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  "Title": "Informatic Sequence Classification Trees",
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  "Authors@R": "person(\"Shaun\", \"Wilkinson\", email = \"shaunpwilkinson@gmail.com\",\nrole = c(\"aut\", \"cre\"))",
  "Author": "Shaun Wilkinson [aut, cre]",
  "Maintainer": "Shaun Wilkinson <shaunpwilkinson@gmail.com>",
  "Description": "Provides tools for probabilistic taxon assignment with\ninformatic sequence classification trees. See Wilkinson et al\n(2018) <doi:10.7287/peerj.preprints.26812v1>.",
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    "char2aa",
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    "classify",
    "decodePHMM",
    "demultiplex",
    "dereplicate",
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    "hash",
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    "prune_taxonomy",
    "purge",
    "qfilter",
    "rc",
    "readFASTA",
    "readFASTQ",
    "rereplicate",
    "searchGB",
    "shave",
    "stitch",
    "subset.AAbin",
    "subset.DNAbin",
    "taxonomy",
    "trim",
    "unique.AAbin",
    "unique.DNAbin",
    "virtualFISH",
    "virtualPCR",
    "writeFASTA",
    "writeFASTQ"
  ],
  "_datasets": [
    {
      "name": "samoa",
      "title": "Table of marine COI amplicon sequence variants from American Samoa",
      "object": "samoa",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "CTTAAGTTCGATTCAAAGTCATTCAGGTGCCGCAGTTGATTTAGCCATTCTCAGTCTACATTTATCAGGAGCTGCTTCTATCTTAGGAGCTGTAAACTTCATATCAACAATTTTAAACATGCGTAATCCAGGTCAAAGCATGTATAGAATGCCGTTATTTGTATGATCTATATTTGTTACAGCGTTCTTACTTTTATTAGCAGTACCAGTTTTAGCCGGTGCAATAACAATGCTTTTAACAGATCGTAATTTTAACACATCATTCTTTGATCCAGCAGGAGGAGGTGATCCTATTCTATATCAACACTTGTTT",
        "CCTTGCAAGAAATTTAGCCCATGCAGGCCCATCTGTAGACTTGGCTATTTTCTCTCTCCATCTTGCAGGTATCTCCTCAATTTTAGGAGCAGTAAATTTTATATCTACAACTTTCAATATACGTCATAAAGGCCTTCTTATGGAACGAATTCCACTATTCGCATGAGCTATTTTAATTACCGTAGTTCTCCTCCTTTTATCTCTCCCAGTACTTGCAGCCGCCATTACTATACTACTTACTGACCGGAACTTTAATACTTCCTTCTTTGACCCAGCCGGTGGAGGAGATCCTATCTTATACCAGCACCTCTTT",
        "ATTAAGTTCTATTCAAAGTCATTCAGGAGCCGCTGTTGATTTAGCCATTTTTAGTCTACATTTATCAGGAGCTGCTTCAATACTTGGAGCGATAAATTTTATCTCTACAATTTTAAATATGCGAAATCCAGGACAAAGTATGTATCGAATGCCTTTATTTGTTTGATCAATATTTGTTACAGCCTTTTTACTTTTGTTGGCAGTCCCTGTTTTAGCGGGAGCTATAACTATGCTTCTAACTGACCGTAATTTTAATACATCGTTTTTCGATCCTGCAGGAGGAGGTGACCCTATTTTATATCAGCATTTGTTT",
