{
  "_id": "6ac8c2f4de46216d5edd6a9a",
  "Package": "FateID",
  "Title": "Quantification of Fate Bias in Multipotent Progenitors",
  "Version": "0.2.2",
  "Date": "2022-06-14",
  "Author": "Dominic Grün <dominic.gruen@gmail.com>",
  "Maintainer": "Dominic Grün <dominic.gruen@gmail.com>",
  "Description": "Application of 'FateID' allows computation and\nvisualization of cell fate bias for multi-lineage single cell\ntranscriptome data. Herman, J.S., Sagar, Grün D. (2018)\n<DOI:10.1038/nmeth.4662>.",
  "biocViews": "",
  "VignetteBuilder": "knitr",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-09 09:53:25 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libpng-dev libssl-dev python3",
  "Repository": "https://dgrun.r-universe.dev",
  "Date/Publication": "2022-06-14 12:17:40 UTC",
  "RemoteUrl": "https://github.com/dgrun/fateid",
  "RemoteRef": "HEAD",
  "RemoteSha": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
  "_user": "dgrun",
  "_type": "src",
  "_file": "FateID_0.2.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/4adb100259bef745484323765b3d723afbb90f8b1a8844baea0106a27d707451",
  "_filesize": 2405289,
  "_sha256": "4adb100259bef745484323765b3d723afbb90f8b1a8844baea0106a27d707451",
  "_expires": "2027-01-17T10:33:21.000Z",
  "_created": "2026-10-09T09:53:25.000Z",
  "_published": "2026-10-09T10:33:24.015Z",
  "_buildurl": "https://github.com/r-universe/dgrun/actions/runs/37913751706",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 113766295699,
      "time": 194,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11609510733"
    },
    {
      "job": 113766295638,
      "time": 180,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11609790449"
    },
    {
      "job": 113766295811,
      "time": 216,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11610832200"
    },
    {
      "job": 113766295624,
      "time": 229,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11610156683"
    },
    {
      "job": 113765042619,
      "time": 215,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11609435103"
    },
    {
      "job": 113766295706,
      "time": 112,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11609795231"
    },
    {
      "job": 113766295527,
      "time": 134,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11608596712"
    },
    {
      "job": 113766295585,
      "time": 104,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11609600328"
    },
    {
      "job": 113766295616,
      "time": 148,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11609700408"
    }
  ],
  "_upstream": "https://github.com/dgrun/fateid",
  "_commit": {
    "id": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
    "author": "Dominic Gruen <dominic.gruen@gmail.com>",
    "committer": "Dominic Gruen <dominic.gruen@gmail.com>",
    "message": "second commit\n",
    "time": 1655209060
  },
  "_maintainer": {
    "name": "Dominic Grün",
    "email": "dominic.gruen@gmail.com",
    "login": "dgrun",
    "description": "",
    "uuid": 11157236
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "locfit",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "princurve",
      "role": "Imports"
    },
    {
      "package": "randomForest",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "Rtsne",
      "role": "Imports"
    },
    {
      "package": "som",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "umap",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "DESeq2",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "dgrun",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [],
  "_tags": [],
  "_stars": 22,
  "_contributors": [
    {
      "user": "dgrun",
      "count": 18,
      "uuid": 11157236
    }
  ],
  "_userbio": {
    "uuid": 11157236,
    "type": "user",
    "name": "dgrun",
    "followers": 55
  },
  "_downloads": {
    "count": 503,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FateID"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/dgrun/fateid",
  "_searchresults": 56,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/FateID.html",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/dgrun/fateid",
  "_realowner": "dgrun",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.0.9",
      "date": "2017-11-15"
    },
    {
      "version": "0.1.0",
      "date": "2017-11-15"
    },
    {
      "version": "0.1.1",
      "date": "2018-03-28"
    },
    {
      "version": "0.1.2",
      "date": "2018-07-05"
    },
    {
      "version": "0.1.3",
      "date": "2018-07-27"
    },
    {
      "version": "0.1.4",
      "date": "2018-08-07"
    },
    {
      "version": "0.1.5",
      "date": "2018-11-13"
    },
    {
      "version": "0.1.6",
      "date": "2019-03-04"
    },
    {
      "version": "0.1.7",
      "date": "2019-03-28"
    },
    {
      "version": "0.1.8",
      "date": "2019-09-02"
    },
    {
      "version": "0.1.9",
      "date": "2019-09-21"
    },
    {
      "version": "0.2.0",
      "date": "2021-04-07"
    },
    {
      "version": "0.2.1",
      "date": "2021-10-05"
    },
    {
      "version": "0.2.2",
      "date": "2022-06-14"
    }
  ],
  "_exports": [
    "compdr",
    "diffexpnb",
    "fateBias",
    "filterset",
    "gene2gene",
    "getFeat",
    "getPart",
    "getsom",
    "impGenes",
    "plotdiffgenesnb",
    "plotexpression",
    "plotexpressionProfile",
    "plotFateMap",
    "plotheatmap",
    "prcurve",
    "procsom",
    "reclassify"
  ],
  "_datasets": [
    {
      "name": "intestine",
      "title": "Single-cell transcriptome data of intestinal epithelial cells",
      "object": "intestine",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "compdr",
      "title": "Computation of dimensional reduction representations",
      "topics": [
        "compdr"
      ]
    },
    {
      "page": "diffexpnb",
      "title": "Function for differential expression analysis",
      "topics": [
        "diffexpnb"
      ]
    },
    {
      "page": "fateBias",
      "title": "Computation of fate bias",
      "topics": [
        "fateBias"
      ]
    },
    {
      "page": "filterset",
      "title": "Function for filtering expression data",
      "topics": [
        "filterset"
      ]
    },
    {
      "page": "gene2gene",
      "title": "Comparative plot of the expression levels of two genes",
      "topics": [
