{
  "_id": "6a1be1571d7bb097a0a186a8",
  "Package": "pandaR",
  "Title": "PANDA Algorithm",
  "Version": "1.45.0",
  "Author": "Dan Schlauch, Joseph N. Paulson, Albert Young, John\nQuackenbush, Kimberly Glass",
  "Maintainer": "Joseph N. Paulson <paulson.joseph@gene.com>, Dan Schlauch\n<dschlauch@genospace.com>",
  "Description": "Runs PANDA, an algorithm for discovering novel network\nstructure by combining information from multiple complementary\ndata sources.",
  "biocViews": "StatisticalMethod, GraphAndNetwork, Microarray,\nGeneRegulation, NetworkInference, GeneExpression,\nTranscription, Network",
  "VignetteBuilder": "knitr",
  "License": "GPL-2",
  "LazyData": "true",
  "RoxygenNote": "6.1.1",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:11 UTC",
  "RemoteUrl": "https://github.com/bioc/pandaR",
  "RemoteRef": "HEAD",
  "RemoteSha": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-31 06:31:02 UTC",
    "User": "root"
  },
  "MD5sum": "eeb5f740696228f59d32cb85bdbd784a",
  "_user": "bioc",
  "_type": "src",
  "_file": "pandaR_1.45.0.tar.gz",
  "_fileid": "c93289e4c8a21097564d719f522cd1cc3cb36c75404e6edd2f5ea792a9f3aaba",
  "_filesize": 9355613,
  "_sha256": "c93289e4c8a21097564d719f522cd1cc3cb36c75404e6edd2f5ea792a9f3aaba",
  "_created": "2026-05-31T06:31:02.000Z",
  "_published": "2026-05-31T07:20:55.505Z",
  "_jobs": [
    {
      "job": 78705701021,
      "time": 150,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7314457847"
    },
    {
      "job": 78705701018,
      "time": 212,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7314464577"
    },
    {
      "job": 78705701013,
      "time": 210,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7314464365"
    },
    {
      "job": 78705701058,
      "time": 121,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7314753170"
    },
    {
      "job": 78705701062,
      "time": 125,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7314748660"
    },
    {
      "job": 78705533550,
      "time": 176,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7314440789"
    },
    {
      "job": 78705701002,
      "time": 111,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314453348"
    },
    {
      "job": 78705701059,
      "time": 472,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7314494572"
    },
    {
      "job": 78705701056,
      "time": 399,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7314486425"
    },
    {
      "job": 78705701064,
      "time": 118,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7314454208"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 4,
    "note": 17
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26705370658",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/pandaR",
  "_commit": {
    "id": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
    "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": 1777380071
  },
  "_maintainer": {
    "name": "Joseph N. Paulson",
    "email": "dschlauch@genospace.com"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Depends"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "reshape",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "role": "Imports"
    },
    {
      "package": "hexbin",
      "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": "1.45.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.44.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "statisticalmethod",
    "graphandnetwork",
    "microarray",
    "generegulation",
    "networkinference",
    "geneexpression",
    "transcription",
    "network"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 452,
    "source": "https://www.bioconductor.org/packages/stats/bioc/pandaR"
  },
  "_mentions": 1,
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/contents.json",
    "extra/pandaR.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calcDegree",
    "calcDegreeDifference",
    "importPandaMatlab",
    "multiplot",
    "panda",
    "plotCommunityDetection",
    "plotGraph",
    "plotZ",
    "plotZbyTF",
    "subnetwork",
    "summary.panda",
    "targetedGenes",
    "testMotif",
    "topedges"
  ],
  "_datasets": [
    {
      "name": "pandaResult",
      "title": "Analysis result from PANDA algorithm on toy data",
      "object": "pandaResult",
      "class": [
        "panda"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pandaResultPairs",
      "title": "Analysis result from PANDA algorithm on toy data converted into pairs",
      "object": "pandaResultPairs",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TF",
        "Gene",
        "initial",
        "Z"
      ],
      "rows": 87000,
      "table": true,
      "tojson": true
    },
    {
      "name": "pandaToyData",
      "title": "Toy gene expression, motif, and ppi data",
      "object": "pandaToyData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calcDegree",
      "title": "Calculate regulatory network degree",
      "topics": [
        "calcDegree"
      ]
    },
    {
      "page": "calcDegreeDifference",
      "title": "Calculate difference in degrees",
      "topics": [
        "calcDegreeDifference"
      ]
    },
    {
      "page": "importPandaMatlab",
      "title": "Panda Matlab importer",
      "topics": [
        "importPandaMatlab"
      ]
    },
    {
      "page": "multiplot",
      "title": "Multiple plots",
