{
  "_id": "6ae76e001e2c7b3a4f5304db",
  "Package": "PANR",
  "Type": "Package",
  "Title": "Posterior association networks and functional modules inferred\nfrom rich phenotypes of gene perturbations",
  "Version": "1.59.0",
  "Date": "2012-06-20",
  "Author": "Xin Wang <xin_wang@hms.harvard.edu>",
  "Maintainer": "Xin Wang <xin_wang@hms.harvard.edu>",
  "Description": "This package provides S4 classes and methods for inferring\nfunctional gene networks with edges encoding posterior beliefs\nof gene association types and nodes encoding perturbation\neffects.",
  "License": "Artistic-2.0",
  "Collate": "classUnions.R assoScore.R panGraphics.R AllGenerics.R\nAllClasses.R BetaMixture-methods.R PAN-methods.R",
  "LazyLoad": "yes",
  "biocViews": "ImmunoOncology, NetworkInference, Visualization,\nGraphAndNetwork, Clustering, CellBasedAssays",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:46 UTC",
  "RemoteUrl": "https://github.com/bioc/PANR",
  "RemoteRef": "HEAD",
  "RemoteSha": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 14:07:33 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "PANR_1.59.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/db22b6c2fe5b1652728676fef7284a32922f3d5655f39b0897e70049b96ab31f",
  "_filesize": 2243349,
  "_sha256": "db22b6c2fe5b1652728676fef7284a32922f3d5655f39b0897e70049b96ab31f",
  "_expires": "2027-02-09T16:51:11.000Z",
  "_created": "2026-11-01T14:07:33.000Z",
  "_published": "2026-11-01T16:51:12.772Z",
  "_upstream": "https://github.com/bioc/PANR",
  "_status": "success",
  "_maintainer": {
    "name": "Xin Wang",
    "email": "xin_wang@hms.harvard.edu"
  },
  "_jobs": [
    {
      "job": 124871985057,
      "time": 138,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13087870599"
    },
    {
      "job": 124871985069,
      "time": 193,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13087421979"
    },
    {
      "job": 124871985042,
      "time": 204,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13086749987"
    },
    {
      "job": 124871985088,
      "time": 73,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13091737921"
    },
    {
      "job": 124871985054,
      "time": 112,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13091674706"
    },
    {
      "job": 124863938100,
      "time": 201,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13085694423"
    },
    {
      "job": 124871985056,
      "time": 105,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13086862721"
    },
    {
      "job": 124871985065,
      "time": 92,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13087085357"
    },
    {
      "job": 124871985129,
      "time": 87,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13087170559"
    },
    {
      "job": 124871985116,
      "time": 87,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13087140594"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 2,
    "note": 18
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41310383713",
  "_commit": {
    "id": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
    "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": 1777379746
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.14",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "pvclust",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "RedeR",
      "role": "Imports"
    },
    {
      "package": "snow",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.59.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.58.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "immunooncology",
    "networkinference",
    "visualization",
    "graphandnetwork",
    "clustering",
    "cellbasedassays"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 654,
    "source": "https://www.bioconductor.org/packages/stats/bioc/PANR"
  },
  "_searchresults": 6,
  "_abi": {
    "exports": [
      {
        "key": "PANR::BetaMixture",
        "hash": "8c9660100cf5f12f"
      },
      {
        "key": "PANR::PAN",
        "hash": "6861bd3539e5ddd8"
      },
      {
        "key": "PANR::generic:SNR2p",
        "hash": "62141c5018b0d41c"
      },
      {
        "key": "PANR::generic:buildPAN",
        "hash": "a90ae55848322676"
      },
      {
        "key": "PANR::generic:edgeWeight",
        "hash": "43a866737ae67216"
      },
      {
        "key": "PANR::generic:exportPAN",
        "hash": "2c304837990bf214"
      },
      {
        "key": "PANR::generic:fitBM",
        "hash": "55e41a24c9788459"
      },
      {
        "key": "PANR::generic:fitNULL",
        "hash": "399c9588ef7521da"
      },
      {
        "key": "PANR::generic:infer",
        "hash": "76caf3be915cf84b"
      },
      {
        "key": "PANR::generic:p2SNR",
        "hash": "e8b552cb0fc1f6eb"
      },
      {
        "key": "PANR::generic:permNULL",
        "hash": "7e32f49b00013321"
      },
      {
        "key": "PANR::generic:pvclustModule",
        "hash": "0ad9f73a922396e6"
      },
      {
        "key": "PANR::generic:sigModules",
        "hash": "419ce28091500ce8"
      },
      {
        "key": "PANR::generic:summarize",
        "hash": "a012ac5ed8c58414"
      },
      {
        "key": "PANR::generic:view",
