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  "Title": "A DNA Reference Library Manager",
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  "Maintainer": "Francois Keck <francois.keck@gmail.com>",
  "Description": "Reference database manager offering a set of functions to\nimport, organize, clean, filter, audit and export reference\ngenetic data. Provide functions to download sequence data from\nNCBI GenBank <https://www.ncbi.nlm.nih.gov/genbank/>. Designed\nas an environment for semi-automatic and assisted construction\nof reference databases and to improve standardization and\nrepeatability in barcoding and metabarcoding studies.",
  "License": "GPL-3",
  "URL": "https://fkeck.github.io/refdb/",
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  "Repository": "https://fkeck.r-universe.dev",
  "Date/Publication": "2026-02-27 15:05:41 UTC",
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    "refdb_check_seq_homogeneity",
    "refdb_check_tax_conflict",
    "refdb_check_tax_typo",
    "refdb_clean_seq_crop_primers",
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    "refdb_export_idtaxa",
    "refdb_export_mothur",
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    "refdb_fill_tax_downstream",
    "refdb_fill_tax_upstream",
    "refdb_filter_ref_scope",
    "refdb_filter_seq_ambiguous",
    "refdb_filter_seq_duplicates",
    "refdb_filter_seq_homopolymers",
    "refdb_filter_seq_length",
    "refdb_filter_seq_primer",
    "refdb_filter_seq_stopcodon",
    "refdb_filter_tax_na",
    "refdb_filter_tax_precision",
    "refdb_get_fields",
    "refdb_import_NCBI",
    "refdb_merge",
    "refdb_plot_map",
    "refdb_plot_seqlen_hist",
    "refdb_plot_tax_barplot",
    "refdb_plot_tax_tree",
    "refdb_plot_tax_treemap",
    "refdb_report",
    "refdb_set_fields",
    "refdb_set_fields_BOLD",
    "refdb_set_fields_diatbarcode",
    "refdb_set_fields_NCBI",
    "refdb_set_fields_PR2",
    "refdb_set_ncbitax",
    "refdb_write_fields",
    "valid_taxo_rank"
  ],
  "_help": [
    {
      "page": "check_fields",
      "title": "Internal check for fields",
      "topics": [
        "check_fields"
      ]
    },
    {
      "page": "fields_dbs",
      "title": "Functions to set fields for various databases",
      "topics": [
        "fields_dbs",
        "refdb_set_fields_BOLD",
        "refdb_set_fields_diatbarcode",
        "refdb_set_fields_NCBI",
        "refdb_set_fields_PR2"
      ]
    },
    {
      "page": "filter_scores",
      "title": "Scores for filtering operations",
      "topics": [
        ".filter_seq_length",
        "filter_scores"
      ]
    },
    {
      "page": "get_ncbi_taxonomy",
      "title": "Get NCBI taxonomy",
      "topics": [
        "get_ncbi_taxonomy"
      ]
    },
    {
      "page": "igraph_from_taxo",
      "title": "Create a graph from a taxonomic table",
      "topics": [
        "igraph_from_taxo"
      ]
    },
    {
      "page": "make_ncbi_table",
      "title": "Parse NCBI XML and make a table",
      "topics": [
        "make_ncbi_table"
      ]
    },
    {
      "page": "ncbi_taxo_rank",
      "title": "Taxonomic ranks of the NCBI Taxonomy database",
      "topics": [
        "ncbi_taxo_rank"
      ]
    },
    {
      "page": "process_geo_ncbi",
      "title": "Process coordinate column returned by NCBI",
      "topics": [
        "process_geo_ncbi"
      ]
    },
    {
      "page": "refdb_check_seq_conflict",
      "title": "Check for conflicts in sequences",
      "topics": [
        "refdb_check_seq_conflict"
      ]
    },
    {
      "page": "refdb_check_seq_homogeneity",
      "title": "Check for genetic homogeneity of taxa",
      "topics": [
        "refdb_check_seq_homogeneity"
      ]
    },
    {
      "page": "refdb_check_tax_conflict",
      "title": "Check for conflicts in taxonomy",
      "topics": [
        "refdb_check_tax_conflict"
      ]
    },
    {
      "page": "refdb_check_tax_typo",
      "title": "Check for typos in taxonomic names",
      "topics": [
        "refdb_check_tax_typo"
      ]
    },
    {
      "page": "refdb_clean_seq_crop_primers",
      "title": "Crop genetic sequences with a set of primers",
      "topics": [
        "refdb_clean_seq_crop_primers"
      ]
    },
    {
      "page": "refdb_clean_seq_remove_gaps",
      "title": "Remove gaps from genetic sequences",
      "topics": [
        "refdb_clean_seq_remove_gaps"
      ]
    },
    {
      "page": "refdb_clean_seq_remove_sideN",
      "title": "Remove repeated side N from genetic sequences",
      "topics": [
        "refdb_clean_seq_remove_sideN"
      ]
    },
    {
      "page": "refdb_clean_tax_harmonize_nomenclature",
      "title": "Harmonize taxonomic name nomenclature",
      "topics": [
        "refdb_clean_tax_harmonize_nomenclature"
      ]
    },
    {
      "page": "refdb_clean_tax_NA",
      "title": "Convert missing taxonomic names to NA",
      "topics": [
        "refdb_clean_tax_NA"
      ]
    },
    {
      "page": "refdb_clean_tax_remove_blank",
      "title": "Remove blank characters from taxonomic names",
      "topics": [
        "refdb_clean_tax_remove_blank"
      ]
    },
    {
      "page": "refdb_clean_tax_remove_extra",
      "title": "Remove extra words from taxonomic names",
      "topics": [
        "refdb_clean_tax_remove_extra"
      ]
    },
    {
      "page": "refdb_clean_tax_remove_subsp",
      "title": "Remove subspecific information from taxonomic names",
      "topics": [
        "refdb_clean_tax_remove_subsp"
      ]
    },
    {
