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  "Title": "SynMut: Designing Synonymously Mutated Sequences with Different\nGenomic Signatures",
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  "Authors@R": "c(person(\"Haogao\", \"Gu\", email = \"hggu@connect.hku.hk\", role = c(\"aut\", \"cre\")),\nperson(\"Leo L.M.\", \"Poon\", email = \"llmpoon@hku.hk\", role = \"led\"))",
  "Description": "There are increasing demands on designing virus mutants\nwith specific dinucleotide or codon composition. This tool can\ntake both dinucleotide preference and/or codon usage bias into\naccount while designing mutants. It is a powerful tool for in\nsilico designs of DNA sequence mutants.",
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  "BugReports": "https://github.com/Koohoko/SynMut/issues",
  "URL": "https://github.com/Koohoko/SynMut",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-09-06 01:12:07 UTC",
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  "Maintainer": "Haogao Gu <hggu@connect.hku.hk>",
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    "codon_mimic",
    "codon_random",
    "codon_to",
    "dinu_dist",
    "dinu_to",
    "get_cu",
    "get_dna",
    "get_du",
    "get_freq",
    "get_nu",
    "get_region",
    "get_rscu",
    "input_seq",
    "seq_random"
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  "_help": [
    {
      "page": "codon_dist-methods",
      "title": "Calculating the codon usage difference between sequences",
      "topics": [
        "codon_dist",
        "codon_dist,ANY-method"
      ]
    },
    {
      "page": "codon_mimic-methods",
      "title": "Mimic a target codon usage bias",
      "topics": [
        "codon_mimic",
        "codon_mimic,DNAStringSet,DNAStringSet-method",
        "codon_mimic,regioned_dna,DNAStringSet-method",
        "codon_mimic,regioned_dna,vector-method"
      ]
    },
    {
      "page": "codon_random-methods",
      "title": "Generate random synonymous mutations",
      "topics": [
        "codon_random",
        "codon_random,DNAStringSet-method",
        "codon_random,regioned_dna-method"
      ]
    },
    {
      "page": "codon_to-methods",
      "title": "Maximize or minimize the usage of certain codon.",
      "topics": [
        "codon_to",
        "codon_to,regioned_dna-method"
      ]
    },
    {
      "page": "dinu_dist-methods",
      "title": "Calculating the dinucleotide usage difference between sequences",
      "topics": [
        "dinu_dist",
        "dinu_dist,ANY-method"
      ]
    },
    {
      "page": "dinu_to-methods",
      "title": "Maximize or minimize the usage of certain dinucleotide.",
      "topics": [
        "dinu_to",
        "dinu_to,regioned_dna-method"
      ]
    },
    {
      "page": "get_cu-methods",
      "title": "Get codon usage matrix",
      "topics": [
        "get_cu",
        "get_cu,DNAStringSet-method",
        "get_cu,regioned_dna-method"
      ]
    },
    {
      "page": "get_dna-methods",
      "title": "Get the DNAStringSet data",
      "topics": [
        "get_dna",
        "get_dna,regioned_dna-method"
      ]
    },
    {
      "page": "get_du-methods",
      "title": "Get dinucleotide usage matrix",
      "topics": [
        "get_du",
        "get_du,DNAStringSet-method",
        "get_du,regioned_dna-method"
      ]
    },
    {
      "page": "get_freq-methods",
      "title": "Get codon usage frequency of synonymous codons",
      "topics": [
        "get_freq",
        "get_freq,DNAStringSet-method",
        "get_freq,matrix-method",
        "get_freq,regioned_dna-method",
        "get_freq,vector-method"
      ]
    },
    {
      "page": "get_nu-methods",
      "title": "Get nucleotide usage matrix",
      "topics": [
        "get_nu",
        "get_nu,DNAStringSet-method",
        "get_nu,regioned_dna-method"
      ]
    },
    {
      "page": "get_region-methods",
      "title": "Get the variable region",
      "topics": [
        "get_region",
        "get_region,regioned_dna-method"
      ]
    },
    {
      "page": "get_rscu-methods",
      "title": "Get Relative Synonymous Codon Usage (rscu) of synonymous codons",
      "topics": [
        "get_rscu",
        "get_rscu,DNAStringSet-method",
        "get_rscu,regioned_dna-method"
      ]
    },
    {
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        "input_seq,character-method",
        "input_seq,DNAString-method",
        "input_seq,DNAStringSet-method"
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    },
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      "title": "An S4 class to record DNA sequences and variable regions for mutations",
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        "regioned_dna-class"
      ]
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      "page": "seq_random-methods",
      "title": "Generate 'n' random DNA sequnces of length 'm'",
      "topics": [
        "seq_random",
        "seq_random,numeric,numeric-method"
      ]
    }
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