{
  "_id": "6a5c5d1b9baadeef8ab4f0c5",
  "Type": "Package",
  "Package": "TFactSR",
  "Title": "Enrichment Approach to Predict Which Transcription Factors are\nRegulated",
  "Version": "0.99.1",
  "Authors@R": "person(given = \"Atsushi\",\nfamily = \"Fukushima\",\nemail = \"afukushima@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9015-1694\"))",
  "Description": "R implementation of 'TFactS' to predict which are the\ntranscription factors (TFs), regulated in a biological\ncondition based on lists of differentially expressed genes\n(DEGs) obtained from transcriptome experiments. This package is\nbased on the 'TFactS' concept by Essaghir et al. (2010)\n<doi:10.1093/nar/gkq149> and expands it. It allows users to\nperform 'TFactS'-like enrichment approach. The package can\nimport and use the original catalogue file from the 'TFactS' as\nwell as users' defined catalogues of interest that are not\nsupported by 'TFactS' (e.g., Arabidopsis).",
  "License": "GPL-3",
  "URL": "https://afukushima.github.io/TFactSR/",
  "VignetteBuilder": "knitr",
  "biocViews": "Network, Software, DifferentialExpression, GeneTarget,\nGeneExpression, Microarray, RNASeq, Transcription,\nNetworkEnrichment",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "Language": "en-US",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://afukushima.r-universe.dev",
  "Date/Publication": "2023-09-01 05:17:20 UTC",
  "RemoteUrl": "https://github.com/afukushima/tfactsr",
  "RemoteRef": "HEAD",
  "RemoteSha": "a9773380be8d622d21a7595b64a1e8ae000706b3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-19 05:10:15 UTC",
    "User": "root"
  },
  "Author": "Atsushi Fukushima [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9015-1694>)",
  "Maintainer": "Atsushi Fukushima <afukushima@gmail.com>",
  "_user": "afukushima",
  "_type": "src",
  "_file": "TFactSR_0.99.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/0aee8f6136468b26d0b554b851cee5d21557ae4c5cdeb0c843f64fb7f0b2e6ee",
  "_filesize": 186166,
  "_sha256": "0aee8f6136468b26d0b554b851cee5d21557ae4c5cdeb0c843f64fb7f0b2e6ee",
  "_expires": "2026-10-27T05:14:01.000Z",
  "_created": "2026-07-19T05:10:15.000Z",
  "_published": "2026-07-19T05:14:03.620Z",
  "_jobs": [
    {
      "job": 88159050416,
      "time": 179,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8438383528"
    },
    {
      "job": 88159050430,
      "time": 187,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8438384778"
    },
    {
      "job": 88159050435,
      "time": 137,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8438373411"
    },
    {
      "job": 88159050418,
      "time": 122,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8438372492"
    },
    {
      "job": 88158807881,
      "time": 201,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8438356117"
    },
    {
      "job": 88159050424,
      "time": 115,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8438374300"
    },
    {
      "job": 88159050441,
      "time": 79,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8438368665"
    },
    {
      "job": 88159050433,
      "time": 78,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8438368607"
    },
    {
      "job": 88159050453,
      "time": 112,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8438373976"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/afukushima/actions/runs/29674350211",
  "_status": "success",
  "_upstream": "https://github.com/afukushima/tfactsr",
  "_commit": {
    "id": "a9773380be8d622d21a7595b64a1e8ae000706b3",
    "author": "afukushima <afukushima@gmail.com>",
    "committer": "afukushima <afukushima@gmail.com>",
    "message": "fix bugs in counting k\n",
    "time": 1693545440
  },
  "_maintainer": {
    "name": "Atsushi Fukushima",
    "email": "afukushima@gmail.com",
    "login": "afukushima",
    "orcid": "0000-0001-9015-1694",
    "description": "",
    "uuid": 1477136
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "qvalue",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "afukushima",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "network",
    "software",
    "differentialexpression",
    "genetarget",
    "geneexpression",
    "microarray",
    "rnaseq",
    "transcription",
    "networkenrichment"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "afukushima",
      "count": 28,
      "uuid": 1477136
    },
    {
      "user": "kozo2",
      "count": 2,
      "uuid": 12192
    }
  ],
  "_userbio": {
    "uuid": 1477136,
    "type": "user",
    "name": "Atsushi Fukushima",
    "followers": 15
  },
