{
  "_id": "6a49ab84ba590bf88b937f9c",
  "Package": "pageRank",
  "Title": "Temporal and Multiplex PageRank for Gene Regulatory Network\nAnalysis",
  "Version": "1.23.0",
  "Authors@R": "person(\"Hongxu\", \"Ding\", role=c(\"aut\", \"cre\", \"ctb\", \"cph\"), email=\"hd2326@columbia.edu\")",
  "Description": "Implemented temporal PageRank analysis as defined by\nRozenshtein and Gionis. Implemented multiplex PageRank as\ndefined by Halu et al. Applied temporal and multiplex PageRank\nin gene regulatory network analysis.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "biocViews": "StatisticalMethod, GeneTarget, Network",
  "URL": "https://github.com/hd2326/pageRank",
  "BugReports": "https://github.com/hd2326/pageRank/issues",
  "RoxygenNote": "6.1.99.9001",
  "Config/pak/sysreqs": "libglpk-dev make libgsl0-dev libbz2-dev liblzma-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:53:44 UTC",
  "RemoteUrl": "https://github.com/bioc/pageRank",
  "RemoteRef": "HEAD",
  "RemoteSha": "400b824fb859d786c3086e5e6ded79e9839097aa",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-05 00:46:43 UTC",
    "User": "root"
  },
  "Author": "Hongxu Ding [aut, cre, ctb, cph]",
  "Maintainer": "Hongxu Ding <hd2326@columbia.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "pageRank_1.23.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b6f306ea5ab3bcb7935218ca9be507a985a04f2aad39bf43c5e097ff27346527",
  "_filesize": 234294,
  "_sha256": "b6f306ea5ab3bcb7935218ca9be507a985a04f2aad39bf43c5e097ff27346527",
  "_expires": "2026-10-13T00:55:31.000Z",
  "_created": "2026-07-05T00:46:43.000Z",
  "_published": "2026-07-05T00:55:32.917Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 4
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28724653272",
  "_status": "success",
  "_upstream": "https://github.com/bioc/pageRank",
  "_commit": {
    "id": "400b824fb859d786c3086e5e6ded79e9839097aa",
    "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": 1777380824
  },
  "_maintainer": {
    "name": "Hongxu Ding",
    "email": "hd2326@columbia.edu"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85180164243,
      "time": 378,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086909917"
    },
    {
      "job": 85180164265,
      "time": 457,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8086918774"
    },
    {
      "job": 85180164253,
      "time": 454,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8086918355"
    },
    {
      "job": 85180164248,
      "time": 250,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8086895279"
    },
    {
      "job": 85180164268,
      "time": 247,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8086895000"
    },
    {
      "job": 85179784640,
      "time": 377,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086864397"
    },
    {
      "job": 85180164262,
      "time": 295,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8086900329"
    },
    {
      "job": 85180164251,
      "time": 343,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8086905701"
    },
    {
      "job": 85180164259,
      "time": 368,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8086908747"
    },
    {
      "job": 85180164260,
      "time": 395,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8086911925"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "motifmatchr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "bcellViper",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Suggests"
    },
    {
      "package": "JASPAR2018",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "TFBSTools",
      "role": "Suggests"
    },
    {
      "package": "GenomicFeatures",
      "role": "Suggests"
    },
    {
      "package": "annotate",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "statisticalmethod",
    "genetarget",
    "network"
  ],
  "_stars": 0,
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/hd2326/pagerank",
  "_searchresults": 7,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/pageRank.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/hd2326/pagerank",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "accessibility_network",
    "adjust_graph",
    "aracne_network",
    "bubble_plot",
    "clean_graph",
    "conformation_network",
    "diff_graph",
    "get_color_gradient",
    "multiplex_page_rank",
    "P_graph",
    "P_null",
    "time_expmat"
  ],
  "_help": [
    {
      "page": "accessibility_network",
      "title": "Build Network from Accessibility Peaks.",
      "topics": [
        "accessibility_network"
      ]
    },
    {
      "page": "adjust_graph",
      "title": "Re-calculate PageRank",
      "topics": [
        "adjust_graph"
      ]
    },
    {
      "page": "aracne_network",
      "title": "Re-format ARACNe Network.",
      "topics": [
        "aracne_network"
      ]
    },
    {