      "page": "refdb_clean_tax_remove_uncertainty",
      "title": "Remove terms indicating uncertainty in taxonomic names",
      "topics": [
        "refdb_clean_tax_remove_uncertainty"
      ]
    },
    {
      "page": "refdb_export_dada2",
      "title": "Export reference database for DADA2",
      "topics": [
        "refdb_export_dada2"
      ]
    },
    {
      "page": "refdb_export_idtaxa",
      "title": "Export reference database for DECIPHER (IDTAXA)",
      "topics": [
        "refdb_export_idtaxa"
      ]
    },
    {
      "page": "refdb_export_mothur",
      "title": "Export reference database for Mothur",
      "topics": [
        "refdb_export_mothur"
      ]
    },
    {
      "page": "refdb_export_utax",
      "title": "Export reference database for USEARCH/VSEARCH",
      "topics": [
        "refdb_export_utax"
      ]
    },
    {
      "page": "refdb_fill_tax_downstream",
      "title": "Fill missing data in taxonomy",
      "topics": [
        "refdb_fill_tax_downstream"
      ]
    },
    {
      "page": "refdb_fill_tax_upstream",
      "title": "Fill missing data in taxonomy",
      "topics": [
        "refdb_fill_tax_upstream"
      ]
    },
    {
      "page": "refdb_filter_ref_scope",
      "title": "Filter records by taxonomic scope of studies",
      "topics": [
        "refdb_filter_ref_scope"
      ]
    },
    {
      "page": "refdb_filter_seq_ambiguous",
      "title": "Filter sequences based on their number of ambiguous character.",
      "topics": [
        "refdb_filter_seq_ambiguous"
      ]
    },
    {
      "page": "refdb_filter_seq_duplicates",
      "title": "Filter duplicated sequences.",
      "topics": [
        "refdb_filter_seq_duplicates"
      ]
    },
    {
      "page": "refdb_filter_seq_homopolymers",
      "title": "Filter sequences based on their number of repeated character.",
      "topics": [
        "refdb_filter_seq_homopolymers"
      ]
    },
    {
      "page": "refdb_filter_seq_length",
      "title": "Filter sequences based on their number of character.",
      "topics": [
        "refdb_filter_seq_length"
      ]
    },
    {
      "page": "refdb_filter_seq_primer",
      "title": "Filter sequences based on the presence of primers.",
      "topics": [
        "refdb_filter_seq_primer"
      ]
    },
    {
      "page": "refdb_filter_seq_stopcodon",
      "title": "Filter sequences based on their number of of stop codons.",
      "topics": [
        "refdb_filter_seq_stopcodon"
      ]
    },
    {
      "page": "refdb_filter_tax_na",
      "title": "Filter records NA taxa",
      "topics": [
        "refdb_filter_tax_na"
      ]
    },
    {
      "page": "refdb_filter_tax_precision",
      "title": "Filter records based on their taxonomic precision.",
      "topics": [
        "refdb_filter_tax_precision"
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    },
    {
      "page": "refdb_get_fields",
      "title": "Get fields of a reference database",
      "topics": [
        "refdb_get_fields"
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    },
    {
      "page": "refdb_import_NCBI",
      "title": "Download and import NCBI Nucleotide records",
      "topics": [
        "refdb_import_NCBI"
      ]
    },
    {
      "page": "refdb_merge",
      "title": "Merge reference databases",
      "topics": [
        "refdb_merge"
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    },
    {
      "page": "refdb_plot_map",
      "title": "Plot an interactive map",
      "topics": [
        "refdb_plot_map"
      ]
    },
    {
      "page": "refdb_plot_seqlen_hist",
      "title": "Plot an histogram of sequence lengths",
      "topics": [
        "refdb_plot_seqlen_hist"
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    },
    {
      "page": "refdb_plot_tax_barplot",
      "title": "Barplots of the number of records for the most represented taxa",
      "topics": [
        "refdb_plot_tax_barplot"
      ]
    },
    {
      "page": "refdb_plot_tax_tree",
      "title": "Reference database taxonomy tree",
      "topics": [
        "refdb_plot_tax_tree"
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    },
    {
      "page": "refdb_plot_tax_treemap",
      "title": "Reference database treemap",
      "topics": [
        "refdb_plot_tax_treemap"
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    },
    {
      "page": "refdb_report",
      "title": "Compile a report with different checks",
      "topics": [
        "refdb_report"
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    },
    {
      "page": "refdb_sample_tax",
      "title": "Sample records within taxa",
      "topics": [
        "refdb_sample_tax"
      ]
    },
    {
      "page": "refdb_set_fields",
      "title": "Associate columns to fields",
      "topics": [
        "refdb_set_fields"
      ]
    },
    {
      "page": "refdb_set_ncbitax",
      "title": "Replace the current taxonomy using the NCBI Taxonomy database",
      "topics": [
        "refdb_set_ncbitax"
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    },
    {
      "page": "refdb_write_fields",
      "title": "Write fields to a file",
      "topics": [
        "refdb_write_fields"
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    },
    {
      "page": "valid_taxo_rank",
      "title": "Ranks considered as valid by refdb",
      "topics": [
        "valid_taxo_rank"
      ]
    },
    {
      "page": "xml_extract",
      "title": "Extract XML elements",
      "topics": [
        "xml_extract"
      ]
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