{
  "_id": "6ae44b6e95ca2370cc8cef7b",
  "Package": "cosmiq",
  "Type": "Package",
  "Title": "cosmiq - COmbining Single Masses Into Quantities",
  "Version": "1.47.0",
  "Authors@R": "c(person(\"David\", \"Fischer\",\nemail = \"dajofischer@googlemail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Christian\", \"Panse\",\nemail = \"cp@fgcz.ethz.ch\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-1975-3064\")),\nperson(\"Endre\", \"Laczko\",\nemail = \"cp@fgcz.ethz.ch\",\nrole = c(\"ctb\")))",
  "Description": "cosmiq is a tool for the preprocessing of liquid- or gas -\nchromatography mass spectrometry (LCMS/GCMS) data with a focus\non metabolomics or lipidomics applications. To improve the\ndetection of low abundant signals, cosmiq generates master maps\nof the mZ/RT space from all acquired runs before a peak\ndetection algorithm is applied. The result is a more robust\nidentification and quantification of low-intensity MS signals\ncompared to conventional approaches where peak picking is\nperformed in each LCMS/GCMS file separately. The cosmiq package\nbuilds on the xcmsSet object structure and can be therefore\nintegrated well with the package xcms as an alternative\npreprocessing step.",
  "License": "GPL-3",
  "URL": "http://www.bioconductor.org/packages/devel/bioc/html/cosmiq.html",
  "Collate": "combine_spectra.R peakdetection.R eicmatrix.R retention_time.R\nquantify_combined.R create_datamatrix.R cosmiq.R",
  "biocViews": "ImmunoOncology, MassSpectrometry, Metabolomics",
  "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 12:39:13 UTC",
  "RemoteUrl": "https://github.com/bioc/cosmiq",
  "RemoteRef": "HEAD",
  "RemoteSha": "e00bfb810b8421ec33b86d1b43a522f39551d020",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-29 12:07:54 UTC",
    "User": "root"
  },
  "Author": "David Fischer [aut, cre],\nChristian Panse [aut] (ORCID: <https://orcid.org/0000-0003-1975-3064>),\nEndre Laczko [ctb]",
  "Maintainer": "David Fischer <dajofischer@googlemail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "cosmiq_1.47.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/69f3c1c88fe886e9728478f9abc4002409da3858b831534ba4c7bf48c85a5f60",
  "_filesize": 670273,
  "_sha256": "69f3c1c88fe886e9728478f9abc4002409da3858b831534ba4c7bf48c85a5f60",
  "_expires": "2027-02-06T13:19:56.000Z",
  "_created": "2026-10-29T12:07:54.000Z",
  "_published": "2026-10-30T07:46:54.790Z",
  "_upstream": "https://github.com/bioc/cosmiq",
  "_status": "success",
  "_maintainer": {
    "name": "David Fischer",
    "email": "dajofischer@googlemail.com",
    "login": "dajofischer",
    "description": "",
    "uuid": 5081190
  },
  "_jobs": [
    {
      "job": 123946201867,
      "time": 171,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12961064244"
    },
    {
      "job": 123946203304,
      "time": 310,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12896506501"
    },
    {
      "job": 123946203607,
      "time": 502,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12895294609"
    },
    {
      "job": 123946204198,
      "time": 295,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12895054869"
    },
    {
      "job": 123946203538,
      "time": 457,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12895814052"
    },
    {
      "job": 123946203492,
      "time": 370,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12898594116"
    },
    {
      "job": 123946204200,
      "time": 727,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12899543622"
    },
    {
      "job": 123946202387,
      "time": 531,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12961812174"
    },
    {
      "job": 123946203506,
      "time": 870,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12900765445"
    },
    {
      "job": 123946203113,
      "time": 488,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12895881844"
    },
    {
      "job": 123946203512,
      "time": 166,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12894969363"
    },
    {
      "job": 123946203772,
      "time": 464,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12896117966"
    },
    {
      "job": 123946203545,
      "time": 448,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12896033393"
    },
    {
      "job": 123946203767,
      "time": 391,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12896206924"
    },
    {
      "job": 123946203979,
      "time": 466,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12896670875"
    },
    {
      "job": 123946203861,
      "time": 387,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12896660580"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940",
  "_commit": {
    "id": "e00bfb810b8421ec33b86d1b43a522f39551d020",
    "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": 1777379953
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "Depends"
    },
    {
      "package": "pracma",
      "role": "Imports"
    },
    {
      "package": "xcms",
      "role": "Imports"
    },
    {
      "package": "MassSpecWavelet",
      "role": "Imports"
    },
    {
      "package": "faahKO",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.47.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.46.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "immunooncology",
    "massspectrometry",
    "metabolomics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 481,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 509,
    "source": "https://www.bioconductor.org/packages/stats/bioc/cosmiq"
  },
  "_mentions": 3,
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/cosmiq.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "combine_spectra",
    "cosmiq",
    "create_datamatrix",
    "eicmatrix",
    "peakdetection",
    "quantify_combined",
    "retention_time"
  ],
