{
  "_id": "6acf2e8dd9de2f3f33fc8bdf",
  "Package": "cellscape",
  "Title": "Explores single cell copy number profiles in the context of a\nsingle cell tree",
  "Version": "1.37.0",
  "Authors@R": "c(\nperson(\"Shixiang\", \"Wang\", , \"w_shixiang@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9855-7357\")),\nperson(\"Maia\", \"Smith\", , \"maiaannesmith@gmail.com\", role = \"aut\")\n)",
  "Description": "CellScape facilitates interactive browsing of single cell\nclonal evolution datasets. The tool requires two main inputs:\n(i) the genomic content of each single cell in the form of\neither copy number segments or targeted mutation values, and\n(ii) a single cell phylogeny. Phylogenetic formats can vary\nfrom dendrogram-like phylogenies with leaf nodes to\nevolutionary model-derived phylogenies with observed or latent\ninternal nodes. The CellScape phylogeny is flexibly input as a\ntable of source-target edges to support arbitrary\nrepresentations, where each node may or may not have associated\ngenomic data. The output of CellScape is an interactive\ninterface displaying a single cell phylogeny and a\ncell-by-locus genomic heatmap representing the mutation status\nin each cell for each locus.",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "biocViews": "Visualization",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:09 UTC",
  "RemoteUrl": "https://github.com/bioc/cellscape",
  "RemoteRef": "HEAD",
  "RemoteSha": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-14 07:10:00 UTC",
    "User": "root"
  },
  "Author": "Shixiang Wang [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9855-7357>),\nMaia Smith [aut]",
  "Maintainer": "Shixiang Wang <w_shixiang@163.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "cellscape_1.37.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/36e28146d9fb40e0521ca104b588b6299aedf3e63f01b5d2d03e7e05c6cecf90",
  "_filesize": 776548,
  "_sha256": "36e28146d9fb40e0521ca104b588b6299aedf3e63f01b5d2d03e7e05c6cecf90",
  "_expires": "2027-01-22T07:26:03.000Z",
  "_created": "2026-10-14T07:10:00.000Z",
  "_published": "2026-10-14T07:26:05.495Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38526245224",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 3,
    "note": 12
  },
  "_upstream": "https://github.com/bioc/cellscape",
  "_commit": {
    "id": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
    "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": 1777380309
  },
  "_maintainer": {
    "name": "Shixiang Wang",
    "email": "w_shixiang@163.com",
    "login": "shixiangwang",
    "orcid": "0000-0001-9855-7357",
    "twitter": "@WangShxiang",
    "description": "形每万变，神唯守一。",
    "uuid": 25057508
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 115728376881,
      "time": 238,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11876063042"
    },
    {
      "job": 115728376751,
      "time": 173,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11876131580"
    },
    {
      "job": 115728376793,
      "time": 206,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11876271597"
    },
    {
      "job": 115728376791,
      "time": 116,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11877055630"
    },
    {
      "job": 115728376856,
      "time": 124,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11876718273"
    },
    {
      "job": 115727280746,
      "time": 195,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11875757849"
    },
    {
      "job": 115728376789,
      "time": 95,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11876635721"
    },
    {
      "job": 115728376929,
      "time": 72,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11876247206"
    },
    {
      "job": 115728376846,
      "time": 72,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11876685904"
    },
    {
      "job": 115728376871,
      "time": 85,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11876312298"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 0.4.3",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "version": ">= 3.5.0",
      "role": "Imports"
    },
    {
      "package": "htmlwidgets",
      "version": ">= 0.5",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "version": ">= 0.9.19",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "version": ">= 1.4.1",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "version": ">= 1.0.0",
      "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": "1.37.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.36.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "visualization"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 477,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 343,
    "source": "https://www.bioconductor.org/packages/stats/bioc/cellscape"
  },
  "_mentions": 1,
  "_searchresults": 7,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/cellscape.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/shixiangwang/cellscape",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "cellscape",
    "cellscapeOutput",
    "checkAlpha",
    "checkClonalPrev",
