{
  "_id": "6a4a02da9ce196b5e5a913ba",
  "Package": "ClussCluster",
  "Type": "Package",
  "Title": "Simultaneous Detection of Clusters and Cluster-Specific Genes in\nHigh-Throughput Transcriptome Data",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(\"Li\", \"Jun\", email = \"jun.li@nd.edu\", role = \"cre\"),\nperson(\"Jiang\", \"Ge\", email = \"gejiang2@illinois.edu\", role = \"aut\"),\nperson(\"Wang\", \"Chuanqi\", email = \"cwang14@nd.edu\", role = 'ctb'))",
  "Description": "Implements a new method 'ClussCluster' descried in Ge\nJiang and Jun Li, \"Simultaneous Detection of Clusters and\nCluster-Specific Genes in High-throughput Transcriptome Data\"\n(Unpublished). Simultaneously perform clustering analysis and\nsignature gene selection on high-dimensional transcriptome data\nsets.  To do so, 'ClussCluster' incorporates a Lasso-type\nregularization penalty term to the objective function of K-\nmeans so that cell-type-specific signature genes can be\nidentified while clustering the cells.",
  "VignetteBuilder": "knitr",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "6.1.1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-05 07:05:04 UTC",
    "User": "root"
  },
  "Author": "Li Jun [cre], Jiang Ge [aut], Wang Chuanqi [ctb]",
  "Maintainer": "Li Jun <jun.li@nd.edu>",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://jli-stat.r-universe.dev",
  "Date/Publication": "2019-07-02 15:30:16 UTC",
  "RemoteUrl": "https://github.com/cran/ClussCluster",
  "RemoteRef": "HEAD",
  "RemoteSha": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
  "_user": "jli-stat",
  "_type": "src",
  "_file": "ClussCluster_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/7e1daf7e81323682e8d2dea8193f6526f034194b45c83089f6656d04748c2eda",
  "_filesize": 517295,
  "_sha256": "7e1daf7e81323682e8d2dea8193f6526f034194b45c83089f6656d04748c2eda",
  "_expires": "2026-10-13T07:08:08.000Z",
  "_created": "2026-07-05T07:05:04.000Z",
  "_published": "2026-07-05T07:08:10.283Z",
  "_jobs": [
    {
      "job": 85201553037,
      "time": 139,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8089333618"
    },
    {
      "job": 85201553019,
      "time": 144,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8089334435"
    },
    {
      "job": 85201553028,
      "time": 118,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8089332738"
    },
    {
      "job": 85201553022,
      "time": 102,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8089328504"
    },
    {
      "job": 85201382860,
      "time": 155,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8089314152"
    },
    {
      "job": 85201553026,
      "time": 153,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8089335582"
    },
    {
      "job": 85201553030,
      "time": 84,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8089326092"
    },
    {
      "job": 85201553101,
      "time": 71,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8089324606"
    },
    {
      "job": 85201553031,
      "time": 94,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8089327384"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/jli-stat/actions/runs/28732762749",
  "_status": "success",
  "_upstream": "https://github.com/cran/ClussCluster",
  "_commit": {
    "id": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
    "author": "Li Jun <jun.li@nd.edu>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.0\n",
    "time": 1562081416
  },
  "_maintainer": {
    "name": "Li Jun",
    "email": "jun.li@nd.edu",
    "login": "jli-stat",
    "description": "",
    "uuid": 196732573
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "version": ">= 3.5.0",
      "role": "Imports"
    },
    {
      "package": "utils",
      "version": ">= 3.5.0",
      "role": "Imports"
    },
    {
      "package": "VennDiagram",
      "role": "Imports"
    },
    {
      "package": "scales",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "version": ">= 1.4.3",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.1.0",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "version": ">= 0.3.4",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "version": ">= 1.13",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "jli-stat",
      "count": 1,
      "uuid": 196732573
    }
  ],
  "_userbio": {
    "uuid": 196732573,
    "type": "user",
    "name": "jli-stat",
    "followers": 0
  },
  "_downloads": {
    "count": 275,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ClussCluster"
  },
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/ClussCluster.html",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "jli-stat",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2019-07-02"
    }
  ],
  "_exports": [
    "ClussCluster",
    "ClussCluster_Gap",
    "filter_gene",
    "plot_ClussCluster",
    "plot_ClussCluster_Gap",
    "print_ClussCluster",
    "print_ClussCluster_Gap",
    "top.m.hm"
  ],
  "_datasets": [
    {
      "name": "Hou_sim",
      "title": "A truncated subset of the scRNA-seq expression data set from Hou et.al (2016)",
      "object": "Hou_sim",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "sim_dat",
      "title": "A simulated expression data set.",
