{
  "_id": "6a196618acfb0bcc41de71fa",
  "Package": "CompensAID",
  "Type": "Package",
  "Title": "Automated detection tool for spillover errors",
  "Version": "1.0.0",
  "Authors@R": "c(person(\"Rosan\", \"Olsman\", \nrole = c(\"aut\", \"cre\"),\nemail = \"r.olsman@erasmusmc.nl\",\ncomment = c(ORCID = \"0000-0001-5070-0476\")),\nperson(\"Sarah\", \"Bonte\",\nrole = c(\"aut\"),\nemail = \"sarahm.bonte@ugent.be\",\ncomment = c(ORCID = \"0000-0002-0637-4893\")),\nperson(\"Mattias\", \"Hofmans\",\nrole = c(\"aut\"),\nemail = \"mattias.hofmans@uzgent.be\",\ncomment = c(ORCID = \"0000-0003-2061-7617\")),\nperson(\"Malicorne\", \"Buysse\",\nrole = c(\"aut\"),\nemail = \"malicorne.buysse@uzgent.be\"),\nperson(\"Katrien\",\"Van der Borght\",\nrole=\"aut\",\nemail=\"katrien.vanderborght@irc.vib-ugent.be\",\ncomment = c(ORCID = \"0000-0003-1635-4359\")),\nperson(\"Yvan\", \"Saeys\",\nrole = \"aut\",\nemail=\"yvan.saeys@ugent.be\",\ncomment = c(ORCID = \"0000-0002-0415-1506\")),\nperson(\"Vincent\", \"van der Velden\",\nrole = \"aut\",\nemail=\"v.h.j.vandervelden@erasmusmc.nl\",\ncomment = c(ORCID = \"0000-0001-9457-3763\")),\nperson(\"Sofie\", \"Van Gassen\",\nrole = \"aut\",\nemail=\"sofie.vangassen@ugent.be\",\ncomment = c(ORCID = \"0000-0002-7119-5330\")))",
  "Description": "The CompensAID is an automated quality control tool, which\ndetermines for each marker combination in the FCS file, whether\nthere a potential presence of reference errors. Such reference\nerrors, which represent themselves in the form of skewed\npopulations, are detected by integrating the Secondary Stain\nIndex (SSI) score. Marker combinations with an SSI < 1 are\nflagged by CompensAID.",
  "URL": "https://github.com/Olsman/CompensAID",
  "BugReports": "https://github.com/Olsman/CompensAID/issues",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "biocViews": "FlowCytometry, QualityControl, Preprocessing",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake make libicu-dev libjpeg-dev libpng-dev\nlibxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:06:16 UTC",
  "RemoteUrl": "https://github.com/bioc/CompensAID",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 08:11:03 UTC",
    "User": "root"
  },
  "Author": "Rosan Olsman [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5070-0476>),\nSarah Bonte [aut] (ORCID: <https://orcid.org/0000-0002-0637-4893>),\nMattias Hofmans [aut] (ORCID: <https://orcid.org/0000-0003-2061-7617>),\nMalicorne Buysse [aut],\nKatrien Van der Borght [aut] (ORCID:\n<https://orcid.org/0000-0003-1635-4359>),\nYvan Saeys [aut] (ORCID: <https://orcid.org/0000-0002-0415-1506>),\nVincent van der Velden [aut] (ORCID:\n<https://orcid.org/0000-0001-9457-3763>),\nSofie Van Gassen [aut] (ORCID: <https://orcid.org/0000-0002-7119-5330>)",
  "Maintainer": "Rosan Olsman <r.olsman@erasmusmc.nl>",
  "MD5sum": "dc395bffcc5c4fd14c94cf0668b49986",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "CompensAID_1.0.0.tar.gz",
  "_fileid": "7c49982f247610ee080ba5be5da9677120a9406647a7d659137152a7a6917ee6",
  "_filesize": 2127947,
  "_sha256": "7c49982f247610ee080ba5be5da9677120a9406647a7d659137152a7a6917ee6",
  "_created": "2026-05-29T08:11:03.000Z",
  "_published": "2026-05-29T10:10:32.434Z",
  "_jobs": [
    {
      "job": 78463137846,
      "time": 199,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286181469"
    },
    {
      "job": 78463137863,
      "time": 267,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7286201378"
    },
    {
      "job": 78463137847,
      "time": 320,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286216557"
    },
    {
      "job": 78463137915,
      "time": 138,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7288234983"
    },
    {
      "job": 78463137873,
      "time": 210,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288255474"
    },
    {
      "job": 78462502294,
      "time": 272,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286125187"
    },
    {
      "job": 78463137922,
      "time": 177,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286175847"
    },
    {
      "job": 78463137862,
      "time": 197,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7286181787"
    },
    {
      "job": 78463137877,
      "time": 283,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7286206402"
    },
    {
      "job": 78463137858,
      "time": 191,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286180219"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625904822",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/CompensAID",
  "_commit": {
    "id": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381576
  },
  "_maintainer": {
    "name": "Rosan Olsman",
    "email": "r.olsman@erasmusmc.nl",
    "login": "lld-erasmusmc",
    "description": "",
    "uuid": 208964195,
    "orcid": "0000-0001-5070-0476"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "flowCore",
      "role": "Imports"
    },
    {
      "package": "flowDensity",
      "role": "Imports"
    },
    {
      "package": "ggcyto",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.5.2",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ParallelLogger",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-26",
      "n": 7
    },
    {
      "week": "2025-27",
      "n": 9
    },
    {
      "week": "2025-32",
      "n": 3
    },
    {
      "week": "2025-50",
      "n": 4
    },
    {
      "week": "2026-03",
      "n": 1
    },
    {
      "week": "2026-17",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "flowcytometry",