    "checkCloneColours",
    "checkGtypePositioning",
    "checkMinDims",
    "checkPerts",
    "checkRequiredInputs",
    "checkTreeEdges",
    "dfs_tree",
    "findMode",
    "getMutationsData",
    "renderCnvTree",
    "replaceSpaces"
  ],
  "_help": [
    {
      "page": "cellscape",
      "title": "CellScape",
      "topics": [
        "cellscape"
      ]
    },
    {
      "page": "helpers",
      "title": "Get depth first search of a tree",
      "topics": [
        "cellscapeOutput",
        "checkAlpha",
        "checkClonalPrev",
        "checkCloneColours",
        "checkGtypePositioning",
        "checkMinDims",
        "checkPerts",
        "checkRequiredInputs",
        "checkTreeEdges",
        "dfs_tree",
        "findMode",
        "getChromBounds",
        "getChromBoxInfo",
        "getCNVHeatmapForEachSC",
        "getEmptyGrid",
        "getGenomeLength",
        "getMutationsData",
        "getMutOrder",
        "getNBPPerPixel",
        "getTargetedHeatmapForEachSC",
        "processUserData",
        "renderCnvTree",
        "replaceSpaces"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/cellscape/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "digest",
    "dplyr",
    "evaluate",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "glue",
    "gtools",
    "highr",
    "htmltools",
    "htmlwidgets",
    "jquerylib",
    "jsonlite",
    "knitr",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "pillar",
    "pkgconfig",
    "plyr",
    "R6",
    "rappdirs",
    "Rcpp",
    "reshape2",
    "rlang",
    "rmarkdown",
    "sass",
    "stringi",
    "stringr",
    "tibble",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "withr",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "cellscape_vignette.Rmd",
      "filename": "cellscape_vignette.html",
      "title": "CellScape vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Examples",
        "Required parameters",
        "Parameters that are optional for CellScape, but required for a TimeScape",
        "Optional parameters",
        "Clone colours",
        "Mutation order",
        "Titles",
        "Interactivity",
        "Obtaining the data",
        "Targeted mutation data:",
        "Copy number data:",
        "Clonal composition data:",
        "Documentation",
        "References"
      ],
      "created": "2017-02-11 19:22:18",
      "modified": "2024-01-21 11:08:34",
      "commits": 8
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "cellscape",
  "_universes": [
    "bioc",
    "shixiangwang"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-10-14T07:12:54.000Z",
      "distro": "resolute",
      "commit": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
      "fileid": "https://r2.ropensci.org/1ad758a16a6a698b58501a2b70e2de68113b5cdb495207443e1388a5545dc771",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38526245224"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-10-14T07:13:27.000Z",
      "distro": "resolute",
      "commit": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
      "fileid": "https://r2.ropensci.org/135efe580cbb467f30951f10436361083beca615db7a72908267ac2f982474c8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38526245224"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-10-14T07:25:10.000Z",
      "commit": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
      "fileid": "https://r2.ropensci.org/c1e35fccc699b4f49979d20b6e98cc4acf72287abe0e095a87a0da7de250f6ea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38526245224"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-10-14T07:25:22.000Z",
      "commit": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
      "fileid": "https://r2.ropensci.org/f7611d71721c268f562afb88d72f5c41fd64599dfa5e0b9f6377cb4a67e09e65",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38526245224"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.37.0",
      "date": "2026-10-14T07:11:55.000Z",
      "commit": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
      "fileid": "https://r2.ropensci.org/d9eb204cf02c6338f425cff9578b6a38365723c6f39da9d507e128ccca43e4a1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38526245224"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-10-14T07:11:07.000Z",
      "commit": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
      "fileid": "https://r2.ropensci.org/9ba6a408f79bbbcbaa6f0a09782f25aac0011a969d1d145cf10125dcfde07bf8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38526245224"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-10-14T07:11:11.000Z",
      "commit": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
      "fileid": "https://r2.ropensci.org/808768624ddcf57f3258058c1bffd53e6f4b9f313855581c4d1a912a501971f2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38526245224"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-10-14T07:11:24.000Z",
      "commit": "99b5d1a61a75d9f95a993b012d2ff2d2dc6d989a",
      "fileid": "https://r2.ropensci.org/63f41c67f886b4ce711a2bc48896f09d049b3cdefe7f1298ad83c3b0bd4fed59",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38526245224"
    }
  ]
}