      "object": "sim_dat",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 200,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ClussCluster",
      "title": "Performs simultaneous detection of cell types and cell-type-specific signature genes",
      "topics": [
        "ClussCluster",
        "ClussCluster_Gap"
      ]
    },
    {
      "page": "filter_gene",
      "title": "Gene Filter",
      "topics": [
        "filter_gene"
      ]
    },
    {
      "page": "Hou_sim",
      "title": "A truncated subset of the scRNA-seq expression data set from Hou et.al (2016)",
      "topics": [
        "Hou_sim"
      ]
    },
    {
      "page": "plot_ClussCluster",
      "title": "Plots the results of 'ClussCluster'",
      "topics": [
        "plot_ClussCluster",
        "top.m.hm"
      ]
    },
    {
      "page": "plot_ClussCluster_Gap",
      "title": "Plots the results of 'ClussCluster_Gap'",
      "topics": [
        "plot_ClussCluster_Gap"
      ]
    },
    {
      "page": "print_ClussCluster",
      "title": "Prints out the results of 'ClussCluster'",
      "topics": [
        "print_ClussCluster"
      ]
    },
    {
      "page": "print_ClussCluster_Gap",
      "title": "Prints out the results of 'ClussCluster_Gap' Prints the gap statistics and number of genes selected for each candidate tuning parameter.",
      "topics": [
        "print_ClussCluster_Gap"
      ]
    },
    {
      "page": "sim_dat",
      "title": "A simulated expression data set.",
      "topics": [
        "sim_dat"
      ]
    }
  ],
  "_readme": "https://github.com/cran/ClussCluster/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lambda.r",
    "lifecycle",
    "magrittr",
    "plyr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "vctrs",
    "VennDiagram",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "ClussCluster.Rmd",
      "filename": "ClussCluster.html",
      "title": "ClussCluster",
      "author": "Ge Jiang, Chuanqi Wang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Load the package",
        "2. Example Data set",
        "3. Pre-processing the data",
        "4. Determine the tuning parameter",
        "5. Run ClussCluster",
        "Viewing Clustering Results",
        "Cell-type-specific signature genes",
        "6. Plot",
        "7. References"
      ],
      "created": "2019-07-02 15:30:16",
      "modified": "2019-07-02 15:30:16",
      "commits": 1
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "clusscluster",
  "_universes": [
    "jli-stat"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-07-05T07:07:13.000Z",
      "distro": "resolute",
      "commit": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
      "fileid": "https://r2.ropensci.org/9f4770807ebff9f7c0c3e8d9f4c9b40f3cd3260d42c1a6246ce6680db89100d6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/jli-stat/actions/runs/28732762749"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-07-05T07:07:22.000Z",
      "distro": "resolute",
      "commit": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
      "fileid": "https://r2.ropensci.org/72f949b3831d9952da858dd8c5172e9c4785b96e4f5135e0cfca1f4e01c8ccec",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/jli-stat/actions/runs/28732762749"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-07-05T07:07:13.000Z",
      "commit": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
      "fileid": "https://r2.ropensci.org/e0190014440647aa51d9800419b64e18130ebb1266404bc401ec80b5114a7b82",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/jli-stat/actions/runs/28732762749"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-07-05T07:06:45.000Z",
      "commit": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
      "fileid": "https://r2.ropensci.org/023b22c1063527bd15e670074b1b67583916318c3dffbe46ed6ac0d4edc1315a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/jli-stat/actions/runs/28732762749"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-07-05T07:07:53.000Z",
      "commit": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
      "fileid": "https://r2.ropensci.org/64d1a32c545c80229d911ecf8a4cda469bd754d4f1427447edd24298d0867db4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/jli-stat/actions/runs/28732762749"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-07-05T07:06:14.000Z",
      "commit": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
      "fileid": "https://r2.ropensci.org/796e4aafcdfbd5644c181ff7ee8da3877bad618d06a801326b91b3070c2d249a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/jli-stat/actions/runs/28732762749"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-07-05T07:06:05.000Z",
      "commit": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
      "fileid": "https://r2.ropensci.org/2be93299c122ee70fb761464b8ace12a3b40d063f19687f0be3d87a74ddf9e8f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/jli-stat/actions/runs/28732762749"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-07-05T07:06:25.000Z",
      "commit": "ac393fec37cb770fb2566eaef1b247ad82a98c6b",
      "fileid": "https://r2.ropensci.org/9d6be8f3b1addf85793e5ea97ebe202a982e43def8f3953824c8901b791a2e57",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/jli-stat/actions/runs/28732762749"
    }
  ]
}