        "CTTAAGATCTACTCTGGGGCACTCAGGTGCCTCGGTTGATTTTGCGATTTTTTCTTTGCACCTCGCAGGAATTTCTTCTTTGCTAGGGGCAGTAAATTTTATTAGAACTCTAAAAAATACACGAACATTCGGCTTGGTTTTAGACCGAATAAGCCTTTTCCCCTGATCCGTGCTGGTAACTGCAATTCTACTTTTGCTTTCTCTCCCTGTCTTAGCAGGAGCAATTACTATGTTATTAACCGATCGAAACTTAAACACAACTTTTTACGACCCAAGAGGGGGGGGAGACCCTGTCCTCTACCAACACCTTTTT",
        "CCTAGCAGGAAACACCGCTCACAATGGTCCACCAGTAGATATGGCTATCTTCTCCCTCCACCTTGCTGGTGCCAGGTCAATCCTCGGAGCAGCTAACTTTATCTCTACTGTTACAAATATGCGAGCTAAGAAACAAAAATCAGAGAAAACATTACTATTTCCATGGTCCGTACTACTAACAGCTATCCTCCTACTTTTATCCCTTCCAGTACTGGCTGGGGCGATTACAATACTCCTAACCGACCGAAACCTGAATACATCATTTTTCGACGTAGGAGGAGGAGGTGATCCTATCCTATACCAACACTTATTT",
        "CTTAAGTTCGATTCAAAGTCATTCAGGAGCCGCAGTTGATTTAGCTATTTTCAGTCTACATTTATCAGGAGCCGCTTCCATTCTAGGAGCCGTAAATTTCATATCAACAATTTTAAACATGCGTAATCCAGGTCAAAGTATGTACAGAATGCCTTTATTCGTATGATCTATATTTGTTACAGCGTTTTTACTTTTACTAGCAGTACCAGTTTTAGCAGGTGCAATAACAATGCTTCTAACAGATCGTAATTTTAACACATCATTTTTTGATCCAGCAGGAGGAGGTGACCCTATTTTGTATCAACACTTGTTT",
        "TCTTGCAAGTAACATCGCCCATGCAGGGCCTTCTGTAGACCTTGCTATCTTCTCATTACACCTCGCAGGTGTATCCTCAATCATAGGAGCTTTAAACTTTATCACCACAGCCATCAATATACGATCGAAAGGGCTAAAGCTAGAACGAATTCCATTATTTGTATGATCAGTATTAATCACAGCGATTTTATTACTTTTAAGACTGCCAGTTCTAGCAGGAGCTATTACAATGCTTCTTACAGACCGAAACCTGAATACTGCTTTTTTTGATCCAGCAGGTGGGGGAGACCCCATTCTCTATCAACATTTATTC",
        "GCTAAGATCCAATATTAGTCACTCTGGTGCCTCGGTTGATTTTGCTATTTTTTCTCTGCATTTAGCGGGAGTGTCTTCTTTATTAGGAGCTGTGAATTTTATTTCTACTCTAGGCAATTTACGAGCTTTTGGTCTTCTTCTGGACCTGATGCCTTTATTCCCATGGGCTGTATTAATTACTGCAATTTTACTTTTGCTGTCTTTACCAGTATTGGCCGGGGCAGTTACCATGCTTTTAACTGATCGAAATTTAAACACCTCTTTTTACGATTCCAGAGGAGGAGGAGATCCCGTGCTTTATCAGCACCTGTTT",
        "TTTAAGTTCTATACAAAGTCATTCTGGGGCTGCAGTAGATTTAGCAATTTTTAGTTTACATTTATCAGGAGCAGCTTCTATTTTAGGAGCAATAAATTTTATTTCTACGATTGTGAATATGCGAAACCCTGGACAAAGTATGTATAGAATGCCTTTATTTGTTTGGTCAATTTTGGTAACTGCTTTTTTATTATTATTAGCGGTTCCTGTCTTAGCAGGCGCTATTACAATGCTATTAACGGATCGTAATTTCAATACTTCCTTTTTTGATCCTGCGGGAGGAGGGGATCCTATTTTATATCAACATTTATTT",
        "CTGAGGTCTAATCTTGGCCACAAGGGGGCCTCGGTAGACCTTGCAATCTTCTCCCTCCATTTAGCGGGAATTTCCTCTTTACTTGGGGCGGTTAACTTCATTACTACAATTCAAAATCTTCGGACTCTCGGGGTGTCGTTAGACCGAATAAGTCTTTTTCCCTGGGCAGTCTTGATTACGGCAGTACTACTCCTGTTATCATTACCAGTATTAGCGGGAGCTATTACCATACTTCTCACGGATCGTAACTTAAACACGTCCTTTTTTGACCCCTCAGGAGGGGGGGATCCGGTCCTTTATCAGCACTTATTT",
        "CCTAGCTAGAAATATTGCTCACGCAGGACCCTCAGTAGATATAGCAATTTTCTCCCTCCATTTAGCAGGAGCTTCATCTATTTTAGGCGCTGTTAACTTTATCTCCACCGTAATAAACATACGTAGGAAAGGCTATCGAATAGAACGAGTGCCTCTATTCGTTTGAGCAGTTAAAATCACTGCCGTGCTACTCCTTCTATCACTTCCTGTCCTTGCCGGTGCAATCACAATACTACTAACAGATCGAAATCTAAATACCTCATTTTTCGACCCAGCAGGGGGAGGAGATCCAGTTCTATTCCAACACCTATTC",