  "_downloads": {
    "count": 190,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TFactSR"
  },
  "_devurl": "https://github.com/afukushima/tfactsr",
  "_pkgdown": "https://afukushima.github.io/TFactSR/",
  "_searchresults": 4,
  "_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/readme.html",
    "extra/readme.md",
    "extra/TFactSR.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/afukushima/tfactsr",
  "_realowner": "afukushima",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.99.0",
      "date": "2023-08-31"
    }
  ],
  "_exports": [
    "calculateEnrichmentTest",
    "calculateEvalue",
    "calculateFDRBH",
    "calculateQvalue",
    "calculateRC",
    "calculateTFactS",
    "extractTFTG",
    "FASTcalculateRC",
    "formatET",
    "formatRC"
  ],
  "_datasets": [
    {
      "name": "ATRM",
      "title": "A list of ATRM TF-target genes (TG) in Arabidopsis thaliana.",
      "object": "ATRM",
      "file": "ATRM.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TF",
        "target.genes"
      ],
      "rows": 1431,
      "table": true,
      "tojson": true
    },
    {
      "name": "catalog",
      "title": "A list of TF-target genes (TG) in TFactS.",
      "object": "catalog",
      "file": "catalog.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Target.gene..OFFICIAL_GENE_NAME.",
        "TF..OFFICIAL_TF_CODING_GENE_NAME.",
        "REFERENCES",
        "SPECIES",
        "ACCESSION..S"
      ],
      "rows": 6838,
      "table": true,
      "tojson": true
    },
    {
      "name": "DEGs",
      "title": "An example list of DEGs from DEMO data in TFactS.",
      "object": "DEGs",
      "file": "DEGs.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "DEGs39",
      "title": "An example list of 39 DEGs from DEMO data in TFactS.",
      "object": "DEGs39",
      "file": "DEGs39.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "example.df",
      "title": "An example result of enrichment analysis",
      "object": "example.df",
      "file": "example.df.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TFs",
        "m",
        "n",
        "N",
        "k",
        "p.value"
      ],
      "rows": 345,
      "table": true,
      "tojson": true
    },
    {
      "name": "example.list",
      "title": "An example list of result of enrichment analysis",
      "object": "example.list",
      "file": "example.list.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "GenesUp_SH1H",
      "title": "An example list of 74 DEGs from AtGenExpress stress dataset.",
      "object": "GenesUp_SH1H",
      "file": "GenesUp_SH1H.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ATRM",
      "title": "A list of ATRM TF-target genes (TG) in Arabidopsis thaliana.",
      "topics": [
        "ATRM"
      ]
    },
    {
      "page": "calculateEnrichmentTest",
      "title": "performs enrichment analysis",
      "topics": [
        "calculateEnrichmentTest"
      ]
    },
    {
      "page": "calculateEvalue",
      "title": "calculates E-value",
      "topics": [
        "calculateEvalue"
      ]
    },
    {
      "page": "calculateFDRBH",
      "title": "calculates FDR by Benjamini and Hochberg method",
      "topics": [
        "calculateFDRBH"
      ]
    },
    {
      "page": "calculateQvalue",
      "title": "calculates Q-value",
      "topics": [
        "calculateQvalue"
      ]
    },
    {
      "page": "calculateRC",
      "title": "calculates Random Control (RC)",
      "topics": [
        "calculateRC"
      ]
    },
    {
      "page": "calculateTFactS",
      "title": "calculates TFactS",
      "topics": [
        "calculateTFactS"
      ]
    },
    {
      "page": "catalog",
      "title": "A list of TF-target genes (TG) in TFactS.",
      "topics": [
        "catalog"
      ]
    },
    {
      "page": "DEGs",
      "title": "An example list of DEGs from DEMO data in TFactS.",
      "topics": [
        "DEGs"
      ]
    },
    {
      "page": "DEGs39",
      "title": "An example list of 39 DEGs from DEMO data in TFactS.",
      "topics": [
        "DEGs39"
      ]
    },
    {
      "page": "example.df",
      "title": "An example result of enrichment analysis",
      "topics": [
        "example.df"
      ]
    },
    {
      "page": "example.list",
      "title": "An example list of result of enrichment analysis",
      "topics": [
        "example.list"
      ]
    },
    {
      "page": "extractTFTG",
      "title": "extracts transcription factor (TF) and target gene (TG) information",
      "topics": [
        "extractTFTG"
      ]
    },
    {