        "hash": "99851c57fbddb754"
      },
      {
        "key": "PANR::generic:viewLegend",
        "hash": "4342b6379dd3244a"
      },
      {
        "key": "PANR::generic:viewNestedModules",
        "hash": "436b33e7fdb2a69c"
      },
      {
        "key": "PANR::generic:viewPAN",
        "hash": "b3ab16224d94b2eb"
      },
      {
        "key": "PANR::igraph",
        "hash": "c187417c40576831"
      }
    ],
    "imports": [
      {
        "key": "RedeR::character_Or_missing",
        "hash": "503a817d772f2c72"
      },
      {
        "key": "RedeR::integer_Or_numeric_Or_character_Or_missing",
        "hash": "07ea52ffcc7ffc58"
      },
      {
        "key": "RedeR::list_Or_missing",
        "hash": "36c4319b89498d74"
      },
      {
        "key": "RedeR::logical_Or_missing",
        "hash": "11be01089c0971ef"
      },
      {
        "key": "RedeR::matrix_Or_missing",
        "hash": "abf7f229a57212da"
      },
      {
        "key": "RedeR::numeric_Or_integer",
        "hash": "bd46272170b5fd65"
      },
      {
        "key": "RedeR::numeric_Or_integer_Or_missing",
        "hash": "235b87d3166d70fb"
      }
    ]
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/PANR.html"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "assoScore",
    "buildPAN",
    "cosineDist",
    "cosineSim",
    "exportPAN",
    "fitBM",
    "fitNULL",
    "infer",
    "p2SNR",
    "permNULL",
    "pvclustModule",
    "sigModules",
    "SNR2p",
    "summarize",
    "view",
    "viewLegend",
    "viewNestedModules",
    "viewPAN"
  ],
  "_datasets": [
    {
      "name": "Bakal2007",
      "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens",
      "object": "Bakal2007",
      "file": "Bakal2007.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "CG3799",
        "RacF28L",
        "RacV12",
        "RhoF30L",
        "RhoV14",
        "del_RhoGEF3",
        "del_Sif"
      ],
      "rows": 273,
      "table": true,
      "tojson": true
    },
    {
      "name": "Bakal2007Cluster",
      "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens",
      "object": "Bakal2007Cluster",
      "file": "Bakal2007Cluster.RData",
      "class": [
        "integer"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "bm1",
      "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens",
      "object": "bm",
      "file": "bm.RData",
      "class": [
        "BetaMixture"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "nodeColor",
      "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens",
      "object": "Bakal2007Cluster",
      "file": "Bakal2007Cluster.RData",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "assoScore",
      "title": "Association scores for gene pairs",
      "topics": [
        "assoScore"
      ]
    },
    {
      "page": "BetaMixture-class",
      "title": "An S4 class for beta mixture modelling of functional gene associations",
      "topics": [
        "BetaMixture",
        "BetaMixture-class"
      ]
    },
    {
      "page": "buildPAN",
      "title": "Build an igraph or RedeR graph for PAN",
      "topics": [
        "buildPAN",
        "buildPAN,PAN,character_Or_missing,list_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "cosineSim",
      "title": "Compute cosine similarities or distances between pairs of genes",
      "topics": [
        "cosineDist",
        "cosineSim"
      ]
    },
    {
      "page": "data-Bakal2007",
      "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens",
      "topics": [
        "Bakal2007",
        "Bakal2007Cluster",
        "bm1",
        "nodeColor"
      ]
    },
    {
      "page": "exportPAN",
      "title": "Export inferred PAN or module graphs to files",
      "topics": [
        "exportPAN",
        "exportPAN,PAN,character_Or_missing,character_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "fitBM",
      "title": "Fit a three-beta mixture model to densities of functional gene associations",
      "topics": [
        "fitBM",
        "fitBM,BetaMixture,list_Or_missing,list_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "fitNULL",
      "title": "Fit the NULL component of a three-beta mixture model for functional gene associations",
      "topics": [
        "fitNULL",
        "fitNULL,BetaMixture,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,character_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "infer",
      "title": "Infer a posterior association network",
      "topics": [
        "infer",
        "infer,PAN,list,logical_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "p2SNR",
      "title": "Translate p-values to Signal-to-Noise Ratios",
      "topics": [
        "p2SNR",
        "p2SNR,BetaMixture,numeric_Or_integer-method"
      ]
    },
    {
      "page": "PAN-class",
      "title": "An S4 class for inferring a posterior association network",
      "topics": [
        "PAN",
        "PAN-class"
      ]
    },
    {
      "page": "pvclustModule",
      "title": "Search enriched functional gene modules by pvclust",
      "topics": [
        "pvclustModule",
        "pvclustModule,PAN,numeric_Or_integer_Or_missing,character_Or_missing,character_Or_missing,logical_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "sigModules",
