{
  "_id": "6a17ee05acfb0bcc41da5315",
  "Package": "flowTraceR",
  "Title": "Tracing Information Flow for Inter-Software Comparisons in Mass\nSpectrometry-Based Bottom-Up Proteomics",
  "Version": "0.1.1",
  "Authors@R": "person(\"Oliver\", \"Kardell\", , \"Okdll@gmx.net\", role = c(\"aut\", \"cre\"))",
  "Description": "Useful functions to standardize software outputs from\nProteomeDiscoverer, Spectronaut, DIA-NN and MaxQuant on\nprecursor, modified peptide and proteingroup level and to trace\nsoftware differences for identifications such as varying\nproteingroup denotations for common precursor.",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "URL": "https://github.com/OKdll/flowTraceR",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.1",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://okdll.r-universe.dev",
  "Date/Publication": "2025-04-29 14:08:44 UTC",
  "RemoteUrl": "https://github.com/okdll/flowtracer",
  "RemoteRef": "HEAD",
  "RemoteSha": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 07:20:17 UTC",
    "User": "root"
  },
  "Author": "Oliver Kardell [aut, cre]",
  "Maintainer": "Oliver Kardell <Okdll@gmx.net>",
  "MD5sum": "dd18074d157d362dbc0915fdb8936aed",
  "_user": "okdll",
  "_type": "src",
  "_file": "flowTraceR_0.1.1.tar.gz",
  "_fileid": "fda14790e66f51954e226ed22bde56e876038ff45db674dcecaef3ce8b267de2",
  "_filesize": 579552,
  "_sha256": "fda14790e66f51954e226ed22bde56e876038ff45db674dcecaef3ce8b267de2",
  "_created": "2026-05-28T07:20:17.000Z",
  "_published": "2026-05-28T07:25:57.108Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78242750337,
      "time": 156,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7259979081"
    },
    {
      "job": 78242750281,
      "time": 166,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259982059"
    },
    {
      "job": 78242750297,
      "time": 160,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7260010796"
    },
    {
      "job": 78242750351,
      "time": 185,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7260014068"
    },
    {
      "job": 78242107012,
      "time": 270,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259933675"
    },
    {
      "job": 78242750302,
      "time": 113,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259966684"
    },
    {
      "job": 78242750364,
      "time": 91,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7259960537"
    },
    {
      "job": 78242750450,
      "time": 89,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7259959760"
    },
    {
      "job": 78242750373,
      "time": 143,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259975895"
    }
  ],
  "_buildurl": "https://github.com/r-universe/okdll/actions/runs/26560498402",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/okdll/flowtracer",
  "_commit": {
    "id": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
    "author": "OKdll <40389089+OKdll@users.noreply.github.com>",
    "committer": "OKdll <40389089+OKdll@users.noreply.github.com>",
    "message": "update version nr\n",
    "time": 1745935724
  },
  "_maintainer": {
    "name": "Oliver Kardell",
    "email": "okdll@gmx.net"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "comprehenr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "okdll",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "okdll",
      "count": 99,
      "uuid": 40389089
    }
  ],
  "_userbio": {
    "uuid": 40389089,
    "type": "user",
    "name": "OKdll"
  },
  "_downloads": {
    "count": 557,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/flowTraceR"
  },
  "_devurl": "https://github.com/okdll/flowtracer",
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/flowTraceR.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/okdll/flowtracer",
  "_realowner": "okdll",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2022-06-03"
    },
    {
      "version": "0.1.1",
      "date": "2025-04-29"
    }
  ],
  "_exports": [
    "analyze_connected_levels",
    "analyze_unknown_mods",
    "connect_traceR_levels",
    "convert_all_levels",
    "convert_modified_peptides",
    "convert_precursor",
    "convert_proteingroups",
    "get_example",
    "get_unknown_mods",
    "trace_all_levels",
    "trace_level",
    "trace_unique_common_pg"
  ],
  "_help": [
    {
      "page": "analyze_connected_levels",
      "title": "Analysis of connected levels",
      "topics": [
        "analyze_connected_levels"
      ]
    },
    {
      "page": "analyze_unknown_mods",
      "title": "Analysis of unknown modifications",
      "topics": [
        "analyze_unknown_mods"
      ]
    },
    {
      "page": "connect_traceR_levels",
      "title": "Connects traced levels",
      "topics": [
        "connect_traceR_levels"
      ]
    },
    {
      "page": "convert_all_levels",
      "title": "Conversion of software specific levels",
      "topics": [
        "convert_all_levels"
      ]
    },
    {
      "page": "convert_modified_peptides",
      "title": "Conversion of software specific modified peptide entries",
      "topics": [
        "convert_modified_peptides"
      ]
    },
    {
      "page": "convert_precursor",
      "title": "Conversion of software specific precursor entries",
      "topics": [
        "convert_precursor"
      ]
    },
    {
      "page": "convert_proteingroups",
      "title": "Conversion of software specific proteinGroups",
      "topics": [
        "convert_proteingroups"
      ]
    },
    {
      "page": "flowTraceR",
      "title": "flowTraceR: a package for standardization of level information and tracking inter-software differences in bottom-up label-free proteomics",