      "page": "FASTcalculateRC",
      "title": "calculates Random Control (RC) fastly?",
      "topics": [
        "FASTcalculateRC"
      ]
    },
    {
      "page": "formatET",
      "title": "formats the result of enrichment test (ET)",
      "topics": [
        "formatET"
      ]
    },
    {
      "page": "formatRC",
      "title": "formats the result of Random Control (RC)",
      "topics": [
        "formatRC"
      ]
    },
    {
      "page": "GenesUp_SH1H",
      "title": "An example list of 74 DEGs from AtGenExpress stress dataset.",
      "topics": [
        "GenesUp_SH1H"
      ]
    },
    {
      "page": "TFactSR",
      "title": "TFactSR: A package for identifying critical transcription factors.",
      "topics": [
        "TFactSR"
      ]
    }
  ],
  "_readme": "https://github.com/afukushima/tfactsr/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "plyr",
    "qvalue",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "TFactSR.Rmd",
      "filename": "TFactSR.html",
      "title": "TFactSR: Enrichment Approach to Predict Which Transcription Factors Are Regulated",
      "author": "Atsushi Fukushima",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Methods - Statistical significance",
        "P-value",
        "E-value",
        "BH-corrected P-value",
        "Random Control (RC)",
        "Prerequisites",
        "Getting started",
        "Acknowledgments",
        "Reference",
        "Session info"
      ],
      "created": "2023-08-18 02:37:18",
      "modified": "2023-09-01 05:17:20",
      "commits": 4
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "tfactsr",
  "_universes": [
    "afukushima"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.1",
      "date": "2026-07-19T05:13:13.000Z",
      "distro": "resolute",
      "commit": "a9773380be8d622d21a7595b64a1e8ae000706b3",
      "fileid": "https://r2.ropensci.org/4610e6739d7c61a8dd4ff19a2f9370267e30b691bf63cebd46ebc0c90ac5a748",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/afukushima/actions/runs/29674350211"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.1",
      "date": "2026-07-19T05:13:20.000Z",
      "distro": "resolute",
      "commit": "a9773380be8d622d21a7595b64a1e8ae000706b3",
      "fileid": "https://r2.ropensci.org/e3c65e4e4b304d68fdae74ae3ca9b84dc9926c59297d0ffc960684172eca5ef7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/afukushima/actions/runs/29674350211"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.1",
      "date": "2026-07-19T05:12:10.000Z",
      "commit": "a9773380be8d622d21a7595b64a1e8ae000706b3",
      "fileid": "https://r2.ropensci.org/74e03186bc83cf95c5eaa885ae4e05f067432ae3219d3e43943f8bbac69ffd2a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/afukushima/actions/runs/29674350211"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.1",
      "date": "2026-07-19T05:12:03.000Z",
      "commit": "a9773380be8d622d21a7595b64a1e8ae000706b3",
      "fileid": "https://r2.ropensci.org/b2cdfd95e43b1abada78eae3713bb676d9f9e38b9e152ea0cea5f12d6dc361c3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/afukushima/actions/runs/29674350211"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.1",
      "date": "2026-07-19T05:12:29.000Z",
      "commit": "a9773380be8d622d21a7595b64a1e8ae000706b3",
      "fileid": "https://r2.ropensci.org/4030a4e9d259ac1c02d3b8313f0de37ca10dff0119b3e3e30ca8e90266343e31",
      "status": "success",
      "buildurl": "https://github.com/r-universe/afukushima/actions/runs/29674350211"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.1",
      "date": "2026-07-19T05:11:25.000Z",
      "commit": "a9773380be8d622d21a7595b64a1e8ae000706b3",
      "fileid": "https://r2.ropensci.org/b0149f58577a898ce7a445c6b367c91f95845626ea0a0a6f325868568477c23e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/afukushima/actions/runs/29674350211"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.1",
      "date": "2026-07-19T05:11:26.000Z",
      "commit": "a9773380be8d622d21a7595b64a1e8ae000706b3",
      "fileid": "https://r2.ropensci.org/893a01ea78a1273d3c515aaf36f97a854b21e76981f235ff933fbf08f16263e6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/afukushima/actions/runs/29674350211"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.1",
      "date": "2026-07-19T05:12:03.000Z",
      "commit": "a9773380be8d622d21a7595b64a1e8ae000706b3",
      "fileid": "https://r2.ropensci.org/0fefe777ca417c0cde671fc0ddb210e991ec8cf602ca206a00d8063aa48ef66a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/afukushima/actions/runs/29674350211"
    }
  ]
}