{
  "_id": "6a453a116ff6f235755274fa",
  "Package": "wTO",
  "Type": "Package",
  "Title": "Computing Weighted Topological Overlaps (wTO) & Consensus wTO\nNetwork",
  "Version": "2.1",
  "Author": "Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind\nAlmaas and Katja Nowick.",
  "Maintainer": "Deisy Morselli Gysi <deisy.ccnr@gmail.com>",
  "Description": "Computes the Weighted Topological Overlap with positive\nand negative signs (wTO) networks given a data frame containing\nthe mRNA count/ expression/ abundance per sample, and a vector\ncontaining the interested nodes of interaction (a subset of the\nelements of the full data frame). It also computes the cut-off\nthreshold or p-value based on the individuals bootstrap or the\nvalues reshuffle per individual. It also allows the\nconstruction of a consensus network, based on multiple wTO\nnetworks. The package includes a visualization tool for the\nnetworks.  More about the methodology can be found at\n<doi:10.1186/s12859-018-2351-7>.",
  "License": "GPL-2",
  "LazyData": "TRUE",
  "RoxygenNote": "7.3.1",
  "Encoding": "UTF-8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-01 15:59:01 UTC",
    "User": "root"
  },
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-07-05 02:43:58 UTC",
  "RemoteUrl": "https://github.com/cran/wTO",
  "RemoteRef": "HEAD",
  "RemoteSha": "0c431a504419c4d47bac6c7aa4dc89958a716c34",
  "_user": "cran",
  "_type": "src",
  "_file": "wTO_2.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/5875806bdd2cadb677f92459224ed011c2a2ba48da1b360d61b1f796ca328d68",
  "_filesize": 209937,
  "_sha256": "5875806bdd2cadb677f92459224ed011c2a2ba48da1b360d61b1f796ca328d68",
  "_expires": "2026-10-09T16:02:25.000Z",
  "_created": "2026-07-01T15:59:01.000Z",
  "_published": "2026-07-01T16:02:25.808Z",
  "_jobs": [
    {
      "job": 84579112016,
      "time": 134,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8015673764"
    },
    {
      "job": 84579111986,
      "time": 139,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8015676206"
    },
    {
      "job": 84578254684,
      "time": 239,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8015614900"
    },
    {
      "job": 84579111973,
      "time": 164,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8015686857"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/28525075076",
  "_status": "success",
  "_upstream": "https://github.com/cran/wTO",
  "_commit": {
    "id": "0c431a504419c4d47bac6c7aa4dc89958a716c34",
    "author": "Deisy Morselli Gysi <deisy.ccnr@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.1\n",
    "time": 1720147438
  },
  "_maintainer": {
    "name": "Deisy Morselli Gysi",
    "email": "deisy.ccnr@gmail.com"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "som",
      "role": "Imports"
    },
    {
      "package": "visNetwork",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "Rfast",
      "role": "Imports"
    },
    {
      "package": "HiClimR",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "deisygysi",
      "count": 12,
      "uuid": 17457373
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 615,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 360,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/wTO"
  },
  "_mentions": 7,
  "_searchresults": 52,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/wTO.html",
    "manual.pdf"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.1.0",
      "date": "2017-05-29"
    },
    {
      "version": "1.2.0",
      "date": "2017-06-08"
    },
    {
      "version": "1.2.2",
      "date": "2017-07-16"
    },
    {
      "version": "1.3.0",
      "date": "2017-10-04"
    },
    {
      "version": "1.4.0",
      "date": "2017-11-12"
    },
    {
      "version": "1.4.1",
      "date": "2017-11-22"
    },
    {
      "version": "1.4.2",