      "topics": [
        "flowTraceR-package",
        "flowTraceR"
      ]
    },
    {
      "page": "get_example",
      "title": "Create example data",
      "topics": [
        "get_example"
      ]
    },
    {
      "page": "get_unknown_mods",
      "title": "Check of converted modifications",
      "topics": [
        "get_unknown_mods"
      ]
    },
    {
      "page": "trace_all_levels",
      "title": "Trace common and unique identifications between different software outputs for all levels",
      "topics": [
        "trace_all_levels"
      ]
    },
    {
      "page": "trace_level",
      "title": "Trace common and unique identifications between different software outputs",
      "topics": [
        "trace_level"
      ]
    },
    {
      "page": "trace_unique_common_pg",
      "title": "Trace unique_common categorization for proteinGroup level",
      "topics": [
        "trace_unique_common_pg"
      ]
    }
  ],
  "_readme": "https://github.com/okdll/flowtracer/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "comprehenr",
    "cpp11",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "Example_RT_distribution.Rmd",
      "filename": "Example_RT_distribution.html",
      "title": "Example Retention Time Distribution",
      "author": "Oliver Kardell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Loading R packages",
        "Preparation",
        "Conversion to standardized format",
        "RT distribution",
        "Without flowTraceR",
        "With flowTraceR",
        "Inter-software comparison",
        "Common entries",
        "Unique entries"
      ],
      "created": "2022-05-31 12:06:46",
      "modified": "2022-06-01 14:59:00",
      "commits": 5
    },
    {
      "source": "Requirements.Rmd",
      "filename": "Requirements.html",
      "title": "Requirements",
      "author": "Oliver Kardell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Spectronaut",
        "MaxQuant",
        "DIA-NN",
        "Proteome Discoverer"
      ],
      "created": "2022-05-31 12:06:46",
      "modified": "2022-06-02 16:04:32",
      "commits": 2
    },
    {
      "source": "Workflow.Rmd",
      "filename": "Workflow.html",
      "title": "Workflow",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Loading R packages",
        "Import",
        "Import your data",
        "Examples",
        "Conversion to standardized format",
        "Precursor",
        "Modified Peptides",
        "ProteinGroups",
        "All Levels",
        "Analyzing Conversion",
        "Example precursor level",
        "For each individual level",
        "All levels",
        "Connect traced levels",
        "Show software differences for modified peptide/proteinGroup denotations",
        "Example proteinGroup level",
        "Get software difference for proteinGroup denotations",
        "Results:"
      ],
      "created": "2022-05-31 12:06:46",
      "modified": "2022-06-23 13:24:56",
      "commits": 8
    }
  ],
  "_score": 5.130333768495006,
  "_indexed": true,
  "_nocasepkg": "flowtracer",
  "_universes": [
    "okdll"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-05-28T07:22:39.000Z",
      "distro": "noble",
      "commit": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
      "fileid": "d52f5d2037f4328f7fd83b0a538a24df93c9ecd1dce9d614cd58aec24edb264c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/okdll/actions/runs/26560498402"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-05-28T07:22:47.000Z",
      "distro": "noble",
      "commit": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
      "fileid": "1878fe42e4c2417c4cf2fb3b2222014a2d9fe7d785dd309e8db399d0dcd0052c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/okdll/actions/runs/26560498402"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-05-28T07:24:27.000Z",
      "commit": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
      "fileid": "258deb82d42fb1d23370b5e05cd9730973de63f2eca798d98617f62f2f69dcc7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/okdll/actions/runs/26560498402"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-05-28T07:24:37.000Z",
      "commit": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
      "fileid": "8ac914b823150fe7a164784f2842d5611182ccfe09ceedb4df6d376e4dc69b01",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/okdll/actions/runs/26560498402"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.1",
      "date": "2026-05-28T07:22:26.000Z",
      "commit": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
      "fileid": "6298ed13c4fc931358524379ac58e528ba70639aa53d9b66e94ecdbe4899e5c6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/okdll/actions/runs/26560498402"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-05-28T07:21:29.000Z",
      "commit": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
      "fileid": "a6acb1c17008fe025997dce0703b8835c287d0f3d53fca274c6403b91fb5b418",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/okdll/actions/runs/26560498402"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-05-28T07:21:26.000Z",
      "commit": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
      "fileid": "6e3f69bb51c3cb5984fa60ef013d8263ced2a235097d15ab093d2e0ae925870f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/okdll/actions/runs/26560498402"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-05-28T07:22:16.000Z",
      "commit": "535be57b4a0096a1eca58d3843ca28c27a4661ed",
      "fileid": "823f4ac9a99386e7844c6db674242f16b1c70238040699db7be53fd2d196af8a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/okdll/actions/runs/26560498402"
    }
  ]
}