{
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  "Title": "Tidy Processing and Analysis of Biological Sequences",
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  "Date": "2024-10-23",
  "Authors@R": "c(person(\"Dominik\", \"Rafacz\", \nemail = \"dominikrafacz@gmail.com\",\ncomment = c(ORCID = \"0000-0003-0925-1909\"),\nrole = c(\"cre\", \"aut\")),\nperson(\"Michal\", \"Burdukiewicz\",\nemail = \"michalburdukiewicz@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8926-582X\"),\nrole = c(\"aut\")),\nperson(\"Laura\", \"Bakala\",\nemail = \"erdaradun.gaztea@gmail.com\",\nrole = c(\"aut\")),\nperson(\"Leon Eyrich\", \"Jessen\",\nemail = \"ljess@dtu.dk\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-2879-2559\")),\nperson(\"Stefan\", \"Roediger\",\nemail = \"stefan.roediger@b-tu.de\",\ncomment = c(ORCID = \"0000-0002-1441-6512\"),\nrole = c(\"ctb\")),\nperson(\"Jadwiga\", \"Slowik\",\nemail = \"jadwigaslowik5@gmail.com\",\ncomment = c(ORCID = \"0000-0003-3466-8933\"),\nrole = c(\"ctb\")),\nperson(\"Weronika\", \"Puchala\",\nemail = \"puchala.weronika@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2163-1429\"),\nrole = c(\"ctb\")),\nperson(\"Katarzyna\", \"Sidorczuk\",\nemail = \"sidorczuk.katarzyna17@gmail.com\",\nrole = c(\"ctb\")),\nperson(\"Filip\", \"Pietluch\",\nemail = \"fpietluch@gmail.com\",\nrole = c(\"ctb\")),\nperson(\"Jaroslaw\", \"Chilimoniuk\",\nemail = \"jaroslaw.chilimoniuk@gmail.com\",\ncomment = c(ORCID = \"0000-0001-5467-018X\"),\nrole = c(\"ctb\")))",
  "Description": "A tidy approach to analysis of biological sequences. All\nprocessing and data-storage functions are heavily optimized to\nallow the fastest and most efficient data storage.",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/BioGenies/tidysq",
  "BugReports": "https://github.com/BioGenies/tidysq/issues",
  "SystemRequirements": "GNU make, C++17",
  "NeedsCompilation": "yes",
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  "VignetteBuilder": "knitr",
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  "Config/pak/sysreqs": "cmake make libuv1-dev",
  "Repository": "https://biogenies.r-universe.dev",
  "Date/Publication": "2025-01-01 13:47:00 UTC",
  "RemoteUrl": "https://github.com/biogenies/tidysq",
  "RemoteRef": "HEAD",
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  "Packaged": {
    "Date": "2026-05-08 09:00:07 UTC",
    "User": "root"
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  "Author": "Dominik Rafacz [cre, aut] (ORCID:\n<https://orcid.org/0000-0003-0925-1909>),\nMichal Burdukiewicz [aut] (ORCID:\n<https://orcid.org/0000-0001-8926-582X>),\nLaura Bakala [aut],\nLeon Eyrich Jessen [ctb] (ORCID:\n<https://orcid.org/0000-0003-2879-2559>),\nStefan Roediger [ctb] (ORCID: <https://orcid.org/0000-0002-1441-6512>),\nJadwiga Slowik [ctb] (ORCID: <https://orcid.org/0000-0003-3466-8933>),\nWeronika Puchala [ctb] (ORCID: <https://orcid.org/0000-0003-2163-1429>),\nKatarzyna Sidorczuk [ctb],\nFilip Pietluch [ctb],\nJaroslaw Chilimoniuk [ctb] (ORCID:\n<https://orcid.org/0000-0001-5467-018X>)",
  "Maintainer": "Dominik Rafacz <dominikrafacz@gmail.com>",
  "MD5sum": "a745d9d16af6798cceb63b4d4c84cb1a",
  "_user": "biogenies",
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  "_created": "2026-05-08T09:00:07.000Z",
  "_published": "2026-05-22T13:52:21.717Z",
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    "%has%",
    "alphabet",
    "as.sq",
    "bite",
    "collapse",
    "complement",
    "export_sq",
    "find_invalid_letters",
    "find_motifs",
    "get_sq_lengths",
    "get_standard_alphabet",
    "get_tidysq_options",
    "import_sq",
    "is_empty_sq",
    "is.sq",
    "is.sq_ami",
    "is.sq_ami_bsc",
    "is.sq_ami_ext",
    "is.sq_atp",
    "is.sq_dna",
    "is.sq_dna_bsc",
    "is.sq_dna_ext",
    "is.sq_rna",
    "is.sq_rna_bsc",
    "is.sq_rna_ext",
    "is.sq_unt",
    "paste",
    "random_sq",
    "read_fasta",
    "remove_ambiguous",