        "ACTTAGTTCGATACAAAGTCATTCAGGTGCTGCCGTTGACTTAGCTATTTTCAGCTTACATTTATCGGGTGCATCGTCTATTTTAGGCGCTGTCAATTTTATATCTACTATCTTGAATATGCGTAATCCAGGACAAAGCATGTATCGAATGCCTTTATTTGTTTGGTCTATTTTTGTGACTGCCATCTTACTTCTTTTAGCAGTACCTGTATTGGCAGGAGCAATTACAATGTTATTAACGGATAGGAATTTTAATACATCGTTTTTTGACCCAGCTGGCGGTGGAGATCCTGTCTTATACCAACATTTATTT",
        "ACTCTCTGCAAACATCTCGCACAGCGGATCTTCTGTAGATATAGCAATTTTCTCACTACATTTCGCTGGAATTAGCTCAATTCTAGGGGCAATTAACTTTATAACCACAGTTATTAACATACGAGTAAACAGAATAACTTTCATAAAAACCACACTTTTAACCTGAGCTGTATTCATCACTGCCATCCTTTTACTTCTATCTTTACCCGTCCTAGCCGGAGCTATTACCATACTCCTAACCGATCGAAACCTTAATACATCTTTCTTCGACCCAGCCGGAGGCGGAGACCCTATTCTCTATCAGCACTTATTC",
        "TCTAGCAGGAAACACCGCTCACAACGGACCACCAGTAGATATGGCTATCTTCTCCCTCCACCTTGCTGGTGCCAGGTCAATCCTCGGAGCAGCTAACTTTATCTCTACTGTTACAAATATACGAGCTAAGAAACAAAAATCAGAGAAAACATTACTATTTCCATGGTCCGTACTACTAACAGCTATCCTCCTACTCTTATCCCTTCCAGTACTGGCTGGGGCGATTACAATACTCCTAACCGACCGAAACCTAAATACATCATTTTTTGATGTAGGAGGGGGAGGTGACCCTATCCTATACCAACACTTATTT",
        "CTTAAGTTCGATTCAAAGTCATTCAGGTGCCGCAGTTGATTTAGCCATTCTCAGTCTACATTTATCAGGAGCTGCTTCTATCTTAGGAGCTGTAAACTTCATATCAACAATTTTAAACATGCGTAGTCCAGGTCAAAGCATGTATAGAATGCCGTTATTTGTATGATCTATATTTGTTACAGCGTTCTTACTTTTATTAGCAGTACCAGTTTTAGCCGGTGCAATAACAATGCTTTTAACAGATCGTAATTTTAACACATCATTCTTTGATCCAGCAGGAGGAGGTGATCCTATTCTATATCAACACTTGTTT",
        "TCTAGCAAGGAACATCGCTCATGCAGGACCTTCTGTAGATCTTGCAATCTTTTCCCTACACTTAGCAGGAGTATCATCAATTATAGGAGCCCTAAATTTCATTACTACGGTAATTAATATACGCTCCAAAGGACTACGCCTAGAACGAGTCCCATTATTTGTATGATCAGTTATAATTACCGCAATCCTTCTTCTCCTAAGCCTTCCTGTTCTAGCAGGAGCTATCACAATACTTTTAACAGATCGTAACCTAAACACTGCATTCTTTGATCCTGCGGGAGGAGGAGACCCCATTCTTTACCAGCATTTATTC"
      ],
      "rows": 2,
      "table": true,
      "tojson": true
    },
    {
      "name": "whale_taxonomy",
      "title": "Cetacean section of NCBI taxonomy database.",
      "object": "whale_taxonomy",
      "class": [
        "data.frame"
      ],
      "fields": [
        "taxID",
        "parent_taxID",
        "rank",
        "name"
      ],
      "rows": 72,
      "table": true,
      "tojson": true
    },
    {
      "name": "whales",
      "title": "Cetacean 16S rDNA sequences.",
      "object": "whales",
      "class": [
        "DNAbin"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "allocateCVI",
      "title": "Allocate sequences for cross validation by identity.",
      "topics": [
        "allocateCVI"
      ]
    },
    {
      "page": "classify",
      "title": "Tree-based sequence classification.",
      "topics": [
        "classify"
      ]
    },
    {
      "page": "conversion",
      "title": "Convert sequences between binary and character string formats.",
