{
  "_id": "6a1e8c171d7bb097a0a69563",
  "Package": "RScelestial",
  "Type": "Package",
  "Title": "Scelestial: Steiner Tree Based Single-Cell Lineage Tree\nInference",
  "Version": "1.0.4",
  "Date": "2023-11-29",
  "Authors@R": "c(person(\"Mohammad Hadi\", \"Foroughmand Araabi\", role = c(\"aut\", \"cre\"),\nemail = \"foroughmand@gmail.com\"),\nperson(\"Sama\", \"Goliaei\", role = c(\"aut\", \"ctb\")),\nperson(\"Alice\", \"McHardy\", role = \"ctb\"))",
  "Maintainer": "Mohammad Hadi Foroughmand Araabi <foroughmand@gmail.com>",
  "Description": "Scelestial infers a lineage tree from single-cell DNA\nmutation matrix. It generates a tree with approximately maximum\nparsimony through a Steiner tree approximation algorithm.",
  "License": "GPL (>= 2)",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr, rmarkdown",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-02 07:46:27 UTC",
    "User": "root"
  },
  "Author": "Mohammad Hadi Foroughmand Araabi [aut, cre], Sama Goliaei [aut,\nctb], Alice McHardy [ctb]",
  "Repository": "https://foroughmand.r-universe.dev",
  "Date/Publication": "2023-12-01 02:43:10 UTC",
  "RemoteUrl": "https://github.com/cran/RScelestial",
  "RemoteRef": "HEAD",
  "RemoteSha": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
  "MD5sum": "5584f20285cd9daef4273356e48c52ab",
  "_user": "foroughmand",
  "_type": "src",
  "_file": "RScelestial_1.0.4.tar.gz",
  "_fileid": "d49b1be0afc18fb12d96b789860a54a0c1306011c73e54ed5d05cb615883c54b",
  "_filesize": 380841,
  "_sha256": "d49b1be0afc18fb12d96b789860a54a0c1306011c73e54ed5d05cb615883c54b",
  "_created": "2026-06-02T07:46:27.000Z",
  "_published": "2026-06-02T07:53:59.921Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79023554806,
      "time": 141,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7351902380"
    },
    {
      "job": 79023554834,
      "time": 137,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7351900142"
    },
    {
      "job": 79023554860,
      "time": 127,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7351897560"
    },
    {
      "job": 79023554811,
      "time": 123,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7351895532"
    },
    {
      "job": 79023554829,
      "time": 159,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7351897334"
    },
    {
      "job": 79023554861,
      "time": 405,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7351979568"
    },
    {
      "job": 79023554805,
      "time": 172,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7351903544"
    },
    {
      "job": 79023554852,
      "time": 255,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7351929463"
    },
    {
      "job": 79022937715,
      "time": 238,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7351853929"
    },
    {
      "job": 79023554784,
      "time": 108,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7351891146"
    },
    {
      "job": 79023554879,
      "time": 126,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7351896848"
    },
    {
      "job": 79023554912,
      "time": 138,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7351900570"
    },
    {
      "job": 79023554826,
      "time": 108,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7351891478"
    }
  ],
  "_buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/RScelestial",
  "_commit": {
    "id": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
    "author": "Mohammad Hadi Foroughmand Araabi <foroughmand@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.4\n",
    "time": 1701398590
  },
  "_maintainer": {
    "name": "Mohammad Hadi Foroughmand Araabi",
    "email": "foroughmand@gmail.com",
    "login": "foroughmand",
    "description": "",
    "uuid": 1122486
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.1",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    },
    {
      "package": "seqinr",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "foroughmand",
      "count": 5,
      "uuid": 1122486
    }
  ],
  "_userbio": {
    "uuid": 1122486,
    "type": "user",
    "name": "foroughmand"
  },
  "_downloads": {
    "count": 174,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RScelestial"
  },
  "_searchresults": 2,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/RScelestial.html",
    "manual.pdf"
  ],
  "_realowner": "foroughmand",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2019-11-28"
    },
    {
      "version": "1.0.1",
      "date": "2020-03-23"
    },
    {
      "version": "1.0.2",
      "date": "2021-11-05"
    },
    {
      "version": "1.0.3",
      "date": "2021-12-09"
    },
    {
      "version": "1.0.4",
      "date": "2023-11-30"
    }
  ],
  "_exports": [
    ".scelestial",
    ".synthesis",
    "as.mutation.matrix",
    "as.ten.state.matrix",
    "as.ten.state.matrix.from.node.seq",
    "distance.matrix.scelestial",
    "distance.matrix.tree",
    "distance.matrix.true.tree",
    "my.dfs",
    "my.general.dfs",
    "read.sequence.table",
    "scelestial",
    "synthesis",
    "tree.plot"
  ],
  "_datasets": [
    {
      "name": "Li",
      "title": "Bladder invasive single cell tumor dataset",
      "object": "Li",
      "file": "Li.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V2",
        "V3",
        "V4",
        "V5",
        "V6",
        "V7",
        "V8",
        "V9",
        "V10",
        "V11",
        "V12",
        "V13",
        "V14",
        "V15",
        "V16",
        "V17",
        "V18",
        "V19",
        "V20",
        "V21",
        "V22",
        "V23",
        "V24",
        "V25",
        "V26",
        "V27",
        "V28",
        "V29",
        "V30",
        "V31",
        "V32",
        "V33",
        "V34",
        "V35",
        "V36",
        "V37",
        "V38",
        "V39",
        "V40",
        "V41",
        "V42",
        "V43",
        "V44",
        "V45",
        "V46",
        "V47",
        "V48",
        "V49",
        "V50",
        "V51",
        "V52",
        "V53",
        "V54",
        "V55",
        "V56",
        "V57",
        "V58"
      ],
      "rows": 443,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dot-scelestial",
