{
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  "Package": "TFutils",
  "Title": "TFutils",
  "Description": "This package helps users to work with TF metadata from\nvarious sources. Significant catalogs of TFs and\nclassifications thereof are made available. Tools for working\nwith motif scans are also provided.",
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  "Date/Publication": "2026-04-28 12:47:44 UTC",
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      "tojson": true
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        "MSource_Author",
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        "MSource_Version",
        "SR_Model",
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        "TfSource_Month",
        "TfSource_Day"
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      "tojson": false
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      "name": "tftCollMap",
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      "object": "tftCollMap",
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  "_help": [
    {
      "page": "anchor_pmids",
      "title": "check columns of a dataframe for numerical tokens of 7 or 8 digits and create HTML anchors to pubmed.gov constituting a link to a PMID",
      "topics": [
        "anchor_pmids"
      ]
    },
    {
      "page": "browse_gotf_main",
      "title": "use DT::datatable to browse the GO catalogue of human DNA-binding transcription factors in Table S1.A of Lovering et al.",
      "topics": [
        "browse_gotf_main"
      ]
    },
    {
      "page": "browse_humantfs_main",
      "title": "use DT::datatable to browse the Lambert's Human Transcription Factors repository",
      "topics": [
        "browse_humantfs_main"
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    },
    {
      "page": "browse_lambert_gwaslinks",
      "title": "browse several hundred disease-TF associations with hyperlinked PMIDs",
      "topics": [
        "browse_lambert_gwaslinks"
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    },
    {
      "page": "browse_lambert_main",
      "title": "use DT::datatable to browse the Lambert table S1",
      "topics": [
        "browse_lambert_main"
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    },
    {
      "page": "ccbr_cell_url",
      "title": "Update Oct 18 2021",
      "topics": [
        "ccbr_cell_url"
      ]
    },
    {
      "page": "cisbpTFcat",
      "title": "cisbpTFcat: data.frame with information on CISBP TFs for human, retained for reproducibility support; see cisbpTFcat_2.0 for a more recent catalog",
      "topics": [
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    },
    {
      "page": "cisbpTFcat_2.0",
      "title": "cisbpTFcat_2.0: data.frame with information on CISBP TFs for human, described in PMID 31133749",
      "topics": [
        "cisbpTFcat_2.0"
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    },
    {
      "page": "defaultCircosParms",
      "title": "basic layout parameters for circos",
      "topics": [
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    },
    {
      "page": "demo_fimo_granges",
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      "topics": [
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    },
    {
      "page": "directHitsInCISBP",
      "title": "demonstrate interoperation of TF catalog with GWAS catalog",
      "topics": [
        "directHitsInCISBP"
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    },
    {
      "page": "encode690",
      "title": "encode690: DataFrame extending AnnotationHub metadata about ENCODE cell line x TF ranges",
      "topics": [
        "encode690"
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    {
      "page": "fimo_granges",
      "title": "create a list of GRanges for FIMO hits in a GenomicFiles instance, corresponding to a GRanges-based query",
      "topics": [
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    {
      "page": "fimo16",
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      "topics": [
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      "page": "fimoMap",
      "title": "fimoMap: table with Mnnnn (motif PWM tags) and HGNC symbols for TFs",
      "topics": [
        "fimoMap"
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    },
    {
      "page": "genemodelDF",
      "title": "use EnsDb to generate an exon-level model of genes identified by symbol",
      "topics": [
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      ]
    },
    {
      "page": "genemodForGviz",
      "title": "create a GeneRegionTrack instance for selected symbols",
      "topics": [
        "genemodForGviz"
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    },
    {
      "page": "get_rslocs_38",
      "title": "utility to obtain location etc. for rsids of SNPs",
      "topics": [
        "get_rslocs_38"
      ]
    },
    {
      "page": "gotf_url",
      "title": "Update Oct 18 2021",
      "topics": [
        "gotf_url"
      ]
    },
    {
      "page": "grabTab",
      "title": "create table of TF targets and related metadata",
      "topics": [
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    {
      "page": "gwascat_hg19_chr17",
      "title": "gwascat_hg19: GRanges of march 21 2018 EBI gwascat, limit to chr17",
      "topics": [
        "gwascat_hg19_chr17"
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    },
    {
      "page": "HGNCmap",
      "title": "simple accessor for HGNCmap component of TFCatalog",
      "topics": [
        "HGNCmap"
      ]
    },
    {
      "page": "hocomoco.mono",
      "title": "hocomoco.mono: data.frame with information on HOCOMOCO TFs for human",
      "topics": [
        "hocomoco.mono"
      ]
    },
    {
      "page": "hocomoco.mono.sep2018",
      "title": "hocomoco.mono.sep2018: data.frame with information on HOCOMOCO TFs for human, Sept 2018 download",
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