{
  "_id": "6a18184dacfb0bcc41db0331",
  "Package": "hierBipartite",
  "Type": "Package",
  "Title": "Bipartite Graph-Based Hierarchical Clustering",
  "Version": "0.0.2",
  "Authors@R": "c(person(\"Calvin\", \"Chi\", email = \"calvin.chi@berkeley.edu\", role = c(\"aut\", \"cre\", \"cph\")),\nperson(\"Woojoo\", \"Lee\", role = c(\"ctb\")),\nperson(\"Donghwan\", \"Lee\", role = c(\"ctb\")),\nperson(\"Youngjo\", \"Lee\", role = c(\"ctb\")),\nperson(\"Yudi\", \"Pawitan\", role = c(\"ctb\")))",
  "Maintainer": "Calvin Chi <calvin.chi@berkeley.edu>",
  "Description": "Bipartite graph-based hierarchical clustering performs\nhierarchical clustering of groups of samples based on\nassociation patterns between two sets of variables. It is\ndeveloped for pharmacogenomic datasets and datasets sharing the\nsame data structure. In the context of pharmacogenomic\ndatasets, the samples are cell lines, and the two sets of\nvariables are typically expression levels and drug sensitivity\nvalues. For this method, sparse canonical correlation analysis\nfrom Lee, W., Lee, D., Lee, Y. and Pawitan, Y. (2011)\n<doi:10.2202/1544-6115.1638> is first applied to extract\nassociation patterns for each group of samples. Then, a nuclear\nnorm-based dissimilarity measure is used to construct a\ndissimilarity matrix between groups based on the extracted\nassociations. Finally, hierarchical clustering is applied.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Repository": "https://calvintchi.r-universe.dev",
  "Date/Publication": "2021-02-20 16:14:25 UTC",
  "RemoteUrl": "https://github.com/calvintchi/hierbipartite",
  "RemoteRef": "HEAD",
  "RemoteSha": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 10:20:01 UTC",
    "User": "root"
  },
  "Author": "Calvin Chi [aut, cre, cph],\nWoojoo Lee [ctb],\nDonghwan Lee [ctb],\nYoungjo Lee [ctb],\nYudi Pawitan [ctb]",
  "MD5sum": "181c04a1e0279b1f01bb4ab97ab5d856",
  "_user": "calvintchi",
  "_type": "src",
  "_file": "hierBipartite_0.0.2.tar.gz",
  "_fileid": "0086d9382760f52fe1367a152ae6c24d47532d844f695460765e06518667c3af",
  "_filesize": 2068601,
  "_sha256": "0086d9382760f52fe1367a152ae6c24d47532d844f695460765e06518667c3af",
  "_created": "2026-05-28T10:20:01.000Z",
  "_published": "2026-05-28T10:26:21.845Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78270610823,
      "time": 318,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7263488137"
    },
    {
      "job": 78270610779,
      "time": 116,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263428229"
    },
    {
      "job": 78270611169,
      "time": 193,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7263439514"
    },
    {
      "job": 78270610788,
      "time": 145,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263427696"
    },
    {
      "job": 78270112435,
      "time": 197,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263392606"
    },
    {
      "job": 78270610807,
      "time": 102,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263424233"
    },
    {
      "job": 78270610832,
      "time": 98,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7263423586"
    },
    {
      "job": 78270610853,
      "time": 74,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7263415982"
    },
    {
      "job": 78270610781,
      "time": 62,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263412796"
    }
  ],
  "_buildurl": "https://github.com/r-universe/calvintchi/actions/runs/26568728764",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/calvintchi/hierbipartite",
  "_commit": {
    "id": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
    "author": "CalvinTChi <calvin.chi@berkeley.edu>",
    "committer": "CalvinTChi <calvin.chi@berkeley.edu>",
    "message": "updated readme\n",
    "time": 1613837665
  },
  "_maintainer": {
    "name": "Calvin Chi",
    "email": "calvin.chi@berkeley.edu",
    "login": "calvintchi",
    "description": "",
    "uuid": 14324978
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "irlba",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "calvintchi",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "calvintchi",
      "count": 16,
      "uuid": 14324978
    }
  ],
  "_userbio": {
    "uuid": 14324978,
    "type": "user",
    "name": "Calvin Chi"
  },
  "_downloads": {
    "count": 173,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hierBipartite"
  },
  "_devurl": "https://github.com/calvintchi/hierbipartite",
  "_searchresults": 4,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/hierBipartite.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/calvintchi/hierbipartite",
  "_realowner": "calvintchi",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.0.2",
      "date": "2021-02-16"
    }
  ],
  "_exports": [
    "constructBipartiteGraph",
    "getSignificantMergedGroups",
    "hierBipartite",
    "matrixDissimilarity",
    "null_distri",
    "p_value",
    "scca"
  ],
  "_datasets": [
    {
      "name": "ctrp2",