      "title": "Retrieve ids for significant gene modules searched by pvclust",
      "topics": [
        "sigModules",
        "sigModules,PAN,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "SNR2p",
      "title": "Translate p-values to Signal-to-Noise Ratios",
      "topics": [
        "SNR2p",
        "SNR2p,BetaMixture,numeric_Or_integer-method"
      ]
    },
    {
      "page": "summarize",
      "title": "Summarize the object of S4 class 'BetaMixture' or 'PAN'",
      "topics": [
        "summarize",
        "summarize,BetaMixture,character_Or_missing-method",
        "summarize,PAN,character_Or_missing-method"
      ]
    },
    {
      "page": "view",
      "title": "View the results of beta-mixture model fitting",
      "topics": [
        "view",
        "view,BetaMixture,character_Or_missing-method"
      ]
    },
    {
      "page": "viewLegend",
      "title": "View the legends for the graph built for PAN",
      "topics": [
        "viewLegend",
        "viewLegend,PAN,character_Or_missing-method"
      ]
    },
    {
      "page": "viewNestedModules",
      "title": "View the nested modules in a posterior association network in RedeR",
      "topics": [
        "viewNestedModules",
        "viewNestedModules,PAN,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "viewPAN",
      "title": "Show posterior association networks or modules in `igraph' or `RedeR'",
      "topics": [
        "viewPAN",
        "viewPAN,PAN,character_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "glue",
    "igraph",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "pkgconfig",
    "pvclust",
    "R6",
    "RColorBrewer",
    "RedeR",
    "rlang",
    "scales",
    "vctrs",
    "viridisLite"
  ],
  "_vignettes": [
    {
      "source": "PANR-Vignette.Rnw",
      "filename": "PANR-Vignette.pdf",
      "title": "Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "An overview of PANR",
        "Methods",
        "Case study I–inferring a functional association network regulating epidermal stem cell fate",
        "Case study II–inferring a functional association network regulating cell morphology",
        "Session info",
        "References"
      ],
      "created": "2013-11-01 20:20:36",
      "modified": "2013-11-01 20:20:36",
      "commits": 1
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "panr",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.59.0",
      "date": "2026-11-01T14:30:11.000Z",
      "distro": "resolute",
      "commit": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
      "fileid": "https://r2.ropensci.org/55537dde18ad9542d94b6a9b351ae152da1925979ded6886c6f7a4e70b747b24",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310383713"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.59.0",
      "date": "2026-11-01T14:30:33.000Z",
      "distro": "resolute",
      "commit": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
      "fileid": "https://r2.ropensci.org/0509ac95e80bd83a2051a7b8f13e6505e1e027f3dd951be954604a3169da2028",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310383713"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.59.0",
      "date": "2026-11-01T16:50:05.000Z",
      "commit": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
      "fileid": "https://r2.ropensci.org/977e4295862e422b569f7baa40359db22841809b8bd5043c96d656ef9fdd46cd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310383713"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.59.0",
      "date": "2026-11-01T16:50:23.000Z",
      "commit": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
      "fileid": "https://r2.ropensci.org/b4840edf1e841d8fa68d52c1a59ff466a5cae550a431e115e85bd3dc41be3926",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310383713"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.59.0",
      "date": "2026-11-01T14:29:15.000Z",
      "commit": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
      "fileid": "https://r2.ropensci.org/e10acaf8b1e42c21411167e4521bc57972e028f503c8301e540f535c2643b0a8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310383713"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.59.0",
      "date": "2026-11-01T14:08:54.000Z",
      "commit": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
      "fileid": "https://r2.ropensci.org/b25092b58b92c4ab89254904f892a54c28a9fd5cae111aa3bd5bfd9a7b500b5c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310383713"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.59.0",
      "date": "2026-11-01T14:09:02.000Z",
      "commit": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
      "fileid": "https://r2.ropensci.org/14358d06fa16cef8dbe855c488b8a80464c66a2ae5b03796926502fa4953403e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310383713"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.59.0",
      "date": "2026-11-01T14:08:55.000Z",
      "commit": "0ce8e4aa6dabe1c7db4a810b7f115b3a15dcdb35",
      "fileid": "https://r2.ropensci.org/e791b0d7c3e8590eed6cc62a218de7c96416a7083f1eaa21a2ee7a9540c4fc31",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310383713"
    }
  ]
}