{
  "_id": "6a1a74411d7bb097a09d150a",
  "Package": "CytoDx",
  "Type": "Package",
  "Title": "Robust prediction of clinical outcomes using cytometry data\nwithout cell gating",
  "Version": "1.32.0",
  "Author": "Zicheng Hu",
  "Maintainer": "Zicheng Hu <zicheng.hu@ucsf.edu>",
  "Description": "This package provides functions that predict clinical\noutcomes using single cell data (such as flow cytometry data,\nRNA single cell sequencing data) without the requirement of\ncell gating or clustering.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr, rmarkdown",
  "RoxygenNote": "6.1.0",
  "biocViews": "ImmunoOncology, CellBiology, FlowCytometry,\nStatisticalMethod, Software, CellBasedAssays, Regression,\nClassification, Survival",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:46 UTC",
  "RemoteUrl": "https://github.com/bioc/CytoDx",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 06:53:11 UTC",
    "User": "root"
  },
  "MD5sum": "94e2daffe5be235e674fb07c08368e88",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "CytoDx_1.32.0.tar.gz",
  "_fileid": "b8a842a435af4a1d8bc4427567a6706890c3e7d2623cf36b71595e6fb6968d12",
  "_filesize": 971875,
  "_sha256": "b8a842a435af4a1d8bc4427567a6706890c3e7d2623cf36b71595e6fb6968d12",
  "_created": "2026-05-29T06:53:11.000Z",
  "_published": "2026-05-30T05:23:13.772Z",
  "_jobs": [
    {
      "job": 78626297982,
      "time": 157,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7305637436"
    },
    {
      "job": 78626298223,
      "time": 270,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7284914328"
    },
    {
      "job": 78626298235,
      "time": 279,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284916406"
    },
    {
      "job": 78626298088,
      "time": 140,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7285844547"
    },
    {
      "job": 78626298095,
      "time": 105,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7285833318"
    },
    {
      "job": 78626297984,
      "time": 255,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284851340"
    },
    {
      "job": 78626298096,
      "time": 126,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284880930"
    },
    {
      "job": 78626298019,
      "time": 149,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7305639582"
    },
    {
      "job": 78626298172,
      "time": 267,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7284914200"
    },
    {
      "job": 78626298156,
      "time": 220,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284902651"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 0,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622725023",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/CytoDx",
  "_commit": {
    "id": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
    "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": 1777380466
  },
  "_maintainer": {
    "name": "Zicheng Hu",
    "email": "zicheng.hu@ucsf.edu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "rpart",
      "role": "Imports"
    },
    {
      "package": "rpart.plot",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "flowCore",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "cellbiology",
    "flowcytometry",
    "statisticalmethod",
    "software",
    "cellbasedassays",
    "regression",
    "classification",
    "survival"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 382,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CytoDx"
  },
  "_searchresults": 8,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/CytoDx.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CytoDx.fit",
    "CytoDx.pred",
    "fcs2DF",
    "meanUnique",
    "pRank",
    "rank.ub.average",
    "set2DF",
    "treeGate"
  ],
  "_help": [
    {
      "page": "CytoDx.fit",
      "title": "Build the CytoDx model",
      "topics": [
        "CytoDx.fit"
      ]
    },
    {
      "page": "CytoDx.pred",
      "title": "Make prediction using the CytoDx model",
      "topics": [
        "CytoDx.pred"
      ]
    },
    {
      "page": "fcs2DF",
      "title": "Convert fcs files to a data frame",
      "topics": [
        "fcs2DF"
      ]
    },
    {
      "page": "meanUnique",
      "title": "Calulate mean or take unique elements of a vector",
      "topics": [
        "meanUnique"
      ]
    },
    {
      "page": "pRank",
      "title": "Percentile rank transformation of the data",
      "topics": [
        "pRank"
      ]
    },
    {
      "page": "rank.ub.average",
      "title": "Percentile rank transformation of a vector",
      "topics": [
        "rank.ub.average"
      ]
    },
    {
      "page": "set2DF",
      "title": "convert a flowSet to a data frame",
      "topics": [
        "set2DF"
      ]
    },
    {
      "page": "treeGate",
      "title": "Use decision tree to find a group of cells that are associated with clinical outcome.",
      "topics": [
        "treeGate"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CytoDx/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "BH",
    "Biobase",
    "BiocGenerics",
    "biocmake",
    "cli",
    "codetools",
    "cpp11",
    "cytolib",
    "dir.expiry",
    "doParallel",
    "dplyr",
    "filelock",
    "flowCore",
    "foreach",
    "generics",
    "glmnet",
    "glue",
    "iterators",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "matrixStats",
    "pillar",
    "pkgconfig",
    "R6",
    "Rcpp",
    "RcppEigen",
    "Rhdf5lib",
    "rlang",
    "rpart",
    "rpart.plot",
    "RProtoBufLib",
    "S4Vectors",
    "shape",
    "survival",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "CytoDx_Vignette.Rmd",
      "filename": "CytoDx_Vignette.pdf",
      "title": "Introduction to CytoDx",
      "author": "Zicheng Hu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Example: diagnosing AML using flow cytometry",
        "Step 1: Prepare data",
        "Step 2: Build CytoDx model",
        "Step 3: Predict AML using testing data",
        "Step 4: Find cell subsets associated with AML",
        "Session Infomation"
      ],
      "created": "2018-02-21 16:42:47",
      "modified": "2018-09-06 15:51:01",
      "commits": 5
    }
  ],
  "_score": 4,
  "_indexed": false,
  "_nocasepkg": "cytodx",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/CytoDx",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.32.0",
      "date": "2026-05-29T06:57:04.000Z",
      "distro": "noble",
      "commit": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
      "fileid": "dea98677df0ade93da7d7233bda028203e53c59ce9fd5d816569428f6c6e52fb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622725023"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.32.0",
      "date": "2026-05-29T06:57:15.000Z",
      "distro": "noble",
      "commit": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
      "fileid": "75579c3360ab3e9feaff1f0adcd7c72390071ff61f4c3f7ca84792b62c24b81c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622725023"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.32.0",
      "date": "2026-05-29T07:53:47.000Z",
      "commit": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
      "fileid": "c3a64d4a1284b824c8937c605f76526f1dd2cdfff99d1fc294cf9b1d977fd99b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622725023"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.32.0",
      "date": "2026-05-29T07:53:19.000Z",
      "commit": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
      "fileid": "0645579ff11ce9886ae63cb02be6b3eba87d1a84ffe6cf1638827a82977c009b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622725023"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.32.0",
      "date": "2026-05-29T06:55:38.000Z",
      "commit": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
      "fileid": "9354364fa61899967ac98fcf19f92db47eea377912786008a7d9c48ea6b2fbd1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622725023"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.32.0",
      "date": "2026-05-30T05:19:41.000Z",
      "commit": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
      "fileid": "1f4eaf0b7d18e03679f7cad6f820cb5f7ef01a11a10053c4628289243e288d75",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622725023"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.32.0",
      "date": "2026-05-29T06:56:01.000Z",
      "commit": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
      "fileid": "7f1e28af0e7bf660b52af108d191cf22ccfa6397a20026f3005e2ae73fe76639",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622725023"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.32.0",
      "date": "2026-05-29T06:55:42.000Z",
      "commit": "6a65eaad35a4c09d559bd7be57a842efec6210b0",
      "fileid": "07e6176e947f9a620b2ba45c02d001519fb3b01bc5066dced9aa1e253c404d55",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622725023"
    }
  ]
}