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  "Package": "tantale",
  "Title": "Mining and Analysis of Transcription Activator-Like Effectors",
  "Version": "0.99.0.9000",
  "Authors@R": "c(\nperson(given = c(\"Bao\", \"Tram\"), family =\"Vi\",\nemail = \"vbt576@gmail.com\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-4319-5544\")),\nperson(given = \"Sebastien\", family = \"Cunnac\",\nemail = \"sebastien.cunnac@ird.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3695-491X\")),\nperson(given = c(\"Alvaro\", \"L.\"), family = \"Pérez-Quintero\",\nrole = \"cph\",\ncomment = \"Author of the bundled TALVEZ 3.2 and of the FuncTAL table behind rvd_dna_specificity\"),\nperson(given = \"Molly\", family = \"Megraw\", role = \"cph\",\ncomment = \"Author of the PlantTFBS Java classes bundled with TALVEZ (simplescancode/)\"),\nperson(given = c(\"Artemis\", \"G.\"), family = \"Hatzigeorgiou\", role = \"cph\",\ncomment = \"Author of the PlantTFBS Java classes bundled with TALVEZ (simplescancode/)\")\n)",
  "Maintainer": "Sebastien Cunnac <sebastien.cunnac@ird.fr>",
  "Description": "A toolkit for the study of transcription activator-like\neffectors (TALEs) of Xanthomonas. tell_tales() finds TALE genes\nin genome assemblies and can correct the frameshifts that make\nthem hard to annotate in error-prone long-read assemblies.\nTALEs are held in S3 classes that record each one as a series\nof parts (N-terminus, repeats with their repeat-variable\ndiresidues (RVDs), C-terminus), with methods to validate,\nsubset, combine and plot them. TALEs are aligned repeat by\nrepeat, compared with R implementations of the 'DisTAL' and\n'FuncTAL' distances <doi:10.3389/fpls.2015.00545>, and grouped\ninto families by hierarchical clustering or k-medoids. Wrappers\nfor 'AnnoTALE' <doi:10.1038/srep21077>, 'TALEcorrection'\n<doi:10.1186/s12864-023-09228-1>, 'TALVEZ'\n<doi:10.1371/journal.pone.0068464> and 'PrediTALE'\n<doi:10.1371/journal.pcbi.1007206> read their results into the\nsame objects; the last two predict target sites in host\ngenomes.",
  "License": "MIT + file LICENSE",
  "Copyright": "tantale authors, except the bundled third-party programs and\ndata listed with their licences in inst/COPYRIGHTS",
  "URL": "https://scunnac.github.io/tantale/,\nhttps://github.com/scunnac/tantale",
  "BugReports": "https://github.com/scunnac/tantale/issues",
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  "Repository": "https://ropensci-staging.r-universe.dev",
  "Date/Publication": "2026-10-09 12:48:37 UTC",
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  "Packaged": {
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  "Author": "Bao Tram Vi [aut] (ORCID: <https://orcid.org/0000-0002-4319-5544>),\nSebastien Cunnac [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3695-491X>),\nAlvaro L. Pérez-Quintero [cph] (Author of the bundled TALVEZ 3.2 and of\nthe FuncTAL table behind rvd_dna_specificity),\nMolly Megraw [cph] (Author of the PlantTFBS Java classes bundled with\nTALVEZ (simplescancode/)),\nArtemis G. Hatzigeorgiou [cph] (Author of the PlantTFBS Java classes\nbundled with TALVEZ (simplescancode/))",
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    "correct_tales",
    "distances_assert_square",
    "distances_restrict",
    "domain_distances",
    "is_pairwise_distances",
    "is_tales",
    "is_tales_msa",
    "pairwise_distances",
    "plot_target_preds",
    "preditale",
    "run_annotale_assign",
    "run_annotale_build",
    "run_annotale_load_classes",
    "run_annotale_predict",
    "tale_distances",
    "tales",
    "tales_align",
    "tales_anchor_codes",
    "tales_anomalies",
    "tales_assert_complete",
    "tales_assign_domain_codes",
    "tales_bind",
    "tales_coded_strings",
    "tales_compare_distal",
    "tales_compare_functal",
    "tales_consensus",
    "tales_consensus_match",
    "tales_domain_codes",
    "tales_domain_distances",
    "tales_from_annotale",
    "tales_from_telltales",
    "tales_get_dna_seq",
    "tales_get_protein_seq",
    "tales_group_hclust",
    "tales_group_kmedoids",
    "tales_msa",
    "tales_msa_params",
    "tales_msa_width",
    "tales_names",
    "tales_namespace",
    "tales_predict_targets",
    "tales_requirements",
    "tales_rvd_strings",
    "tales_tale_distances",
    "tales_to_universalmotif",
    "talomes_heatmap",
    "talvez",
    "tantale_genome",
    "tantale_setup",
    "tell_tales",
    "validate_pairwise_distances",
    "validate_tales",
    "validate_tales_msa"
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      "title": "RVD-to-DNA-binding-specificity weights",
      "object": "rvd_dna_specificity",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
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        "A",
        "C",
        "G",
        "T"
      ],
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      "table": true,
      "tojson": true
    },
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      "title": "Curated TALE annotations for ten published _Xanthomonas oryzae_ genomes",
      "object": "tale_annotations",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
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        "label",
        "tal_name",
        "annotale_class",
        "replicon_id",
        "genome_id",
        "pubmed",
        "truncTALE",
        "rvd_seq",
        "unusual_feature"
      ],
      "rows": 128,
      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "tantale-package",
      "title": "tantale: Transcription Activator-Like Effectors (TALEs) tools",
      "topics": [
        "tantale-package",
        "tantale"
