{
  "_id": "6a4965313c3572b93bf7eb49",
  "Package": "topdownr",
  "Title": "Investigation of Fragmentation Conditions in Top-Down Proteomics",
  "Version": "1.35.0",
  "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/",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown=TRUE)",
  "RoxygenNote": "7.3.3",
  "biocViews": "ImmunoOncology, Infrastructure, Proteomics,\nMassSpectrometry, Coverage",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:43 UTC",
  "RemoteUrl": "https://github.com/bioc/topdownr",
  "RemoteRef": "HEAD",
  "RemoteSha": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-23 06:38:14 UTC",
    "User": "root"
  },
  "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>)",
  "Maintainer": "Sebastian Gibb <mail@sebastiangibb.de>",
  "_user": "bioc",
  "_type": "src",
  "_file": "topdownr_1.35.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/64b4cc4741410fda5853016246f3af3ad8df97a2d23b33019a800fca7ff74f62",
  "_filesize": 1218661,
  "_sha256": "64b4cc4741410fda5853016246f3af3ad8df97a2d23b33019a800fca7ff74f62",
  "_expires": "2026-10-12T19:55:27.000Z",
  "_created": "2026-06-23T06:38:14.000Z",
  "_published": "2026-07-04T19:55:29.637Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 11
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28007125670",
  "_status": "success",
  "_upstream": "https://github.com/bioc/topdownr",
  "_commit": {
    "id": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380403
  },
  "_maintainer": {
    "name": "Sebastian Gibb",
    "email": "mail@sebastiangibb.de",
    "login": "sgibb",
    "mastodon": "@sgibb@floss.social",
    "orcid": "0000-0001-7406-4443",
    "description": "",
    "uuid": 1828443
  },
  "_distro": "noble",
  "_jobs": [
    {
      "job": 85162282360,
      "time": 258,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7813335596"
    },
    {
      "job": 85162282199,
      "time": 820,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7813503561"
    },
    {
      "job": 85162282313,
      "time": 503,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7813406772"
    },
    {
      "job": 85162282323,
      "time": 223,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7813325951"
    },
    {
      "job": 85162282295,
      "time": 253,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7813334399"
    },
    {
      "job": 85162282104,
      "time": 339,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7813263473"
    },
    {
      "job": 85162282170,
      "time": 209,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7813322083"
    },
    {
      "job": 85162282507,
      "time": 442,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7813388987"
    },
    {
      "job": 85162282233,
      "time": 499,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7813406291"
    },
    {
      "job": 85162282396,
      "time": 404,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7813377252"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "version": ">= 0.20.0",
      "role": "Depends"
    },
    {
      "package": "ProtGenerics",
      "version": ">= 1.10.0",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "version": ">= 2.42.1",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.12.2",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "version": ">= 1.4-2",
      "role": "Imports"
    },
    {
      "package": "MSnbase",
      "version": ">= 2.33.5",
      "role": "Imports"
    },
    {
      "package": "PSMatch",
      "version": ">= 1.11.4",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.2.1",
      "role": "Imports"
    },
    {
      "package": "mzR",
      "version": ">= 2.27.5",
      "role": "Imports"
    },
    {
      "package": "topdownrdata",
      "version": ">= 0.2",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ranger",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "xml2",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-42",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.35.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "infrastructure",
    "proteomics",
    "massspectrometry",
    "coverage"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 441,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://codeberg.org/sgibb/topdownr",
  "_searchresults": 0,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/topdownr.html",
    "manual.pdf"
  ],
  "_homeurl": "https://codeberg.org/sgibb/topdownr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aggregate",
    "assayData",
    "bestConditions",
    "colData",
    "colData<-",
    "combine",
    "conditionData",
    "conditionData<-",
    "conditionNames",
    "createExperimentsFragmentOptimisation",
    "createTngFusionMethFiles",
    "expandMs1Conditions",
    "expandTms2Conditions",
    "filterCv",
    "filterInjectionTime",
    "filterIntensity",
    "filterNonReplicatedFragments",
    "fragmentationMap",
    "FragmentViews",