      "topics": [
        "multiplot"
      ]
    },
    {
      "page": "panda",
      "title": "Passing Messages between Biological Networks to Refine Predicted Interactions",
      "topics": [
        "panda"
      ]
    },
    {
      "page": "pandaR",
      "title": "pandaR: Passing Messages between Biological Networks to Refine Predicted Interactions.",
      "topics": [
        "pandaR-package",
        "pandaR"
      ]
    },
    {
      "page": "pandaResult",
      "title": "Analysis result from PANDA algorithm on toy data",
      "topics": [
        "pandaResult"
      ]
    },
    {
      "page": "pandaResultPairs",
      "title": "Analysis result from PANDA algorithm on toy data converted into pairs",
      "topics": [
        "pandaResultPairs"
      ]
    },
    {
      "page": "pandaToyData",
      "title": "Toy gene expression, motif, and ppi data",
      "topics": [
        "pandaToyData"
      ]
    },
    {
      "page": "plotCommunityDetection",
      "title": "Community detection plot",
      "topics": [
        "plotCommunityDetection"
      ]
    },
    {
      "page": "plotGraph",
      "title": "Plot graph",
      "topics": [
        "plotGraph"
      ]
    },
    {
      "page": "plotZ",
      "title": "Comparison of Z scores between two PANDA runs",
      "topics": [
        "plotZ"
      ]
    },
    {
      "page": "plotZbyTF",
      "title": "Plot Z by TF out-degree quantiles",
      "topics": [
        "plotZbyTF"
      ]
    },
    {
      "page": "print.panda",
      "title": "print.panda",
      "topics": [
        "print.panda"
      ]
    },
    {
      "page": "subnetwork",
      "title": "Subnetwork",
      "topics": [
        "subnetwork"
      ]
    },
    {
      "page": "summary.panda",
      "title": "Summary.panda",
      "topics": [
        "summary.panda"
      ]
    },
    {
      "page": "targetedGenes",
      "title": "targetedGenes",
      "topics": [
        "targetedGenes"
      ]
    },
    {
      "page": "testMotif",
      "title": "Check motif",
      "topics": [
        "testMotif"
      ]
    },
    {
      "page": "topedges",
      "title": "Top edges",
      "topics": [
        "topedges"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "hexbin",
    "igraph",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "matrixStats",
    "pkgconfig",
    "plyr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape",
    "rlang",
    "RUnit",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "pandaR.Rmd",
      "filename": "pandaR.html",
      "title": "An Introduction to the pandaR Package",
      "author": "Daniel Schlauch, Albert Young, Joseph N. Paulson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Example",
        "Comparing state-specific PANDA networks",
        "Other helpful functions",
        "Session information"
      ],
      "created": "2015-04-06 22:04:26",
      "modified": "2016-05-01 20:07:12",
      "commits": 6
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "pandar",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-05-31T06:34:07.000Z",
      "distro": "noble",
      "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
      "fileid": "fc5d28d915fafc1380ef07c0cf85c523dbc9d7354c29ce264d1bba026201788b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705370658"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-05-31T06:34:05.000Z",
      "distro": "noble",
      "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
      "fileid": "b4229091458ef2793c60bd375979cada989f088e8e735df2051701ef42088f42",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705370658"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-05-31T07:19:56.000Z",
      "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
      "fileid": "abf7cb8c08f116719d1d7be7e2e904157e5d00becc585e3ef4e0b71cb5ab1161",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705370658"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-05-31T07:19:18.000Z",
      "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
      "fileid": "29ac747439e8214a587aa6aeaab59a7473e86a388b85bca827794f090d26e917",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705370658"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.45.0",
      "date": "2026-05-31T06:33:10.000Z",
      "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
      "fileid": "efc546c0c10ac3a76a8c44e0e6f292dc6882d3c3f1381620990768a8adc055c2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705370658"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-05-31T06:38:27.000Z",
      "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
      "fileid": "51ad906a019295a4ba8584b7b98336303e1456d5a2a650d31f75266b2f87e681",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705370658"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-05-31T06:37:09.000Z",
      "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
      "fileid": "2e2eb30f4bddacbedd5a427a496136c29f7348f294c6cf29b74c972f33a51930",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705370658"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-05-31T06:32:23.000Z",
      "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c",
      "fileid": "1875c3f1cb56281d98486b19421193a446644cfb53d1d5a063aabc0a5f82bedd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705370658"
    }
  ]
}