      ]
    },
    {
      "page": "sub-.pairwise_distances",
      "title": "Subset a pairwise_distances object",
      "concept": [
        "pairwise distances"
      ],
      "topics": [
        "[.pairwise_distances"
      ]
    },
    {
      "page": "sub-.tales",
      "title": "Subset a tales object",
      "concept": [
        "tales objects"
      ],
      "topics": [
        "[.tales"
      ]
    },
    {
      "page": "as_tales",
      "title": "Coerce sequences of TALE parts to a tales object",
      "concept": [
        "tales objects"
      ],
      "topics": [
        "as_tales",
        "as_tales.data.frame",
        "as_tales.default"
      ]
    },
    {
      "page": "as.matrix.pairwise_distances",
      "title": "Render a distance table as a square matrix",
      "concept": [
        "pairwise distances"
      ],
      "topics": [
        "as.matrix.pairwise_distances"
      ]
    },
    {
      "page": "as.matrix.tales_msa",
      "title": "Render a TALE alignment as a matrix",
      "concept": [
        "TALE alignment"
      ],
      "topics": [
        "as.matrix.tales_msa"
      ]
    },
    {
      "page": "correct_tales",
      "title": "Correct TALE ORFs in error-prone sequences",
      "concept": [
        "TALE discovery"
      ],
      "topics": [
        "correct_tales"
      ]
    },
    {
      "page": "distances_assert_square",
      "title": "Assert that a distance table is complete and square",
      "concept": [
        "pairwise distances"
      ],
      "topics": [
        "distances_assert_square"
      ]
    },
    {
      "page": "distances_restrict",
      "title": "Restrict a distance table to a set of entities",
      "concept": [
        "pairwise distances"
      ],
      "topics": [
        "distances_restrict"
      ]
    },
    {
      "page": "format.tales",
      "title": "Render a tales object as lines of text",
      "concept": [
        "tales objects"
      ],
      "topics": [
        "format.tales"
      ]
    },
    {
      "page": "format.tales_msa",
      "title": "Render a tales_msa object as lines of text",
      "concept": [
        "tales objects"
      ],
      "topics": [
        "format.tales_msa"
      ]
    },
    {
      "page": "is_pairwise_distances",
      "title": "Is this a pairwise distance table?",
      "concept": [
        "pairwise distances"
      ],
      "topics": [
        "is_pairwise_distances"
      ]
    },
    {
      "page": "is_tales",
      "title": "Is this a tales object?",
      "concept": [
        "tales objects"
      ],
      "topics": [
        "is_tales"
      ]
    },
    {
      "page": "is_tales_msa",
      "title": "Is this a tales_msa object?",
      "concept": [
        "TALE alignment"
      ],
      "topics": [
        "is_tales_msa"
      ]
    },
    {
      "page": "pairwise_distances",
      "title": "Create a pairwise distance table",
      "concept": [
        "pairwise distances"
      ],
      "topics": [
        "domain_distances",
        "pairwise_distances",
        "tale_distances"
      ]
    },
    {
      "page": "plot_target_preds",
      "title": "Plot TALE RVD sequences along a potential DNA target region",
      "concept": [
        "TALE plots",
        "target prediction"
      ],
      "topics": [
        "plot_target_preds"
      ]
    },
    {
      "page": "plot.tales",
      "title": "Plot the domain composition of a set of TALE arrays",
      "concept": [
        "TALE plots"
      ],
      "topics": [
        "plot.tales"
      ]
    },
    {
      "page": "plot.tales_msa",
      "title": "Plot a multiple alignment of TALEs",
      "concept": [
        "TALE plots"
      ],
      "topics": [
        "plot.tales_msa"
      ]
    },
    {
      "page": "preditale",
      "title": "Run TALE target predictions on DNA sequence(s) using PrediTale",
      "concept": [
        "target prediction"
      ],
      "topics": [
        "preditale"
      ]
    },
    {
      "page": "print.tales",
      "title": "Print a tales object",
      "concept": [
        "tales objects"
      ],
      "topics": [
        "print.tales"
      ]
    },
    {
      "page": "print.tales_msa",
      "title": "Print a tales_msa object",
      "concept": [
        "tales objects"
      ],
      "topics": [
        "print.tales_msa"
      ]
    },
    {
      "page": "run_annotale_assign",
      "title": "Assign TALEs to AnnoTALE's published classes",
      "concept": [
        "external TALE tools"
      ],
      "topics": [
        "run_annotale_assign"
      ]
    },
    {
      "page": "run_annotale_build",
      "title": "Run the \"build\" stage of AnnoTALE",
      "concept": [
        "external TALE tools"
      ],
      "topics": [
        "run_annotale_build"
      ]
    },
    {
      "page": "run_annotale_load_classes",
      "title": "Download AnnoTALE's catalogue of TALE classes",
      "concept": [
        "external TALE tools"
      ],
      "topics": [
        "run_annotale_load_classes"
      ]
    },
    {
      "page": "run_annotale_predict",
      "title": "Runs the \"predict\" and \"analyze\" steps of AnnoTALE on a fasta file",
      "concept": [
        "external TALE tools"
      ],
      "topics": [
        "run_annotale_predict"
      ]
    },
    {
      "page": "rvd_dna_specificity",
      "title": "RVD-to-DNA-binding-specificity weights",
      "concept": [
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      "page": "tales_names",
      "title": "The names of the TALEs in a tales object",
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        "Checking for trouble",
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