    "mz",
    "normalize",
    "readTopDownFiles",
    "removeEmptyConditions",
    "rowViews",
    "runScanHeadsman",
    "runXmlMethodChanger",
    "show",
    "summary",
    "updateConditionNames",
    "updateMedianInjectionTime",
    "validMs1Settings",
    "validTms2Settings",
    "writeMethodXmls"
  ],
  "_datasets": [
    {
      "name": "tds",
      "title": "TopDownSet Example Data",
      "object": "tds",
      "class": [
        "TopDownSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "topdownr-package",
      "title": "Investigation of Fragmentation Conditions in Top-Down Proteomics",
      "topics": [
        "topdownr-package",
        "topdownr"
      ]
    },
    {
      "page": "AbstractTopDownSet-class",
      "title": "The AbstractTopDownSet class",
      "topics": [
        "$,AbstractTopDownSet-method",
        "$<-,AbstractTopDownSet-method",
        "AbstractTopDownSet-class",
        "assayData,AbstractTopDownSet-method",
        "colData",
        "colData,AbstractTopDownSet-method",
        "colData<-",
        "colData<-,AbstractTopDownSet-method",
        "combine",
        "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"
      ]
    },
    {
      "page": "createExperimentsFragmentOptimisation",
      "title": "Create fragment optimisation experiment",
      "topics": [
        "createExperimentsFragmentOptimisation"
      ]
    },
    {
      "page": "windows-specific-functions",
      "title": "Windows specific functions.",
      "topics": [
        "createTngFusionMethFiles",
        "runScanHeadsman",
        "runXmlMethodChanger"
      ]
    },
    {
      "page": "expandMsConditions",
      "title": "Expand MS Conditions",
      "topics": [
        "expandMs1Conditions",
        "expandTms2Conditions"
      ]
    },
    {
      "page": "FragmentViews-class",
      "title": "The FragmentViews class",
      "topics": [
        "coerce,FragmentViews,data.frame-method",
        "combine,FragmentViews,FragmentViews-method",
        "combine,FragmentViews-method",
        "FragmentViews",
        "FragmentViews-class",
        "mz,FragmentViews-method",
        "show,FragmentViews-method"
      ]
    },
    {
      "page": "NCBSet-class",
      "title": "The NCBSet class",
      "topics": [
        "bestConditions",
        "bestConditions,NCBSet-method",
        "fragmentationMap",
        "fragmentationMap,NCBSet-method",
        "NCBSet-class",
        "show,NCBSet-method",
        "summary,NCBSet-method"
      ]
    },
    {
      "page": "readTopDownFiles",
      "title": "Read top-down files.",
      "topics": [
        "readTopDownFiles"
      ]
    },
    {
      "page": "tds",
      "title": "TopDownSet Example Data",
      "topics": [
        "tds"
      ]
    },
    {
      "page": "topdownr-deprecated",
      "title": "Deprecated functions in topdownr",
      "topics": [
        "topdownr-deprecated"
      ]
    },
    {
      "page": "TopDownSet-class",
      "title": "The TopDownSet class",
      "topics": [
        "aggregate,TopDownSet-method",
        "coerce,TopDownSet,MSnSet-method",
        "coerce,TopDownSet,NCBSet-method",
        "combine,TopDownSet,TopDownSet-method",
        "filterCv",
        "filterCv,TopDownSet-method",
        "filterInjectionTime",
        "filterInjectionTime,TopDownSet-method",
        "filterIntensity",
        "filterIntensity,TopDownSet-method",
        "filterNonReplicatedFragments",
        "filterNonReplicatedFragments,TopDownSet-method",
        "normalize,TopDownSet-method",
        "plot,TopDownSet,missing-method",
        "show,TopDownSet-method",
        "summary,TopDownSet-method",
        "TopDownSet-class"
      ]
    },
    {
      "page": "validMsSettings",
      "title": "List valid MS settings.",
      "topics": [
        "validMs1Settings",
        "validTms2Settings"
      ]
    },
    {
      "page": "writeMethodXmls",
      "title": "Create Orbitrap Fusion Lumos method.xml files.",
      "topics": [
        "writeMethodXmls"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/topdownr/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "affy",
    "affyio",
    "AnnotationFilter",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bslib",
    "cachem",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "doParallel",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "impute",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "magrittr",
    "MALDIquant",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "MetaboCoreUtils",
    "mime",
    "MsCoreUtils",
    "MSnbase",
    "MultiAssayExperiment",
    "mzID",
    "mzR",
    "ncdf4",
    "openssl",
    "otel",
    "pcaMethods",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "preprocessCore",
    "promises",
    "ProtGenerics",
    "PSMatch",
    "PTMods",
    "purrr",
    "QFeatures",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "Rhdf5lib",
    "rlang",
