{
  "_id": "6ace2dbea14063b82c3b0db0",
  "Package": "CytoDx",
  "Type": "Package",
  "Title": "Robust prediction of clinical outcomes using cytometry data\nwithout cell gating",
  "Version": "1.33.0",
  "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": "libssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:46 UTC",
  "RemoteUrl": "https://github.com/bioc/CytoDx",
  "RemoteRef": "HEAD",
  "RemoteSha": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-13 12:30:03 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "CytoDx_1.33.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/0c52cf00a477fe9e6a220aa2ca8b16a7c885f837735203af3b8bfe3ca1a65c64",
  "_filesize": 970795,
  "_sha256": "0c52cf00a477fe9e6a220aa2ca8b16a7c885f837735203af3b8bfe3ca1a65c64",
  "_expires": "2027-01-21T13:10:18.000Z",
  "_created": "2026-10-13T12:30:03.000Z",
  "_published": "2026-10-13T13:10:22.080Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38397362991",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 2,
    "warning": 0,
    "note": 11
  },
  "_upstream": "https://github.com/bioc/CytoDx",
  "_commit": {
    "id": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
    "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": 1777380466
  },
  "_maintainer": {
    "name": "Zicheng Hu",
    "email": "zicheng.hu@ucsf.edu"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 115297314690,
      "time": 205,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11814575428"
    },
    {
      "job": 115297314623,
      "time": 261,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11814660548"
    },
    {
      "job": 115297314527,
      "time": 413,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11814766050"
    },
    {
      "job": 115297314523,
      "time": 139,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11815487241"
    },
    {
      "job": 115297314570,
      "time": 163,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11815997706"
    },
    {
      "job": 115296048294,
      "time": 180,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11813286152"
    },
    {
      "job": 115297314606,
      "time": 129,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11814720112"
    },
    {
      "job": 115297314619,
      "time": 136,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11814785090"
    },
    {
      "job": 115297314652,
      "time": 135,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11813151628"
    },
    {
      "job": 115297314548,
      "time": 141,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11814645166"
    }
  ],
  "_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": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "immunooncology",
    "cellbiology",
    "flowcytometry",
    "statisticalmethod",
    "software",
    "cellbasedassays",
    "regression",
    "classification",
    "survival"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 492,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CytoDx"
  },
  "_searchresults": 8,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/CytoDx.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_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/HEAD/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": true,
  "_nocasepkg": "cytodx",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-10-13T12:33:42.000Z",
      "distro": "resolute",
      "commit": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
      "fileid": "https://r2.ropensci.org/c8cc824d8a4610a5d44804fbb6380dbdd9c3a0dc31016e3762e20a89694246fa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38397362991"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-10-13T12:36:26.000Z",
      "distro": "resolute",
      "commit": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
      "fileid": "https://r2.ropensci.org/680b40f582ec67f4dc4330bddec511077a9b963d1da1b44f2e3e59f926c1b88d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38397362991"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-10-13T13:05:21.000Z",
      "commit": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
      "fileid": "https://r2.ropensci.org/99af8649d50cca96f424f7a04cb53efdfcf2b5ec28a97aebc81a236874b98078",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38397362991"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-10-13T13:08:53.000Z",
      "commit": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
      "fileid": "https://r2.ropensci.org/f8794dd9eb6ea755cee96a69cea0f4648c7d4ac806ae7e4828757cf4c3300073",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38397362991"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.0",
      "date": "2026-10-13T12:32:30.000Z",
      "commit": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
      "fileid": "https://r2.ropensci.org/de4375d051a797149331e61c70d1de4d7767a8d77a2f6ec971c1fa3b8afa5e6c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38397362991"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-10-13T12:31:35.000Z",
      "commit": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
      "fileid": "https://r2.ropensci.org/06937a4bb6dae9fa64636173e9de6def8649064c451c5ebc8eecda4e4a850d70",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38397362991"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-10-13T12:31:40.000Z",
      "commit": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
      "fileid": "https://r2.ropensci.org/a3ae67ca1657baa2efa725cf6a076767d8c467782811c0f4d2abec926a3c7fb7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38397362991"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-10-13T12:31:42.000Z",
      "commit": "0f9a68173a2adf4ef0dc85112ecddf95b90567e9",
      "fileid": "https://r2.ropensci.org/12baef5e3d6043aba3333a631c6060e8dd8ad4e0acbd682824e11ca04a29e653",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38397362991"
    }
  ]
}