    "remove_na",
    "reverse",
    "sq",
    "sq_type",
    "sq_type<-",
    "sqapply",
    "substitute_letters",
    "translate",
    "typify",
    "write_fasta"
  ],
  "_help": [
    {
      "page": "tidysq-package",
      "title": "tidysq: tidy analysis of biological sequences",
      "topics": [
        "tidysq-package",
        "tidysq"
      ]
    },
    {
      "page": "grapes-has-grapes",
      "title": "Test sq object for presence of given motifs",
      "concept": [
        "bio_functions"
      ],
      "topics": [
        "%has%"
      ]
    },
    {
      "page": "equals-.sq",
      "title": "Compare sq objects",
      "concept": [
        "util_functions"
      ],
      "topics": [
        "==.sq"
      ]
    },
    {
      "page": "alphabet",
      "title": "Get alphabet of given sq object.",
      "concept": [
        "alphabet_functions"
      ],
      "topics": [
        "alphabet"
      ]
    },
    {
      "page": "as.character.sq",
      "title": "Convert sq object into character vector",
      "concept": [
        "output_functions"
      ],
      "topics": [
        "as.character.sq"
      ]
    },
    {
      "page": "as.matrix.sq",
      "title": "Convert sq object into matrix",
      "concept": [
        "output_functions"
      ],
      "topics": [
        "as.matrix.sq"
      ]
    },
    {
      "page": "as.sq",
      "title": "Convert an object to sq",
      "concept": [
        "output_functions"
      ],
      "topics": [
        "as.sq",
        "as.sq.character",
        "as.sq.default"
      ]
    },
    {
      "page": "bite",
      "title": "Subset sequences from sq objects",
      "concept": [
        "order_functions"
      ],
      "topics": [
        "bite",
        "bite.sq"
      ]
    },
    {
      "page": "collapse",
      "title": "Collapse multiple sequences into one",
      "concept": [
        "order_functions"
      ],
      "topics": [
        "collapse",
        "collapse.sq"
      ]
    },
    {
      "page": "complement",
      "title": "Create complement sequence from dnasq or rnasq object",
      "concept": [
        "bio_functions"
      ],
      "topics": [
        "complement",
        "complement.sq_dna_bsc",
        "complement.sq_dna_ext",
        "complement.sq_rna_bsc",
        "complement.sq_rna_ext"
      ]
    },
    {
      "page": "export_sq",
      "title": "Export sq objects into other formats",
      "concept": [
        "output_functions"
      ],
      "topics": [
        "export_sq"
      ]
    },
    {
      "page": "find_invalid_letters",
      "title": "Find elements which are not suitable for specified type.",
      "concept": [
        "type_functions"
      ],
      "topics": [
        "find_invalid_letters",
        "find_invalid_letters.sq"
      ]
    },
    {
      "page": "find_motifs",
      "title": "Find given motifs",
      "concept": [
        "bio_functions"
      ],
      "topics": [
        "find_motifs",
        "find_motifs.data.frame",
        "find_motifs.sq"
      ]
    },
    {
      "page": "get_sq_lengths",
      "title": "Get lengths of sequences in sq object",
      "concept": [
        "util_functions"
      ],
      "topics": [
        "get_sq_lengths"
      ]
    },
    {
      "page": "get_standard_alphabet",
      "title": "Get standard alphabet for given type.",
      "concept": [
        "alphabet_functions"
      ],
      "topics": [
        "get_standard_alphabet"
      ]
    },
    {
      "page": "get_tidysq_options",
      "title": "Obtain current state of tidysq options",
      "concept": [
        "display_functions"
      ],
      "topics": [
        "get_tidysq_options",
        "tidysq-options"
      ]
    },
    {
      "page": "import_sq",
      "title": "Import sq objects from other objects",
      "concept": [
        "input_functions"
      ],
      "topics": [
        "import_sq"
      ]
    },
    {
      "page": "is_empty_sq",
      "title": "Test if sequence is empty",
