{
  "_id": "6ac0a9b891601a2ad2996f6a",
  "Package": "BioNet",
  "Type": "Package",
  "Title": "Routines for the functional analysis of biological networks",
  "Version": "1.73.0",
  "Date": "2015-09-11",
  "Author": "Marcus Dittrich and Daniela Beisser",
  "Maintainer": "Marcus Dittrich\n<marcus.dittrich@biozentrum.uni-wuerzburg.de>",
  "Description": "This package provides functions for the integrated\nanalysis of protein-protein interaction networks and the\ndetection of functional modules. Different datasets can be\nintegrated into the network by assigning p-values of\nstatistical tests to the nodes of the network. E.g. p-values\nobtained from the differential expression of the genes from an\nAffymetrix array are assigned to the nodes of the network. By\nfitting a beta-uniform mixture model and calculating scores\nfrom the p-values, overall scores of network regions can be\ncalculated and an integer linear programming algorithm\nidentifies the maximum scoring subnetwork.",
  "License": "GPL (>= 2)",
  "LazyLoad": "yes",
  "URL": "http://bionet.bioapps.biozentrum.uni-wuerzburg.de/",
  "biocViews": "Microarray, DataImport, GraphAndNetwork, Network,\nNetworkEnrichment, GeneExpression, DifferentialExpression",
  "Config/pak/sysreqs": "libglpk-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:46 UTC",
  "RemoteUrl": "https://github.com/bioc/BioNet",
  "RemoteRef": "HEAD",
  "RemoteSha": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-03 07:00:49 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "BioNet_1.73.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/9c8bc028c0c640993bd0ed7a2c5dfbe76e1a6b18ed6781bd7617528ec812c2f8",
  "_filesize": 1872907,
  "_sha256": "9c8bc028c0c640993bd0ed7a2c5dfbe76e1a6b18ed6781bd7617528ec812c2f8",
  "_expires": "2027-01-11T07:07:33.000Z",
  "_created": "2026-10-03T07:00:49.000Z",
  "_published": "2026-10-03T07:07:36.035Z",
  "_bioccheck": {
    "error": 1,
    "warning": 7,
    "note": 18
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37104681411",
  "_status": "success",
  "_upstream": "https://github.com/bioc/BioNet",
  "_commit": {
    "id": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
    "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": 1777379686
  },
  "_maintainer": {
    "name": "Marcus Dittrich",
    "email": "marcus.dittrich@biozentrum.uni-wuerzburg.de"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 111151538269,
      "time": 155,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11268026866"
    },
    {
      "job": 111151538276,
      "time": 293,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11267527584"
    },
    {
      "job": 111151538265,
      "time": 357,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11268002198"
    },
    {
      "job": 111151538295,
      "time": 315,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11267188064"
    },
    {
      "job": 111151538268,
      "time": 288,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11267271795"
    },
    {
      "job": 111150837618,
      "time": 268,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11267737002"
    },
    {
      "job": 111151538296,
      "time": 152,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11267766334"
    },
    {
      "job": 111151538302,
      "time": 276,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11267472652"
    },
    {
      "job": 111151538397,
      "time": 210,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11267992047"
    },
    {
      "job": 111151538281,
      "time": 228,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11267906303"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10.0",
      "role": "Depends"
    },
    {
      "package": "graph",
      "role": "Depends"
    },
    {
      "package": "RBGL",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "version": ">= 1.0.1",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "rgl",
      "role": "Suggests"
    },
    {
      "package": "impute",
      "role": "Suggests"
    },
    {
      "package": "DLBCL",
      "role": "Suggests"
    },
    {
      "package": "genefilter",
      "role": "Suggests"
    },
    {
      "package": "xtable",
      "role": "Suggests"
    },
    {
      "package": "ALL",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "hgu95av2.db",
      "role": "Suggests"
    },
    {
      "package": "XML",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.73.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.72.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "dataimport",
    "graphandnetwork",
    "network",
    "networkenrichment",
    "geneexpression",
    "differentialexpression"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 470,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 819,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BioNet"
  },
  "_mentions": 40,
  "_searchresults": 178,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/BioNet.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aggrPvals",
    "bumOptim",
    "compareNetworks",
    "consensusScores",
    "fbum",
    "fbumLL",
    "fdrThreshold",
    "fitBumModel",
    "getCompScores",
    "getEdgeList",
    "hist.bum",
    "largestComp",
    "largestScoreComp",
    "loadNetwork.sif",
