rmd",
      "filename": "wrProteoVignette1.html",
      "title": "Getting started with wrProteo",
      "author": "Wolfgang Raffelsberger",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Calculating Molecular Masses From Composition Formulas",
        "Molecular masses based on (summed) chemical formulas",
        "Molecular masses based on amino-acid sequence",
        "Working With Fasta(Files)",
        "Reading Fasta Files (from Uniprot)",
        "Writing Sequences As Fasta Files",
        "Analyzing Label-Free Quantitative Proteomics Data",
        "Label-free Quantitative Proteomics Introduction",
        "Import From Dedicated Quantification Algorithms/Software",
        "MaxQuant: Import Protein Quantification Data",
        "Adding Meta-Data at Import (Example MaxQuant)",
        "Adding Experimental Setup (Sdrf) to Meta-Data at Import (Example MaxQuant)",
        "Exporting Experimental Setup from MaxQuant to Draft-Sdrf",
        "MaxQuant : Import Peptide Data",
        "ProteomeDiscoverer : Import Protein Quantification",
        "ProteomeDiscoverer : Import Peptide Data",
        "DIA-NN: Import Protein Quantification Data",
        "DIA-NN : Import Peptide Data",
        "Proline : Import Protein Quantification Data",
        "Fragpipe : Import Protein Quantification Data",
        "MassChroQ : Import Protein Quantification Data",
        "AlphaPept : Import Protein Quantification Data",
        "Ionbot : Import Peptide Identification And  Quantification Data",
        "Wombat-P : Import Protein Quantification Data",
        "OpenMS : Import Protein Quantification Data",
        "Importing Sdrf Meta-Data",
        "Removing Samples From Proteomics Projects",
        "Combining Proteomics Projects",
        "Normalization",
        "Imputation of NA-values",
        "Filtering",
        "Statistical Testing",
        "Data Exploration With Graphical Support",
        "PCA",
        "MA-plot",
        "",
        "Volcano-Plot",
        "Reporting Results",
        "Further Steps",
        "Protein Annotation",
        "Appendix",
        "Acknowledgements",
        "Session-Info"
      ],
      "created": "2020-04-29 13:00:02",
      "modified": "2026-04-29 14:35:29",
      "commits": 23
    }
  ],
  "_score": 3.494697123110737,
  "_indexed": true,
  "_nocasepkg": "wrproteo",
  "_universes": [
    "wraff"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.0.2",
      "date": "2026-06-08T23:15:24.000Z",
      "distro": "noble",
      "commit": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
      "fileid": "4a18d3b14347b27d38e4fbe6a92ca4b50c102029def5d6b0c789d1204e692506",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wraff/actions/runs/27172718927"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.0.2",
      "date": "2026-06-08T23:15:20.000Z",
      "distro": "noble",
      "commit": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
      "fileid": "bf8b74fe54802d32339bd61ff777a08cd978410aa932ae1759a397b63069729a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wraff/actions/runs/27172718927"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.0.2",
      "date": "2026-06-08T23:14:40.000Z",
      "commit": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
      "fileid": "80e5cdff56e68e031dfc717ba25cb67917da0b4ae8cec92c6285478d8d2c0d2d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wraff/actions/runs/27172718927"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.0.2",
      "date": "2026-06-08T23:14:42.000Z",
      "commit": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
      "fileid": "862929c24112164b7a3a8fce667521d5744a2d108e6d760ae12b716ad0db52c0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wraff/actions/runs/27172718927"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.0.2",
      "date": "2026-06-08T23:15:49.000Z",
      "commit": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
      "fileid": "f48abe2946c9a13a3898a9d9315d364d5e93a450493b81e2912f1ce1deb2a065",
      "status": "success",
      "buildurl": "https://github.com/r-universe/wraff/actions/runs/27172718927"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.0.2",
      "date": "2026-06-08T23:14:17.000Z",
      "commit": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
      "fileid": "f246f44e258faa4ab5ec17b31eea197c5242f2ee508259ec581dca261c2507fa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wraff/actions/runs/27172718927"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.0.2",
      "date": "2026-06-08T23:14:36.000Z",
      "commit": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
      "fileid": "145b8e458c7f58ddd480948351c6f9ea01c31f4baf61798110de3e19550a6ba6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wraff/actions/runs/27172718927"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.0.2",
      "date": "2026-06-08T23:14:42.000Z",
      "commit": "7bbf5f94df2bcc53629367ea25db6f2d30e37edf",
      "fileid": "69b3ff7148c7ce6ef5b15f86152ba8ca9f9124b05ca531b8b45fdce8ba42b8e4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wraff/actions/runs/27172718927"
    }
  ]
}