      "concept": [
        "cleaning_functions"
      ],
      "topics": [
        "is_empty_sq",
        "is_empty_sq.sq"
      ]
    },
    {
      "page": "is.sq",
      "title": "Check if object has specified type",
      "concept": [
        "type_functions",
        "util_functions"
      ],
      "topics": [
        "is.sq",
        "is.sq_ami",
        "is.sq_ami_bsc",
        "is.sq_ami_ext",
        "is.sq_atp",
        "is.sq_dna",
        "is.sq_dna_bsc",
        "is.sq_dna_ext",
        "is.sq_rna",
        "is.sq_rna_bsc",
        "is.sq_rna_ext",
        "is.sq_unt"
      ]
    },
    {
      "page": "paste",
      "title": "Paste sequences in string-like fashion",
      "concept": [
        "order_functions"
      ],
      "topics": [
        "paste",
        "paste.sq"
      ]
    },
    {
      "page": "random_sq",
      "title": "Generate random sequences",
      "concept": [
        "input_functions"
      ],
      "topics": [
        "random_sq"
      ]
    },
    {
      "page": "read_fasta",
      "title": "Read a FASTA file",
      "concept": [
        "input_functions"
      ],
      "topics": [
        "read_fasta"
      ]
    },
    {
      "page": "remove_ambiguous",
      "title": "Remove sequences that contain ambiguous elements",
      "concept": [
        "cleaning_functions"
      ],
      "topics": [
        "remove_ambiguous",
        "remove_ambiguous.sq"
      ]
    },
    {
      "page": "remove_na",
      "title": "Remove sequences that contain NA values",
      "concept": [
        "cleaning_functions"
      ],
      "topics": [
        "remove_na",
        "remove_na.sq"
      ]
    },
    {
      "page": "reverse",
      "title": "Reverse sequence",
      "concept": [
        "order_functions"
      ],
      "topics": [
        "reverse",
        "reverse.sq"
      ]
    },
    {
      "page": "sq",
      "title": "Construct sq object from character vector",
      "concept": [
        "input_functions"
      ],
      "topics": [
        "sq"
      ]
    },
    {
      "page": "sq_type",
      "title": "Get type of an sq object",
      "concept": [
        "type_functions"
      ],
      "topics": [
        "sq_type",
        "sq_type.sq",
        "sq_type<-",
        "sq_type<-.sq"
      ]
    },
    {
      "page": "sq-class",
      "title": "sq: class for keeping biological sequences tidy",
      "topics": [
        "sq-class"
      ]
    },
    {
      "page": "sqapply",
      "title": "Apply function to each sequence",
      "topics": [
        "sqapply",
        "sqapply.sq"
      ]
    },
    {
      "page": "sqconcatenate",
      "title": "Concatenate sq objects",
      "concept": [
        "util_functions"
      ],
      "topics": [
        "sq-concatenate",
        "sqconcatenate"
      ]
    },
    {
      "page": "sqextract",
      "title": "Extract parts of a sq object",
      "concept": [
        "util_functions"
      ],
      "topics": [
        "sq-extract",
        "sqextract"
      ]
    },
    {
      "page": "sqprint",
      "title": "Print sq object",
      "concept": [
        "display_functions"
      ],
      "topics": [
        "sq-print",
        "sqprint"
      ]
    },
    {
      "page": "substitute_letters",
      "title": "Substitute letters in a sequence",
      "concept": [
        "type_functions"
      ],
      "topics": [
        "substitute_letters",
        "substitute_letters.sq"
      ]
    },
    {
      "page": "translate",
      "title": "Convert DNA or RNA into proteins using genetic code",
      "concept": [
        "bio_functions"
      ],
      "topics": [
        "translate",
        "translate.sq_dna_bsc",
        "translate.sq_rna_bsc"
      ]
    },
    {
      "page": "typify",
      "title": "Set type of an sq object",
      "concept": [
        "type_functions"
      ],
      "topics": [
        "typify",
        "typify.sq"
      ]
    },
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