    "rmarkdown",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "Spectra",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "vsn",
    "withr",
    "xfun",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "data-generation.Rmd",
      "filename": "data-generation.html",
      "title": "Data Generation for topdownr",
      "author": "Pavel V. Shliaha, Sebastian Gibb, Ole Nørregaard Jensen",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Foreword",
        "Questions and bugs",
        "Introduction",
        "The topdownr Data Generation Workflow",
        "Installation of Additional Software",
        "Setup the Thermo Software",
        "Setup XMLMethodChanger",
        "Setup Operating System",
        "Setup ScanHeadsman",
        "Creating Methods",
        "Data preparation with topdownr",
        "Data Acquisition",
        "Data Preparation",
        "Extracting Header Information",
        "Convert .raw files into mzML",
        "Session Info",
        "References"
      ],
      "created": "2017-08-01 19:51:18",
      "modified": "2018-12-07 09:04:37",
      "commits": 9
    },
    {
      "source": "analysis.Rmd",
      "filename": "analysis.html",
      "title": "Fragmentation Analysis with topdownr",
      "author": "Pavel V. Shliaha, Sebastian Gibb, Ole Nørregaard Jensen",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Foreword",
        "Questions and bugs",
        "Introduction/Working with topdownr",
        "Importing Files",
        "The TopDownSet Anatomy",
        "Technical Details",
        "Fragment data",
        "Condition data",
        "Assay data",
        "Subsetting a TopDownSet",
        "Plotting a TopDownSet",
        "Fragmentation Data Analysis of Myoglobin",
        "Filter Conditions on Injection Times",
        "Filter Fragments on CV",
        "Filter Fragments on Intensity",
        "Data Aggregation",
        "Random Forest",
        "Combining Fragmentation Conditions to Maximize Coverage",
        "Building a Fragmentation Map",
        "Session Information",
        "References"
      ],
      "created": "2017-08-01 19:51:18",
      "modified": "2019-11-22 20:10:15",
      "commits": 16
    }
  ],
  "_score": 4.698970004336019,
  "_indexed": true,
  "_nocasepkg": "topdownr",
  "_universes": [
    "bioc",
    "sgibb",
    "codeberg-sgibb"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-06-23T06:49:52.000Z",
      "distro": "noble",
      "commit": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
      "fileid": "https://r2.ropensci.org/0f5e1a774c2deaae7005d409b925a0b504f6cb3627b399a31d0e5147b078daff",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007125670"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-06-23T06:43:14.000Z",
      "distro": "noble",
      "commit": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
      "fileid": "https://r2.ropensci.org/bdb95da3d0883434009e0b2b7e37f53e1e3426eaebbbfe7676b6829d190c86a0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007125670"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-06-23T06:40:34.000Z",
      "commit": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
      "fileid": "https://r2.ropensci.org/44371aded1818141921a5cf7702611afcf4d0c78f158aa5e3fff74fda96ec994",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007125670"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-06-23T06:41:02.000Z",
      "commit": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
      "fileid": "https://r2.ropensci.org/3cd4d231299134e97cb039a055bd6c4f5076a860615ee42dd9076b4ea5ab50e8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007125670"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.35.0",
      "date": "2026-06-23T06:42:29.000Z",
      "commit": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
      "fileid": "https://r2.ropensci.org/bf677c44dec725c40b204886f90ede11d09d3b28ad93ad7e8e9ad11f57f7d61b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007125670"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-06-23T06:42:06.000Z",
      "commit": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
      "fileid": "https://r2.ropensci.org/5626944a4da75a348a49252f9947bbbabf27e33a7195f8a439ff66b80b0ff5bc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007125670"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-06-23T06:43:10.000Z",
      "commit": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
      "fileid": "https://r2.ropensci.org/4e2b1becda6f11aa084cef94a5cf9a3b7aecc695695e58d6e91c35c6bc7c9332",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007125670"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-06-23T06:42:14.000Z",
      "commit": "b3262a2923148d7b3b64672fbfc23f3a8e3e953c",
      "fileid": "https://r2.ropensci.org/65ad91280e4c6ab98aaf17534e980f9cab3bc86c40f89a80b059e3e6b88866e7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007125670"
    }
  ]
}