      "date": "2018-02-01"
    },
    {
      "version": "1.5",
      "date": "2018-03-02"
    },
    {
      "version": "1.6",
      "date": "2018-05-30"
    },
    {
      "version": "1.6.1",
      "date": "2018-06-28"
    },
    {
      "version": "1.6.2",
      "date": "2018-10-14"
    },
    {
      "version": "1.6.3",
      "date": "2018-11-17"
    },
    {
      "version": "2.0",
      "date": "2022-05-10"
    },
    {
      "version": "2.0.1",
      "date": "2022-05-24"
    },
    {
      "version": "2.0.2",
      "date": "2023-03-22"
    },
    {
      "version": "2.1",
      "date": "2024-07-04"
    }
  ],
  "_exports": [
    "CorrelationOverlap",
    "NetVis",
    "wTO",
    "wTO.Complete",
    "wTO.Consensus",
    "wTO.export",
    "wTO.fast",
    "wTO.in.line",
    "wTO.rep_measure"
  ],
  "_datasets": [
    {
      "name": "ExampleGRF",
      "title": "ExampleGRF",
      "object": "ExampleGRF",
      "class": [
        "data.frame"
      ],
      "fields": [
        "x"
      ],
      "rows": 168,
      "table": true,
      "tojson": true
    },
    {
      "name": "metagenomics_abundance",
      "title": "metagenomics_abundance",
      "object": "metagenomics_abundance",
      "class": [
        "data.frame"
      ],
      "fields": [
        "OTU",
        "Week1",
        "Week2",
        "Week3",
        "Week4",
        "Week5",
        "Week6",
        "Week7",
        "Week8",
        "Week9",
        "Week10",
        "Week11",
        "Week12",
        "Week13",
        "Week14",
        "Week15",
        "Week16",
        "Week17",
        "Week18",
        "Week19",
        "Week20",
        "Week21",
        "Week22",
        "Week23",
        "Week24",
        "Week25",
        "Week26",
        "Week27",
        "Week28",
        "Week29",
        "Week30",
        "Week31",
        "Week32",
        "Week33",
        "Week34",
        "Week35",
        "Week36",
        "Week37",
        "Week38",
        "Week39",
        "Week40",
        "Week41",
        "Week42",
        "Week43",
        "Week44",
        "Week45",
        "Week46",
        "Week47",
        "Week48",
        "Week49",
        "Week50",
        "Week51",
        "Week52",
        "Week53",
        "Week54",
        "Week55",
        "Week56",
        "Week57",
        "Week58",
        "Week59",
        "Week60",
        "Week61",
        "Week62",
        "Week63",
        "Week64",
        "Week65",
        "Week66",
        "Week67",
        "Week68",
        "Week69",
        "Week70",
        "Week71",
        "Week72",
        "Week73",
        "Week74",
        "Week75",
        "Week76",
        "Week77",
        "Week78",
        "Week79",
        "Week80",
        "Week81",
        "Week82",
        "Week83",
        "Week84",
        "Week85",
        "Week86",
        "Week87",
        "Week88",
        "Week89",
        "Week90",
        "Week91",
        "Week92",
        "Week93",
        "Week94",
        "Week95",
        "Week96",
        "Week97",
        "Week98"
      ],
      "rows": 67,
      "table": true,
      "tojson": true
    },
    {
      "name": "Microarray_Expression1",
      "title": "Microarray_Expression1",
      "object": "Microarray_Expression1",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID1",
        "ID2",
        "ID3",
        "ID4",
        "ID5",
        "ID6",
        "ID7",
        "ID8",
        "ID9",
        "ID10",
        "ID11",
        "ID12",
        "ID13",
        "ID14",
        "ID15",
        "ID16",
        "ID17",
        "ID18"
      ],
      "rows": 268,
      "table": true,
      "tojson": true
    },
    {
      "name": "Microarray_Expression2",
      "title": "Microarray_Expression2",
      "object": "Microarray_Expression2",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID1",
