{
  "_id": "6a212829cd65a98ecbd21bc4",
  "Package": "TFARM",
  "Type": "Package",
  "Title": "Transcription Factors Association Rules Miner",
  "Version": "1.34.0",
  "Date": "2021-11-21",
  "Author": "Liuba Nausicaa Martino, Alice Parodi, Gaia Ceddia, Piercesare\nSecchi, Stefano Campaner, Marco Masseroli",
  "Maintainer": "Liuba Nausicaa Martino <liuban.martino@gmail.com>",
  "Description": "It searches for relevant associations of transcription\nfactors with a transcription factor target, in specific genomic\nregions. It also allows to evaluate the Importance Index\ndistribution of transcription factors (and combinations of\ntranscription factors) in association rules.",
  "License": "Artistic-2.0",
  "VignetteBuilder": "knitr",
  "biocViews": "BiologicalQuestion, Infrastructure, StatisticalMethod,\nTranscription",
  "LazyData": "TRUE",
  "RoxygenNote": "6.1.1",
  "NeedsCompilation": "no",
  "Encoding": "UTF-8",
  "Packaged": {
    "Date": "2026-06-04 07:16:32 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:23 UTC",
  "RemoteUrl": "https://github.com/bioc/TFARM",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
  "MD5sum": "8dc81eb34181ccb81e6a39b4bf5a1413",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "TFARM_1.34.0.tar.gz",
  "_fileid": "2fc0f15b10245a0ef536db313ef79cb1c2aee37df502a4e0710e5295a0e453ea",
  "_filesize": 609822,
  "_sha256": "2fc0f15b10245a0ef536db313ef79cb1c2aee37df502a4e0710e5295a0e453ea",
  "_created": "2026-06-04T07:16:32.000Z",
  "_published": "2026-06-04T07:24:25.411Z",
  "_jobs": [
    {
      "job": 79468875643,
      "time": 156,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7405343950"
    },
    {
      "job": 79468875745,
      "time": 242,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7405365989"
    },
    {
      "job": 79468875707,
      "time": 210,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405357619"
    },
    {
      "job": 79468875699,
      "time": 114,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7405408708"
    },
    {
      "job": 79468875688,
      "time": 142,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405417176"
    },
    {
      "job": 79468169639,
      "time": 307,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7405300124"
    },
    {
      "job": 79468875656,
      "time": 111,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7405331233"
    },
    {
      "job": 79468875698,
      "time": 149,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7405341988"
    },
    {
      "job": 79468875783,
      "time": 131,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7405336176"
    },
    {
      "job": 79468875714,
      "time": 164,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405345609"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 16
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936603550",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/TFARM",
  "_commit": {
    "id": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380383
  },
  "_maintainer": {
    "name": "Liuba Nausicaa Martino",
    "email": "liuban.martino@gmail.com",
    "login": "liubanm",
    "description": "",
    "uuid": 23261040
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "arules",
      "role": "Imports"
    },
    {
      "package": "fields",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "plyr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.35.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "biologicalquestion",
    "infrastructure",
    "statisticalmethod",
    "transcription"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 344,
    "source": "https://www.bioconductor.org/packages/stats/bioc/TFARM"
  },
  "_searchresults": 4,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/TFARM.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "distribViz",
    "heatI",
    "IComp",
    "IPCA",
    "items",
    "itemset",
    "presAbs",
    "rulesGen",
    "rulesTF",
    "rulesTF0",
    "search_rule"
  ],
  "_datasets": [
    {
      "name": "DELTA",
      "title": "Contains the delta variations of support, confidence and lift.",
      "object": "data_man",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "I_c_2",
      "title": "Contains the mean Importance Index of pairs of transcription factors which are present in at least one association rule.",
      "object": "data_man",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TF",
        "imp"
      ],
      "rows": 67,
      "table": true,
      "tojson": true
    },
    {
      "name": "IMP",
      "title": "Contains the mean Importance Index of each co-regulator.",
      "object": "data_man",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TF",
        "imp",
        "sd",
        "nrules"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    },
    {
      "name": "imp_FOSL2",
      "title": "Contains the set of Importance Indexes of FOSL2 in a given set of rules.",
      "object": "data_man",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "IMP_Z",
      "title": "Contains the Importance Index associated with each co-regulator which is present in at least one association rule.",
