{
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  "Package": "topdownr",
  "Title": "Investigation of Fragmentation Conditions in Top-Down Proteomics",
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  "Authors@R": "c(person(\"Sebastian\", \"Gibb\", role=c(\"aut\", \"cre\"),\nemail=\"mail@sebastiangibb.de\",\ncomment=c(ORCID=\"0000-0001-7406-4443\")),\nperson(\"Pavel\", \"Shliaha\", role=\"aut\",\nemail=\"pavels@bmb.sdu.dk\",\ncomment=c(ORCID=\"0000-0003-3092-0724\")),\nperson(c(\"Ole\", \"Nørregaard\"), \"Jensen\", role=\"aut\",\nemail=\"jenseno@bmb.sdu.dk\",\ncomment=c(ORCID=\"0000-0003-1862-8528\")))",
  "Description": "The topdownr package allows automatic and systemic\ninvestigation of fragment conditions. It creates Thermo\nOrbitrap Fusion Lumos method files to test hundreds of\nfragmentation conditions. Additionally it provides functions to\nanalyse and process the generated MS data and determine the\nbest conditions to maximise overall fragment coverage.",
  "License": "GPL (>= 3)",
  "URL": "https://codeberg.org/sgibb/topdownr/",
  "BugReports": "https://codeberg.org/sgibb/topdownr/issues/",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:43 UTC",
  "RemoteUrl": "https://github.com/bioc/topdownr",
  "RemoteRef": "RELEASE_3_23",
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  "Author": "Sebastian Gibb [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7406-4443>),\nPavel Shliaha [aut] (ORCID: <https://orcid.org/0000-0003-3092-0724>),\nOle Nørregaard Jensen [aut] (ORCID:\n<https://orcid.org/0000-0003-1862-8528>)",
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    "colData",
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    "conditionNames",
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    "expandMs1Conditions",
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    "fragmentationMap",
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    "updateConditionNames",
    "updateMedianInjectionTime",
    "validMs1Settings",
    "validTms2Settings",
    "writeMethodXmls"
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      "tojson": false
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      "title": "Investigation of Fragmentation Conditions in Top-Down Proteomics",
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        "topdownr-package",
        "topdownr"
      ]
    },
    {
      "page": "AbstractTopDownSet-class",
      "title": "The AbstractTopDownSet class",
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        "$<-,AbstractTopDownSet-method",
        "AbstractTopDownSet-class",
        "assayData,AbstractTopDownSet-method",
        "colData",
        "colData,AbstractTopDownSet-method",
        "colData<-",
        "colData<-,AbstractTopDownSet-method",
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        "combine,AbstractTopDownSet,AbstractTopDownSet-method",
        "conditionData",
        "conditionData,AbstractTopDownSet-method",
        "conditionData<-",
        "conditionData<-,AbstractTopDownSet-method",
        "conditionNames",
        "conditionNames,AbstractTopDownSet-method",
        "dim,AbstractTopDownSet-method",
        "dimnames,AbstractTopDownSet-method",
        "removeEmptyConditions",
        "removeEmptyConditions,AbstractTopDownSet-method",
        "rowViews",
        "rowViews,AbstractTopDownSet-method",
        "show,AbstractTopDownSet-method",
        "summary,AbstractTopDownSet-method",
        "updateConditionNames",
        "updateConditionNames,AbstractTopDownSet-method",
        "updateMedianInjectionTime",
        "updateMedianInjectionTime,AbstractTopDownSet-method",
        "updateMedianInjectionTime,TopDownSet-method",
        "[,AbstractTopDownSet,ANY,ANY,ANY-method",
        "[[,AbstractTopDownSet,ANY,missing,-method",
        "[[,AbstractTopDownSet,ANY,missing-method",
        "[[<-,AbstractTopDownSet,ANY,missing,-method",
        "[[<-,AbstractTopDownSet,ANY,missing-method"
      ]
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    {
      "page": "createExperimentsFragmentOptimisation",
      "title": "Create fragment optimisation experiment",
      "topics": [
        "createExperimentsFragmentOptimisation"
      ]
    },
    {
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      "title": "Windows specific functions.",
      "topics": [
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        "runScanHeadsman",
        "runXmlMethodChanger"
      ]
    },
    {
      "page": "expandMsConditions",
      "title": "Expand MS Conditions",
      "topics": [
        "expandMs1Conditions",
        "expandTms2Conditions"
      ]
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    {
      "page": "FragmentViews-class",
      "title": "The FragmentViews class",
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        "combine,FragmentViews,FragmentViews-method",
        "combine,FragmentViews-method",
        "FragmentViews",
        "FragmentViews-class",
        "mz,FragmentViews-method",
        "show,FragmentViews-method"
      ]
    },
    {
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        "bestConditions,NCBSet-method",
        "fragmentationMap",
        "fragmentationMap,NCBSet-method",
        "NCBSet-class",
        "show,NCBSet-method",
        "summary,NCBSet-method"
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      "topics": [
        "tds"
      ]
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        "summary,TopDownSet-method",
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