      "title": "Processed Cancer Cell Line Encyclopedia (CCLE) and Cancer Therapeutics Response Portal (CTRP2) Dataset",
      "object": "ctrp2",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "constructBipartiteGraph",
      "title": "Construct Bipartite Graph Edge Weight Matrix of Gene-drug Association Patterns",
      "topics": [
        "constructBipartiteGraph"
      ]
    },
    {
      "page": "ctrp2",
      "title": "Processed Cancer Cell Line Encyclopedia (CCLE) and Cancer Therapeutics Response Portal (CTRP2) Dataset",
      "topics": [
        "ctrp2"
      ]
    },
    {
      "page": "getSignificantMergedGroups",
      "title": "Select Significant Results from 'HierBipartite'",
      "topics": [
        "getSignificantMergedGroups"
      ]
    },
    {
      "page": "hierBipartite",
      "title": "Bipartite Graph-based Hierarchical Clustering",
      "topics": [
        "hierBipartite"
      ]
    },
    {
      "page": "matrixDissimilarity",
      "title": "Matrix dissimilarity",
      "topics": [
        "matrixDissimilarity"
      ]
    },
    {
      "page": "null_distri",
      "title": "Null distribution of dissimilarity measures",
      "topics": [
        "null_distri"
      ]
    },
    {
      "page": "p_value",
      "title": "P-value of Similarity in Gene-drug Associations",
      "topics": [
        "p_value"
      ]
    },
    {
      "page": "scca",
      "title": "Sparse canonical covariance analysis",
      "topics": [
        "scca"
      ]
    }
  ],
  "_readme": "https://github.com/calvintchi/hierbipartite/raw/HEAD/README.md",
  "_rundeps": [
    "irlba",
    "lattice",
    "magrittr",
    "Matrix"
  ],
  "_vignettes": [
    {
      "source": "hierBipartite.Rmd",
      "filename": "hierBipartite.html",
      "title": "hierBipartite Vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Introduction",
        "2. Load Data",
        "3. Bipartite Graph-based Hierarchical Clustering",
        "3.1 Using $\\texttt{hierBipartite}$",
        "3.2 Examining Results",
        "References"
      ],
      "created": "2020-03-18 10:27:42",
      "modified": "2021-02-12 15:04:04",
      "commits": 8
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "hierbipartite",
  "_universes": [
    "calvintchi"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.2",
      "date": "2026-05-28T10:24:53.000Z",
      "distro": "noble",
      "commit": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
      "fileid": "8c8c5c749db452c08fc469cc7f62d3a60d240f8190ed029c04f1b0b564e0cd44",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/calvintchi/actions/runs/26568728764"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.2",
      "date": "2026-05-28T10:22:05.000Z",
      "distro": "noble",
      "commit": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
      "fileid": "c385dd8be27151ed23c11fc93f6f67d0722f2cbda26742167a7588fd4a471d77",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/calvintchi/actions/runs/26568728764"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.2",
      "date": "2026-05-28T10:22:45.000Z",
      "commit": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
      "fileid": "ab3ee7738295728e64f0e51b6945f75d146aa872ff65a329938507c78e7b20b8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/calvintchi/actions/runs/26568728764"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.2",
      "date": "2026-05-28T10:22:06.000Z",
      "commit": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
      "fileid": "a0be1c7fc48373ed64dfe58b0c2f8c254dc1c66fde3c438d9500f56edc130a64",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/calvintchi/actions/runs/26568728764"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.0.2",
      "date": "2026-05-28T10:22:05.000Z",
      "commit": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
      "fileid": "5c84c1865e974ac4b2896a6f0e59ae0c59f0e465dc6af2337b460abb1e8fecad",
      "status": "success",
      "buildurl": "https://github.com/r-universe/calvintchi/actions/runs/26568728764"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.2",
      "date": "2026-05-28T10:21:44.000Z",
      "commit": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
      "fileid": "a4aa193a520c7af7b98f47d34ab5db9abf7fc53d8c1bc9e3e204070f85d40ef9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/calvintchi/actions/runs/26568728764"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.2",
      "date": "2026-05-28T10:21:18.000Z",
      "commit": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
      "fileid": "a3dcc64ac40bef56f81e0847f6e093fac320e5f0f10a92305dea298157caa68a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/calvintchi/actions/runs/26568728764"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.0.2",
      "date": "2026-05-28T10:21:08.000Z",
      "commit": "02d69545d0ff3998c72e4068592c1116f62eb0bb",
      "fileid": "dfddb46a8a4ed51674ba2d60f9965f0087c75094c7cba09a9116a5bccceb41b8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/calvintchi/actions/runs/26568728764"
    }
  ]
}