    "qualitycontrol",
    "preprocessing"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "lld-erasmusmc",
      "count": 46,
      "uuid": 208964195
    },
    {
      "user": "olsman",
      "count": 2,
      "uuid": 96538703
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 180,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CompensAID"
  },
  "_devurl": "https://github.com/olsman/compensaid",
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/CompensAID.html",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/olsman/compensaid",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CompensAID",
    "PlotDotSSI",
    "PlotMatrix"
  ],
  "_help": [
    {
      "page": "CompensAID",
      "title": "CompensAID",
      "topics": [
        "CompensAID"
      ]
    },
    {
      "page": "PlotDotSSI",
      "title": "Plot dot plot of Secondary Stain Index scores",
      "topics": [
        "PlotDotSSI"
      ]
    },
    {
      "page": "PlotMatrix",
      "title": "Plot Secondary Stain Index matrix",
      "topics": [
        "PlotMatrix"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CompensAID/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "BH",
    "Biobase",
    "BiocGenerics",
    "biocmake",
    "bitops",
    "boot",
    "broom",
    "car",
    "carData",
    "caTools",
    "checkmate",
    "cli",
    "colorspace",
    "cowplot",
    "cpp11",
    "cytolib",
    "data.table",
    "DelayedArray",
    "deldir",
    "Deriv",
    "dir.expiry",
    "doBy",
    "dplyr",
    "farver",
    "filelock",
    "flowCore",
    "flowDensity",
    "flowViz",
    "flowWorkspace",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "ggcyto",
    "ggplot2",
    "glue",
    "gplots",
    "graph",
    "gridExtra",
    "gtable",
    "gtools",
    "hexbin",
    "IDPmisc",
    "interp",
    "IRanges",
    "isoband",
    "jpeg",
    "jsonlite",
    "KernSmooth",
    "labeling",
    "lattice",
    "latticeExtra",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memuse",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "ncdfFlow",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "ParallelLogger",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polyclip",
    "purrr",
    "quantreg",
    "R6",
    "RBGL",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "reshape2",
    "Rgraphviz",
    "Rhdf5lib",
    "rlang",
    "RProtoBufLib",
    "rstudioapi",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "snow",
    "SparseArray",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "CompensAID.Rmd",
      "filename": "CompensAID.html",
      "title": "CompensAID workflow",
      "author": "Rosan Olsman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installing CompensAID",
        "Pre-processing",
        "Final data",
        "CompensAID: run tool",
        "Secondary Stain Index Matrix",
        "Identify flagged marker combinations",
        "Dot plots",
        "Session info"
      ],
      "created": "2025-06-24 09:44:05",
      "modified": "2026-04-21 17:19:12",
      "commits": 11
    }
  ],
  "_score": 5.243038048686294,
  "_indexed": false,
  "_nocasepkg": "compensaid",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/CompensAID",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-29T08:14:31.000Z",
      "distro": "noble",
      "commit": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
      "fileid": "9d7f54136f78e787518f753057bc80397c7b49d1aa4d2baf6124a15ec28739c7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625904822"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-29T08:15:08.000Z",
      "distro": "noble",
      "commit": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
      "fileid": "433fa261da485917c960531d34885db72580c2437bcf24cd2945b7634fc73a30",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625904822"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-29T10:07:58.000Z",
      "commit": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
      "fileid": "4db69ac98a3155b2cea291d7e54a54fa3360d6c4ff584f04c12857794c885824",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625904822"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-29T10:08:37.000Z",
      "commit": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
      "fileid": "7bb4d3e5f13bb38d4f22bab667efddf295b861cc1c6b7bdfb9f50a22178ce0be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625904822"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-05-29T08:14:26.000Z",
      "commit": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
      "fileid": "1f60b539837938176b23f04ef197f1968d31a05b746d8ad8e55c507875f1a967",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625904822"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T08:12:56.000Z",
      "commit": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
      "fileid": "4fc68cf6b47b8797c871441b6cce68d8f139c3763cdccb69abdc97bc88e6f58a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625904822"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T08:14:22.000Z",
      "commit": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
      "fileid": "2d762dc80ecf4a0adc5d9507cace0e708a1501ad734bc3ff30140aee40185c45",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625904822"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T08:12:52.000Z",
      "commit": "80ad4954699ed0d366cebda295f8e1c7a2a0f80c",
      "fileid": "9a308f417b03d3dd3454c929c8de52a10d28ff0e690f157fe9e0e0319638eb3a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625904822"
    }
  ]
}