      "page": "bubble_plot",
      "title": "Make Bubbleplot",
      "topics": [
        "bubble_plot"
      ]
    },
    {
      "page": "clean_graph",
      "title": "Clean Graph",
      "topics": [
        "clean_graph"
      ]
    },
    {
      "page": "conformation_network",
      "title": "Build Network from Conformation Peaks.",
      "topics": [
        "conformation_network"
      ]
    },
    {
      "page": "diff_graph",
      "title": "Calculate Temporal PageRank from Two Graphs",
      "topics": [
        "diff_graph"
      ]
    },
    {
      "page": "get_color_gradient",
      "title": "Generate Color Gradient",
      "topics": [
        "get_color_gradient"
      ]
    },
    {
      "page": "multiplex_page_rank",
      "title": "Calculate Multiplex PageRank",
      "topics": [
        "multiplex_page_rank"
      ]
    },
    {
      "page": "P_graph",
      "title": "Build Probability-Based Network",
      "topics": [
        "P_graph"
      ]
    },
    {
      "page": "P_null",
      "title": "Build Null Distribution of Probability-Based Distance",
      "topics": [
        "P_null"
      ]
    },
    {
      "page": "time_expmat",
      "title": "Generate Timewise Average Gene Expression",
      "topics": [
        "time_expmat"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "caTools",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "DirichletMultinomial",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "glue",
    "gtools",
    "httr",
    "igraph",
    "IRanges",
    "jsonlite",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "motifmatchr",
    "openssl",
    "pkgconfig",
    "pwalign",
    "R6",
    "Rcpp",
    "RcppArmadillo",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "seqLogo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "TFBSTools",
    "TFMPvalue",
    "vctrs",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "introduction.rnw",
      "filename": "introduction.pdf",
      "title": "pageRank",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "PageRank Analysis",
        "Prioritizing TFs in GRNs",
        "References"
      ],
      "created": "2020-09-04 06:40:04",
      "modified": "2020-09-15 19:42:48",
      "commits": 6
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "pagerank",
  "_universes": [
    "bioc",
    "hd2326"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-07-05T00:51:50.000Z",
      "distro": "resolute",
      "commit": "400b824fb859d786c3086e5e6ded79e9839097aa",
      "fileid": "https://r2.ropensci.org/6a3ed2e2b1fa6facab3e6125fabb1e312f5ea7661d0815468feb86da7ba9cf24",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28724653272"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-07-05T00:51:45.000Z",
      "distro": "resolute",
      "commit": "400b824fb859d786c3086e5e6ded79e9839097aa",
      "fileid": "https://r2.ropensci.org/da646ecc15aa1a81d72f7d24adb8a16ebab935388b64c79a48ef877e7b0ffc52",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28724653272"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-07-05T00:49:43.000Z",
      "commit": "400b824fb859d786c3086e5e6ded79e9839097aa",
      "fileid": "https://r2.ropensci.org/733b79718e7e33b7c413f8ef8e1ad1771e8667b2a2df2f1bcedf5cd8a77a0e21",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28724653272"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-07-05T00:49:28.000Z",
      "commit": "400b824fb859d786c3086e5e6ded79e9839097aa",
      "fileid": "https://r2.ropensci.org/e2944d94f46fb51ad27c1783445111511458802b7cec19df90c92ac9f1e320b7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28724653272"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.23.0",
      "date": "2026-07-05T00:52:16.000Z",
      "commit": "400b824fb859d786c3086e5e6ded79e9839097aa",
      "fileid": "https://r2.ropensci.org/2770b5391c72990d619570d1fef0acbd152436cac88f22bc2e55d94161f81b28",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28724653272"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-07-05T00:49:49.000Z",
      "commit": "400b824fb859d786c3086e5e6ded79e9839097aa",
      "fileid": "https://r2.ropensci.org/eae75daab78599dfede854ca4603e738db120f144ad8c3ddd8026e5f9cefbb0d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28724653272"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-07-05T00:50:03.000Z",
      "commit": "400b824fb859d786c3086e5e6ded79e9839097aa",
      "fileid": "https://r2.ropensci.org/954b300e98c3d9e471625a08e53671c65a5f7c53b8a92be91cab73d207faa832",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28724653272"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-07-05T00:50:32.000Z",
      "commit": "400b824fb859d786c3086e5e6ded79e9839097aa",
      "fileid": "https://r2.ropensci.org/1ded36433b26a56fb8d16576eb2a7bdd78c62ec9262c3ef8708fd87938fd3590",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28724653272"
    }
  ]
}