        "ID2",
        "ID3",
        "ID4",
        "ID5",
        "ID6",
        "ID7",
        "ID8",
        "ID9",
        "ID10",
        "ID11",
        "ID12",
        "ID13",
        "ID14",
        "ID15",
        "ID16",
        "ID17",
        "ID18"
      ],
      "rows": 268,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "CorrelationOverlap",
      "title": "CorrelationOverlap",
      "topics": [
        "CorrelationOverlap"
      ]
    },
    {
      "page": "ExampleGRF",
      "title": "ExampleGRF",
      "topics": [
        "ExampleGRF"
      ]
    },
    {
      "page": "metagenomics_abundance",
      "title": "metagenomics_abundance",
      "topics": [
        "metagenomics_abundance"
      ]
    },
    {
      "page": "Microarray_Expression1",
      "title": "Microarray_Expression1",
      "topics": [
        "Microarray_Expression1"
      ]
    },
    {
      "page": "Microarray_Expression2",
      "title": "Microarray_Expression2",
      "topics": [
        "Microarray_Expression2"
      ]
    },
    {
      "page": "NetVis",
      "title": "NetVis",
      "topics": [
        "NetVis"
      ]
    },
    {
      "page": "wTO",
      "title": "wTO",
      "topics": [
        "wTO"
      ]
    },
    {
      "page": "wTO.Complete",
      "title": "wTO.Complete",
      "topics": [
        "wTO.Complete"
      ]
    },
    {
      "page": "wTO.Consensus",
      "title": "wTO.Consensus",
      "topics": [
        "wTO.Consensus"
      ]
    },
    {
      "page": "wTO.export",
      "title": "wTO.export",
      "topics": [
        "wTO.export"
      ]
    },
    {
      "page": "wTO.fast",
      "title": "wTO.fast",
      "topics": [
        "wTO.fast"
      ]
    },
    {
      "page": "wTO.in.line",
      "title": "wTO.in.line",
      "topics": [
        "wTO.in.line"
      ]
    },
    {
      "page": "wTO.rep_measure",
      "title": "wTO.rep_measure",
      "topics": [
        "wTO.rep_measure"
      ]
    }
  ],
  "_readme": "https://github.com/cran/wTO/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "cpp11",
    "data.table",
    "digest",
    "evaluate",
    "fastmap",
    "fontawesome",
    "fs",
    "glue",
    "HiClimR",
    "highr",
    "htmltools",
    "htmlwidgets",
    "igraph",
    "jquerylib",
    "jsonlite",
    "knitr",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "ncdf4",
    "pkgconfig",
    "plyr",
    "R6",
    "rappdirs",
    "Rcpp",
    "RcppArmadillo",
    "RcppParallel",
    "reshape2",
    "Rfast",
    "rlang",
    "rmarkdown",
    "sass",
    "som",
    "stringi",
    "stringr",
    "tinytex",
    "vctrs",
    "visNetwork",
    "xfun",
    "yaml",
    "zigg"
  ],
  "_score": 3.7371926427047373,
  "_indexed": true,
  "_nocasepkg": "wto",
  "_universes": [
    "cran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1",
      "date": "2026-07-01T16:01:12.000Z",
      "distro": "resolute",
      "commit": "0c431a504419c4d47bac6c7aa4dc89958a716c34",
      "fileid": "https://r2.ropensci.org/e647e0319ea63fdeca16b5b183715b23d19dd4e94acf12ca14f42cdfd3420967",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/28525075076"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.1",
      "date": "2026-07-01T16:01:15.000Z",
      "distro": "resolute",
      "commit": "0c431a504419c4d47bac6c7aa4dc89958a716c34",
      "fileid": "https://r2.ropensci.org/44f4957e6a84edebf03ed8ffbbfc8d97cb6d7202ca66e39e3c49c3d2e9f1ea43",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/28525075076"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1",
      "date": "2026-07-01T16:02:01.000Z",
      "commit": "0c431a504419c4d47bac6c7aa4dc89958a716c34",
      "fileid": "https://r2.ropensci.org/60b5e27ad9381ce360936ab563845dc10d9a5f39ab9055e526e335406bfbbdd3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/28525075076"
    }
  ]
}