    "loadNetwork.tab",
    "makeNetwork",
    "mapByVar",
    "permutateNodes",
    "piUpper",
    "plot.bum",
    "plot3dModule",
    "plotLLSurface",
    "plotModule",
    "print.bum",
    "readHeinzGraph",
    "readHeinzTree",
    "resamplingPvalues",
    "rmSelfLoops",
    "runFastHeinz",
    "runHeinz",
    "save3dModule",
    "saveNetwork",
    "scanFDR",
    "scoreFunction",
    "scoreNodes",
    "scoreOffset",
    "sortedEdgeList",
    "subNetwork",
    "summary.bum",
    "writeHeinz",
    "writeHeinzEdges",
    "writeHeinzNodes"
  ],
  "_datasets": [
    {
      "name": "pvaluesExample",
      "title": "Example p-values for aggregation statistics",
      "object": "pvaluesExample",
      "file": "pvaluesExample.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "p.vals1",
        "p.vals2"
      ],
      "rows": 6154,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "BioNet-package",
      "title": "Routines for the functional analysis of biological networks",
      "topics": [
        "BioNet-package",
        "BioNet"
      ]
    },
    {
      "page": "aggrPvals",
      "title": "Aggregate several p-values into one p-value",
      "topics": [
        "aggrPvals"
      ]
    },
    {
      "page": "bumOptim",
      "title": "Fitting a beta-uniform mixture model to p-value distribution",
      "topics": [
        "bumOptim"
      ]
    },
    {
      "page": "compareNetworks",
      "title": "Compare parameters of two networks",
      "topics": [
        "compareNetworks"
      ]
    },
    {
      "page": "consensusScores",
      "title": "Calculation of a consensus score for a network",
      "topics": [
        "consensusScores"
      ]
    },
    {
      "page": "fbum",
      "title": "Compute the density of the bum distribution",
      "topics": [
        "fbum"
      ]
    },
    {
      "page": "fbumLL",
      "title": "Calculate log likelihood of BUM model",
      "topics": [
        "fbumLL"
      ]
    },
    {
      "page": "fdrThreshold",
      "title": "Calculate p-value threshold for given FDR",
      "topics": [
        "fdrThreshold"
      ]
    },
    {
      "page": "fitBumModel",
      "title": "Fit beta-uniform mixture model to a p-value distribution",
      "topics": [
        "fitBumModel"
      ]
    },
    {
      "page": "getCompScores",
      "title": "Partition scores for subgraphs of the network",
      "topics": [
        "getCompScores"
      ]
    },
    {
      "page": "getEdgeList",
      "title": "Get representation of graph as edgelist",
      "topics": [
        "getEdgeList"
      ]
    },
    {
      "page": "hist.bum",
      "title": "Histogram of the p-value distribution with the fitted bum model",
      "topics": [
        "hist.bum"
      ]
    },
    {
      "page": "largestComp",
      "title": "Extract largest component of network",
      "topics": [
        "largestComp"
      ]
    },
    {
      "page": "largestScoreComp",
      "title": "Component with largest score",
      "topics": [
        "largestScoreComp"
      ]
    },
    {
      "page": "loadNetwork.sif",
      "title": "Load network from Cytoscape sif file",
      "topics": [
        "loadNetwork.sif"
      ]
    },
    {
      "page": "loadNetwork.tab",
      "title": "Load network from tabular format",
      "topics": [
        "loadNetwork.tab"
      ]
    },
    {
      "page": "makeNetwork",
      "title": "Create graph from source and target vectors",
      "topics": [
        "makeNetwork"
      ]
    },
    {
      "page": "mapByVar",
      "title": "Select probeset by variance and get PPI ID",
      "topics": [
        "mapByVar"
      ]
    },
    {
      "page": "permutateNodes",
      "title": "Permute node labels",
      "topics": [
        "permutateNodes"
      ]
    },
    {
      "page": "piUpper",
      "title": "Upper bound pi for the fraction of noise",
      "topics": [
        "piUpper"
      ]
    },
    {
      "page": "plot.bum",
      "title": "Quantile-quantile plot for the beta-uniform mixture model",
      "topics": [
        "plot.bum"
      ]
    },
    {
      "page": "plot3dModule",
      "title": "3D plot of the network",
      "topics": [
        "plot3dModule"
      ]
    },
    {
      "page": "plotLLSurface",
      "title": "Log likelihood surface plot",
      "topics": [
        "plotLLSurface"
      ]
    },
    {
      "page": "plotModule",
      "title": "Plot of the network",
      "topics": [
        "plotModule"
      ]
    },
    {
      "page": "print.bum",
      "title": "Print information about bum model",
      "topics": [
        "print.bum"
      ]
    },
    {
      "page": "pvaluesExample",
      "title": "Example p-values for aggregation statistics",
      "topics": [
        "pvaluesExample"
      ]
    },
    {
      "page": "readHeinzGraph",
      "title": "Convert HEINZ output to graph",
      "topics": [
        "readHeinzGraph"
      ]
    },
    {
      "page": "readHeinzTree",
      "title": "Convert HEINZ output to tree",
      "topics": [
        "readHeinzTree"
      ]
    },
    {
      "page": "resamplingPvalues",
      "title": "Resampling of microarray expression values and test for differential expression.",
      "topics": [
        "resamplingPvalues"
      ]
    },
    {
      "page": "rmSelfLoops",