      "title": "Internal function for running scelestial algorithm.",
      "topics": [
        ".scelestial"
      ]
    },
    {
      "page": "dot-synthesis",
      "title": "Internal function for generating synthetic single-cell data through simulation of tumor growth and evolution.",
      "topics": [
        ".synthesis"
      ]
    },
    {
      "page": "as.mutation.matrix",
      "title": "Conversion of ten-state sequencing matrix to 0/1-mutation matrix.",
      "topics": [
        "as.mutation.matrix"
      ]
    },
    {
      "page": "as.ten.state.matrix",
      "title": "Conversion of 0/1 matrix to 10-state matrix",
      "topics": [
        "as.ten.state.matrix"
      ]
    },
    {
      "page": "as.ten.state.matrix.from.node.seq",
      "title": "Generates 10-state sequence matrix from name/10-char string matrix.",
      "topics": [
        "as.ten.state.matrix.from.node.seq"
      ]
    },
    {
      "page": "distance.matrix.scelestial",
      "title": "Calculates distance matrix for result of scelestial",
      "topics": [
        "distance.matrix.scelestial"
      ]
    },
    {
      "page": "distance.matrix.tree",
      "title": "Calculates distance matrix for a nodes on a tree.",
      "topics": [
        "distance.matrix.tree"
      ]
    },
    {
      "page": "distance.matrix.true.tree",
      "title": "Calculates distance matrix for a synthetized data",
      "topics": [
        "distance.matrix.true.tree"
      ]
    },
    {
      "page": "Li",
      "title": "Bladder invasive single cell tumor dataset",
      "topics": [
        "Li"
      ]
    },
    {
      "page": "my.dfs",
      "title": "Runs DFS on tree and calculates parent of each node as well as depth and upper-depth of nodes.",
      "topics": [
        "my.dfs"
      ]
    },
    {
      "page": "my.general.dfs",
      "title": "Running depth first search on a tree and calling functions on entrance/exit events",
      "topics": [
        "my.general.dfs"
      ]
    },
    {
      "page": "read.sequence.table",
      "title": "Read mutation table",
      "topics": [
        "read.sequence.table"
      ]
    },
    {
      "page": "RScelestial",
      "title": "RScelestial: An R wrapper for scelestial algorithm for single-cell lineage tree reconstruction through an approximation algorithm based on Steiner tree problem",
      "topics": [
        "RScelestial"
      ]
    },
    {
      "page": "scelestial",
      "title": "Infer the single-cell phylogenetic tree",
      "topics": [
        "scelestial"
      ]
    },
    {
      "page": "synthesis",
      "title": "Synthesize single-cell data through tumor simulation",
      "topics": [
        "synthesis"
      ]
    },
    {
      "page": "tree.plot",
      "title": "Plotting the tree",
      "topics": [
        "tree.plot"
      ]
    }
  ],
  "_rundeps": [
    "Rcpp"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "RScelestial-vignette.Rmd",
      "filename": "RScelestial-vignette.html",
      "title": "RScelestial Vignette",
      "author": "Mohammad-Hadi Foroughmand-Araabi",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installing RScelestial",
        "Simulation",
        "Inferring the phylogenetic tree",
        "Evaluating results",
        "Running Scelestial on multiple sequence alignment"
      ],
      "created": "2019-11-28 13:10:02",
      "modified": "2023-12-01 02:43:10",
      "commits": 3
    }
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "rscelestial",
  "_universes": [
    "foroughmand"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-06-02T07:49:01.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "d0f13cd13f57e9b2ab1c0e09d24a35ce2b07bc9bd8e92b7eb9e9820208399125",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-06-02T07:48:50.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "d7c37f8eabe21f304c4c892b150ea74263a696638e43a48591a5ebe93645c235",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-06-02T07:48:48.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "32b647458911c32bdf6bd08d5f944600b3b0d80d0cbb1c43e1b2b6eeab5aaa32",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-06-02T07:48:40.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "07ba7a7ec5fc7bdb58365863c19cf54f9545642f87bf16f9c626de90c1c23c2e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-06-02T07:48:48.000Z",
      "arch": "aarch64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "fbb8eff80bca7c14abd3ee536beede80a52ee1ded4d996255d9e707e7a750a71",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-06-02T07:51:50.000Z",
      "arch": "x86_64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "14627ada3775035ebfdd612240fa4c8eaacae73dfc90de0403b8a049c681648b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-06-02T07:48:58.000Z",
      "arch": "aarch64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "d3d6b177a3d087d539d805692df9ddac8efe4cd862fb44221fc3409421378733",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-06-02T07:50:05.000Z",
      "arch": "x86_64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "d0bb1730cfa2025d715a3e87c7b791db7917cf779f82c63b78cadfc5d55a7429",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.4",
      "date": "2026-06-02T07:48:40.000Z",
      "arch": "emscripten",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "2ffd1ea1d44e39a714cd16bba1a3d4f50c1985d4b8e7ea076b8a0eb527a40c77",
      "status": "success",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-06-02T07:48:11.000Z",
      "arch": "x86_64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "774c622126c369f491a4565c6df430c68fe9e1fafbec3348fe7843bc075c6a1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-06-02T07:48:15.000Z",
      "arch": "x86_64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "b9e1c882ac3ce4029d5ef214b46b2cefc368e3836319d68a40279ffdd2e35bfe",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-06-02T07:47:57.000Z",
      "arch": "x86_64",
      "commit": "cdb757ecd6ff7da3777822f236f0cfd0e4956694",
      "fileid": "0b8b4cf01abe0e97d1bd255851ca115e6a8d7dba4c34102338cec4914ce04750",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/foroughmand/actions/runs/26805810684"
    }
  ]
}