      "object": "data_man",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MCF7_chr1",
      "title": "Contains genomic regions in the first chromosome of the MCF-7 human breast adenocarcinoma cell line at the ranges side, and the presence indexes of transcription factors in such regions at the metadata side.",
      "object": "MCF7_chr1",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "p_TFs",
      "title": "Contains co-regulators found in at least one association rule.",
      "object": "data_man",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "r_FOSL2",
      "title": "Represents an example of rulesTF output, i.e. the subset of rules whose left-hand-sides contain FOSL2, and the correspondent quality measures.",
      "object": "data_man",
      "class": [
        "data.frame"
      ],
      "fields": [
        "lhs",
        "rhs",
        "support",
        "confidence",
        "lift"
      ],
      "rows": 28,
      "table": true,
      "tojson": true
    },
    {
      "name": "r_noFOSL2",
      "title": "Represents an example of rulesTF0 output, where the presence of FOSL2 was replaced with its absence.",
      "object": "data_man",
      "class": [
        "data.frame"
      ],
      "fields": [
        "lhs",
        "rhs",
        "support",
        "confidence",
        "lift"
      ],
      "rows": 28,
      "table": true,
      "tojson": true
    },
    {
      "name": "r_TEAD4",
      "title": "Contains the association rules for the prediction of the presence of the transcription factor TEAD4 in the considered genomic regions, i.e., with TEAD4 in the right-hand-side of the association rules.",
      "object": "data_man",
      "class": [
        "data.frame"
      ],
      "fields": [
        "lhs",
        "rhs",
        "support",
        "confidence",
        "lift",
        "count"
      ],
      "rows": 30,
      "table": true,
      "tojson": true
    },
    {
      "name": "TF_Imp",
      "title": "Contains the candidate co-regulators and the number of rules associated with them.",
      "object": "data_man",
      "class": [
        "data.frame"
      ],
      "fields": [
        "IMP.TF",
        "IMP.imp",
        "IMP.nrules"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "DELTA",
      "title": "Contains the delta variations of support, confidence and lift.",
      "topics": [
        "DELTA"
      ]
    },
    {
      "page": "distribViz",
      "title": "Boxplots visualization of the Importance Index distribution of a set of transcription factors.",
      "topics": [
        "distribViz"
      ]
    },
    {
      "page": "heatI",
      "title": "Generates an heatmap visualization of the mean Importance Index of pairs of transcription factors.",
      "topics": [
        "heatI"
      ]
    },
    {
      "page": "I_c_2",
      "title": "Contains the mean Importance Index of pairs of transcription factors which are present in at least one association rule.",
      "topics": [
        "I_c_2"
      ]
    },
    {
      "page": "IComp",
      "title": "Computes the Importance Index of a transcription factor in a set of association rules.",
      "topics": [
        "IComp"
      ]
    },
    {
      "page": "IMP",
      "title": "Contains the mean Importance Index of each co-regulator.",
      "topics": [
        "IMP"
      ]
    },
    {
      "page": "imp_FOSL2",
      "title": "Contains the set of Importance Indexes of FOSL2 in a given set of rules.",
      "topics": [
        "imp_FOSL2"
      ]
    },
    {
      "page": "IMP_Z",
      "title": "Contains the Importance Index associated with each co-regulator which is present in at least one association rule.",
      "topics": [
        "IMP_Z"
      ]
    },
    {
      "page": "IPCA",
      "title": "Principal Components Analysis for distributions of variations of support and confidence obtained removing a transcription factor from a set of rules.",
      "topics": [
        "IPCA"
      ]
    },
    {
      "page": "items",
      "title": "Extracts items in the left-hand-side of an association rule.",
      "topics": [
        "items"
      ]
    },
    {
      "page": "itemset",
      "title": "Builds the itemset in the left-hand-side of an association rule.",
      "topics": [
        "itemset"
      ]
    },
    {
      "page": "MCF7_chr1",
      "title": "Contains genomic regions in the first chromosome of the MCF-7 human breast adenocarcinoma cell line at the ranges side, and the presence indexes of transcription factors in such regions at the metadata side.",
      "topics": [
        "MCF7_chr1"
      ]
    },
    {
      "page": "p_TFs",
      "title": "Contains co-regulators found in at least one association rule.",
      "topics": [
        "p_TFs"
      ]
    },
    {
      "page": "presAbs",
      "title": "Splits a set of transcription factors in 'present' or 'absent' transcription factors in a set of rules.",
      "topics": [
        "presAbs"
      ]
    },
    {
      "page": "r_FOSL2",
      "title": "Represents an example of rulesTF output, i.e. the subset of rules whose left-hand-sides contain FOSL2, and the correspondent quality measures.",