  "_help": [
    {
      "page": "combine_spectra",
      "title": "Combine mass spectra of each scan and each file into a single master spectrum",
      "topics": [
        "combine_spectra"
      ]
    },
    {
      "page": "cosmiq",
      "title": "cosmiq - main wrapper function",
      "topics": [
        "cosmiq"
      ]
    },
    {
      "page": "create_datamatrix",
      "title": "Quantifying mz/RT intensities using peak locations from master map",
      "topics": [
        "create_datamatrix"
      ]
    },
    {
      "page": "eicmatrix",
      "title": "Generate matrix of combined extraced ion chromatograms (EICs)",
      "topics": [
        "eicmatrix"
      ]
    },
    {
      "page": "peakdetection",
      "title": "An algorithm for the detection of peak locations and boundaries in mass spectra or ion chromatograms",
      "topics": [
        "peakdetection"
      ]
    },
    {
      "page": "quantify_combined",
      "title": "Generate report with combined ion intensities",
      "topics": [
        "quantify_combined"
      ]
    },
    {
      "page": "retention_time",
      "title": "Detection of chromatographic peak locations from extracted ion chromatograms (EICs)",
      "topics": [
        "retention_time"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/cosmiq/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "affy",
    "affyio",
    "AnnotationFilter",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "bslib",
    "cachem",
    "Chromatograms",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "doParallel",
    "dplyr",
    "evaluate",
    "faahKO",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "impute",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "magrittr",
    "MALDIquant",
    "MASS",
    "MassSpecWavelet",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "MetaboCoreUtils",
    "mime",
    "MsCoreUtils",
    "MsExperiment",
    "MsFeatures",
    "MSnbase",
    "MultiAssayExperiment",
    "mzID",
    "mzR",
    "ncdf4",
    "openssl",
    "otel",
    "pcaMethods",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "pracma",
    "preprocessCore",
    "prettyunits",
    "progress",
    "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",
    "xcms",
    "xfun",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "cosmiq.Rnw",
      "filename": "cosmiq.pdf",
      "title": "cosmiq primer",
      "engine": "utils::Sweave",
      "headings": [
        "1 Introduction",
        "2 LCMS feature detection step by step using cosmiq",
        "3 Session information"
      ],
      "created": "2014-05-27 19:16:28",
      "modified": "2014-06-17 04:54:46",
      "commits": 3
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "cosmiq",
  "_universes": [
    "bioc",
    "dajofischer"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-10-29T12:10:40.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/19a075879a66d553c870583d7f4a03f873c512c0c88e87b68ea71313a9dbd8d8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-10-29T12:12:34.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/a295f155452aced38176633fbf6ecdab8d5c92bad705f5cafef2df0210a708b7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-10-29T12:10:34.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/c87dfdb0793689bb22185b869c6a4477131afec1c1eb83006f5383f9751581e1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-10-29T12:11:40.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/1d83536a8cf5975525318e7b4326798360f85607d963ff58230e7a1501a82c5f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-10-29T13:07:03.000Z",
      "arch": "aarch64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/6ce298fa58d5300ff7f771ab6de9cad4f7743b0c5e0f032fd6fb57484eb89c61",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-10-29T13:10:11.000Z",
      "arch": "x86_64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/e75f6bf63e5c20a325079059801fcfd82389d08f5b3bf350bab20523898fceb7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-10-30T07:41:09.000Z",
      "arch": "aarch64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/383a3c0a9751a673ee1307114dc0b544196c42842f8d007a773951e6d8b34ae5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-10-29T13:12:02.000Z",
      "arch": "x86_64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/1b90e8f6dfd1f71509eb01f137bb542e6dbd21082677a157cd3b44eacf863c9f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.47.0",
      "date": "2026-10-29T12:11:13.000Z",
      "arch": "emscripten",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/bd5fc4b2e6c3b106fe121cd6cb2d988db25b0984f2ec045192c275a4208ec028",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-10-29T12:12:25.000Z",
      "arch": "aarch64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/2b9cb977ca6c3915e53a833e12de72f54aa32bbd51ef727766c80706f0d9d18f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-10-29T12:10:50.000Z",
      "arch": "x86_64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/e40d10568ff772071dd5631457ce883d19e1093fb0a43161ccee5b48c740e665",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-10-29T12:10:51.000Z",
      "arch": "x86_64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/d5c828774ba25a18eda20ab9d42e54b286f7a4ba81a3dfc3ceda7e27f3ed8684",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-10-29T12:12:43.000Z",
      "arch": "aarch64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/3c59b36545d56c035f43a3f7952a771546d3e7c8c3e3b3b3ed81358c6d3e5de8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-10-29T12:10:52.000Z",
      "arch": "x86_64",
      "commit": "e00bfb810b8421ec33b86d1b43a522f39551d020",
      "fileid": "https://r2.ropensci.org/a8d63a575da90382b1fd977d8b2e54350a197db073297535f75b9653567dd59c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40869713940"
    }
  ]
}