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  "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",
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  "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",
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  "Packaged": {
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    "User": "root"
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  "Author": "Atsushi Fukushima [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9015-1694>)",
  "Maintainer": "Atsushi Fukushima <afukushima@gmail.com>",
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    "message": "fix bugs in counting k\n",
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  "_tags": [],
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    "software",
    "differentialexpression",
    "genetarget",
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    "microarray",
    "rnaseq",
    "transcription",
    "networkenrichment"
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      "date": "2023-08-31"
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    "calculateFDRBH",
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    "calculateRC",
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      "object": "catalog",
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      ],
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        "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
    },
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      "name": "DEGs39",
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "example.df",
      "title": "An example result of enrichment analysis",
      "object": "example.df",
      "file": "example.df.rda",
      "class": [
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      ],
      "fields": [
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        "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": [
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      ],
      "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"
      ]
    },
    {
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      "topics": [
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      ]
    },
    {
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      "title": "calculates Q-value",
      "topics": [
        "calculateQvalue"
      ]
    },
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      "topics": [
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      ]
    },
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      "topics": [
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      ]
    },
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      "title": "A list of TF-target genes (TG) in TFactS.",
      "topics": [
        "catalog"
      ]
    },
    {
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      "title": "An example list of DEGs from DEMO data in TFactS.",
      "topics": [
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      ]
    },
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      ]
    },
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      "title": "calculates Random Control (RC) fastly?",
      "topics": [
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      "title": "formats the result of enrichment test (ET)",
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    },
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      "title": "TFactSR: A package for identifying critical transcription factors.",
      "topics": [
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