      "topics": [
        "r_FOSL2"
      ]
    },
    {
      "page": "r_noFOSL2",
      "title": "Represents an example of rulesTF0 output, where the presence of FOSL2 was replaced with its absence.",
      "topics": [
        "r_noFOSL2"
      ]
    },
    {
      "page": "r_TEAD4",
      "title": "Contains the association rules for the prediction of the presence of the transcription factor TEAD4 in the considered genomic regions, i.e., with TEAD4 in the right-hand-side of the association rules.",
      "topics": [
        "r_TEAD4"
      ]
    },
    {
      "page": "rulesGen",
      "title": "Exctracts relevant association rules.",
      "topics": [
        "rulesGen"
      ]
    },
    {
      "page": "rulesTF",
      "title": "Extracts a subset of rules that contain a certain transcription factor (or a combination of transcription factors) in their left-hand-side.",
      "topics": [
        "rulesTF"
      ]
    },
    {
      "page": "rulesTF0",
      "title": "Substitutes the presence of a transcription factor (or a combination of transcription factors) in the left-hand-side of a set of rules, with its absence.",
      "topics": [
        "rulesTF0"
      ]
    },
    {
      "page": "search_rule",
      "title": "Finds an association rule in a dataset.",
      "topics": [
        "search_rule"
      ]
    },
    {
      "page": "TF_Imp",
      "title": "Contains the candidate co-regulators and the number of rules associated with them.",
      "topics": [
        "TF_Imp"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/TFARM/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "arules",
    "BiocGenerics",
    "bitops",
    "caTools",
    "cli",
    "dotCall64",
    "fields",
    "generics",
    "GenomicRanges",
    "glue",
    "gplots",
    "gtools",
    "IRanges",
    "KernSmooth",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "Matrix",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S4Vectors",
    "Seqinfo",
    "spam",
    "stringi",
    "stringr",
    "vctrs",
    "viridisLite"
  ],
  "_vignettes": [
    {
      "source": "TFARM.Rnw",
      "filename": "TFARM.pdf",
      "title": "Transcription Factor Association Rule Miner",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2016-11-04 13:49:07",
      "modified": "2019-06-24 09:55:01",
      "commits": 11
    }
  ],
  "_score": 4,
  "_indexed": false,
  "_nocasepkg": "tfarm",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/TFARM",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.34.0",
      "date": "2026-06-04T07:19:43.000Z",
      "distro": "noble",
      "commit": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
      "fileid": "952da31d7ff73deee570b594f67ccc7de06f90db75fbe7c6caa57fe3dfd2b9ec",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936603550"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.34.0",
      "date": "2026-06-04T07:19:20.000Z",
      "distro": "noble",
      "commit": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
      "fileid": "3f364508bd0b8e05280541583c920e37503cf18a1d9c8742b2bd2a4ab090c428",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936603550"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.34.0",
      "date": "2026-06-04T07:22:49.000Z",
      "commit": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
      "fileid": "d948f72902ab94e3d771f2e9f1dacc483691bbca3b9bd70a94107fe339b658c5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936603550"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.34.0",
      "date": "2026-06-04T07:23:06.000Z",
      "commit": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
      "fileid": "db06543d7e481b7d22bda045220cbbfbf3cd6e5b1383906e02111338d6b9f8f6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936603550"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.34.0",
      "date": "2026-06-04T07:18:47.000Z",
      "commit": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
      "fileid": "c86f2f6f77ca83213e42bdbdd0df1c72e39f3f9d577854872fc4b44216848c08",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936603550"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.34.0",
      "date": "2026-06-04T07:17:53.000Z",
      "commit": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
      "fileid": "88a56b652716869b3fdb9cc1340ed5d2f3d701275e55d4bc023c5ac9dbf19672",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936603550"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.34.0",
      "date": "2026-06-04T07:17:46.000Z",
      "commit": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
      "fileid": "69744ee23fefdfe3c3fd56de60b208f487a6d476b780c96e9a143eeb38c4a968",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936603550"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.34.0",
      "date": "2026-06-04T07:18:09.000Z",
      "commit": "7c565059ba84b03c215c737c7e9ebd8fd4e82ba4",
      "fileid": "0cdf591c5f00258d97de560fc9f1495631ac15eb9fae5de51de21bc887305914",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936603550"
    }
  ]
}