      "title": "Remove self-loops in a graph",
      "topics": [
        "rmSelfLoops"
      ]
    },
    {
      "page": "runFastHeinz",
      "title": "Calculate heuristically maximum scoring subnetwork",
      "topics": [
        "runFastHeinz"
      ]
    },
    {
      "page": "runHeinz",
      "title": "Start HEINZ",
      "topics": [
        "runHeinz"
      ]
    },
    {
      "page": "save3dModule",
      "title": "Save a 3D plot of the network",
      "topics": [
        "save3dModule"
      ]
    },
    {
      "page": "saveNetwork",
      "title": "Save undirected network in various formats",
      "topics": [
        "saveNetwork"
      ]
    },
    {
      "page": "scanFDR",
      "title": "Dataframe of scores over a given range of FDRs",
      "topics": [
        "scanFDR"
      ]
    },
    {
      "page": "scoreFunction",
      "title": "Scoring function for p-values",
      "topics": [
        "scoreFunction"
      ]
    },
    {
      "page": "scoreNodes",
      "title": "Score the nodes of a network",
      "topics": [
        "scoreNodes"
      ]
    },
    {
      "page": "scoreOffset",
      "title": "Change score offset for 2 FDRs",
      "topics": [
        "scoreOffset"
      ]
    },
    {
      "page": "sortedEdgeList",
      "title": "Get a sorted edgelist",
      "topics": [
        "sortedEdgeList"
      ]
    },
    {
      "page": "subNetwork",
      "title": "Create a subGraph",
      "topics": [
        "subNetwork"
      ]
    },
    {
      "page": "summary.bum",
      "title": "Print summary of informations about bum model",
      "topics": [
        "summary.bum"
      ]
    },
    {
      "page": "writeHeinz",
      "title": "Write input files for HEINZ",
      "topics": [
        "writeHeinz"
      ]
    },
    {
      "page": "writeHeinzEdges",
      "title": "Write edge input file for HEINZ",
      "topics": [
        "writeHeinzEdges"
      ]
    },
    {
      "page": "writeHeinzNodes",
      "title": "Write node input file for HEINZ",
      "topics": [
        "writeHeinzNodes"
      ]
    }
  ],
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "fastmap",
    "generics",
    "glue",
    "graph",
    "httr",
    "igraph",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "RBGL",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "sys",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "Tutorial.Rnw",
      "filename": "Tutorial.pdf",
      "title": "BioNet Tutorial",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:14:05",
      "modified": "2020-10-05 16:38:09",
      "commits": 6
    }
  ],
  "_score": 6.329601248356519,
  "_indexed": true,
  "_nocasepkg": "bionet",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-10-03T07:04:29.000Z",
      "distro": "resolute",
      "commit": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
      "fileid": "https://r2.ropensci.org/87654fe8cb5441cb999263784755f96eacb2b68cc2abd0e37ccb33404dea611a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37104681411"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-10-03T07:05:28.000Z",
      "distro": "resolute",
      "commit": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
      "fileid": "https://r2.ropensci.org/6cf0c64d754c5c6c1b2ea24aa254d13790c70a1827e1317e015a01b58dd77e9f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37104681411"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-10-03T07:05:10.000Z",
      "commit": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
      "fileid": "https://r2.ropensci.org/d50dad6559d57ac1479956a4343eda8763185326ff0816c5a56a1184313bec72",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37104681411"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-10-03T07:04:56.000Z",
      "commit": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
      "fileid": "https://r2.ropensci.org/1ffb22ef211e6389851aab38e3032f5a2ec003921cca956f8c45add5105c4494",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37104681411"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.73.0",
      "date": "2026-10-03T07:03:46.000Z",
      "commit": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
      "fileid": "https://r2.ropensci.org/76b2dbf6878b3da616321bf8301b611f90cbc8d07b0adcab40687a22fb1acd94",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37104681411"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-10-03T07:03:36.000Z",
      "commit": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
      "fileid": "https://r2.ropensci.org/1009c1111f59d45edda3c21f4fbd2c606bd4732c50c9ad5345d9b6b3f2bbfb8d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37104681411"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-10-03T07:02:50.000Z",
      "commit": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
      "fileid": "https://r2.ropensci.org/e59ec6ce15184a07ae9c31e3f9c2a5d7aed7973764ea35674c089027875b651c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37104681411"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-10-03T07:03:01.000Z",
      "commit": "52d7a61b57fb54e8cefb3d64bed2aeb926a4ad94",
      "fileid": "https://r2.ropensci.org/d1e4c8df7081b764b082077c509345d228062b4a3e28f3ac5938198c450a3410",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37104681411"
    }
  ]
}