        "gene2gene"
      ]
    },
    {
      "page": "getFeat",
      "title": "Feature selection based on differentially expressed genes",
      "topics": [
        "getFeat"
      ]
    },
    {
      "page": "getPart",
      "title": "Inference of a cell type partition",
      "topics": [
        "getPart"
      ]
    },
    {
      "page": "getsom",
      "title": "Topological ordering of pseudo-temporal expression profiles",
      "topics": [
        "getsom"
      ]
    },
    {
      "page": "impGenes",
      "title": "Extract genes with high importance values for random forest classification",
      "topics": [
        "impGenes"
      ]
    },
    {
      "page": "intestine",
      "title": "Single-cell transcriptome data of intestinal epithelial cells",
      "topics": [
        "intestine"
      ]
    },
    {
      "page": "plotdiffgenesnb",
      "title": "Function for plotting differentially expressed genes",
      "topics": [
        "plotdiffgenesnb"
      ]
    },
    {
      "page": "plotexpression",
      "title": "Plotting of pseudo-temporal expression profiles",
      "topics": [
        "plotexpression"
      ]
    },
    {
      "page": "plotexpressionProfile",
      "title": "Plotting smoothed pseudo-temporal expression profiles for groups of genes",
      "topics": [
        "plotexpressionProfile"
      ]
    },
    {
      "page": "plotFateMap",
      "title": "Plot dimensional reduction representation of the expression data",
      "topics": [
        "plotFateMap"
      ]
    },
    {
      "page": "plotheatmap",
      "title": "Heatmap of expression profiles",
      "topics": [
        "plotheatmap"
      ]
    },
    {
      "page": "prcurve",
      "title": "Computation of a principal curve for a given dimensional reduction representation",
      "topics": [
        "prcurve"
      ]
    },
    {
      "page": "procsom",
      "title": "Processing of self-organizing maps for pseudo-temporal expression profiles",
      "topics": [
        "procsom"
      ]
    },
    {
      "page": "reclassify",
      "title": "Reclassification of cells",
      "topics": [
        "reclassify"
      ]
    }
  ],
  "_readme": "https://github.com/dgrun/fateid/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "cli",
    "farver",
    "glue",
    "gtable",
    "here",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "locfit",
    "Matrix",
    "matrixStats",
    "openssl",
    "pheatmap",
    "png",
    "princurve",
    "R6",
    "randomForest",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppTOML",
    "reticulate",
    "rlang",
    "rprojroot",
    "RSpectra",
    "Rtsne",
    "scales",
    "som",
    "sys",
    "umap",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "FateID.Rmd",
      "filename": "FateID.html",
      "title": "FateID reference manual",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Prerequisites",
        "Input data",
        "Computing the fate bias",
        "Visualization of fate bias",
        "Inspecting pseudo-temporal gene expression changes",
        "Differential gene expression analysis",
        "Inspecting fate bias of gene expression",
        "References"
      ],
      "created": "2017-11-07 09:30:55",
      "modified": "2022-06-14 12:17:40",
      "commits": 7
    }
  ],
  "_score": 6.868761958212049,
  "_indexed": true,
  "_nocasepkg": "fateid",
  "_universes": [
    "dgrun"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.2",
      "date": "2026-10-09T09:56:01.000Z",
      "distro": "resolute",
      "commit": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
      "fileid": "https://r2.ropensci.org/bef69f86f067c1a9c2bd2ca173a1c677948e05a9b916509130dd7b001f3d3e59",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dgrun/actions/runs/37913751706"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.2.2",
      "date": "2026-10-09T09:55:48.000Z",
      "distro": "resolute",
      "commit": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
      "fileid": "https://r2.ropensci.org/c3a03c1f71261a84f0799e4e983b97db1c9a6d9b1aab471f31f0a8faa8f25157",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dgrun/actions/runs/37913751706"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.2",
      "date": "2026-10-09T10:31:35.000Z",
      "commit": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
      "fileid": "https://r2.ropensci.org/c635608f49654c83a7291a5ce7ed5b0f2381fb90932a80b5a52ad23bed63d047",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dgrun/actions/runs/37913751706"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.2.2",
      "date": "2026-10-09T10:28:57.000Z",
      "commit": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
      "fileid": "https://r2.ropensci.org/bdba279c0f11c6440914eb6a4a01ccdf53b685a4f7914b4a86d5759ce723d8c1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dgrun/actions/runs/37913751706"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.2",
      "date": "2026-10-09T09:55:37.000Z",
      "commit": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
      "fileid": "https://r2.ropensci.org/3a57c4ea9b2344462ca48bb3fbaca5f28fabc97af5fbc0189123357ec67d09f7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/dgrun/actions/runs/37913751706"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.2",
      "date": "2026-10-09T09:54:54.000Z",
      "commit": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
      "fileid": "https://r2.ropensci.org/93bd16f1ce40cb53f21e28bbe51303f7ba6bea4d47a6e851749c3df8ff7984d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dgrun/actions/runs/37913751706"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.2",
      "date": "2026-10-09T09:54:45.000Z",
      "commit": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
      "fileid": "https://r2.ropensci.org/cf15b13e33a96ecd40251be50b7f1c9d5db56fd2779284a6054bac37dd8a8857",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dgrun/actions/runs/37913751706"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.2.2",
      "date": "2026-10-09T09:55:06.000Z",
      "commit": "f2ea6f9b4981ae47cb1e5fd55d38ae9de144ad52",
      "fileid": "https://r2.ropensci.org/8a292340d1ff06b9e3ed13f66056ab9b6120e2b53a47f804cb91687c93f7c266",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dgrun/actions/runs/37913751706"
    }
  ]
}