      "topics": [
        "aa2char",
        "char2aa",
        "char2dna",
        "conversion",
        "dna2char"
      ]
    },
    {
      "page": "demultiplex",
      "title": "Demultiplex merged FASTQ",
      "topics": [
        "demultiplex"
      ]
    },
    {
      "page": "disambiguate",
      "title": "Convert oligonucleotide sequences into regular expressions.",
      "topics": [
        "disambiguate"
      ]
    },
    {
      "page": "encoding",
      "title": "Encode and decode profile HMMs in raw byte format.",
      "topics": [
        "decodePHMM",
        "encodePHMM",
        "encoding"
      ]
    },
    {
      "page": "expand",
      "title": "Expand an existing classification tree.",
      "topics": [
        "expand"
      ]
    },
    {
      "page": "get_lineage",
      "title": "Get full lineage details from a taxonomic ID number.",
      "topics": [
        "get_lineage"
      ]
    },
    {
      "page": "get_taxID",
      "title": "Get taxon ID from taxonomy database.",
      "topics": [
        "get_taxID"
      ]
    },
    {
      "page": "hash",
      "title": "Convert sequences to MD5 hashes.",
      "topics": [
        "hash"
      ]
    },
    {
      "page": "insect",
      "title": "Informatic sequence classification trees.",
      "topics": [
        "insect-package",
        "insect"
      ]
    },
    {
      "page": "join",
      "title": "Concatenate DNAbin objects while preserving attributes.",
      "topics": [
        "join"
      ]
    },
    {
      "page": "learn",
      "title": "Informatic sequence classification tree learning.",
      "topics": [
        "learn"
      ]
    },
    {
      "page": "manipulate",
      "title": "Further bit-level manipulation of DNA and amino acid sequences.",
      "topics": [
        "duplicated.AAbin",
        "duplicated.DNAbin",
        "manipulate",
        "subset.AAbin",
        "subset.DNAbin",
        "unique.AAbin",
        "unique.DNAbin"
      ]
    },
    {
      "page": "prune_taxonomy",
      "title": "Prune taxonomy database.",
      "topics": [
        "prune_taxonomy"
      ]
    },
    {
      "page": "purge",
      "title": "Identify and remove erroneous reference sequences.",
      "topics": [
        "purge"
      ]
    },
    {
      "page": "qfilter",
      "title": "Quality filtering for amplicon sequences.",
      "topics": [
        "qfilter"
      ]
    },
    {
      "page": "rc",
      "title": "Reverse complement DNA in character string format.",
      "topics": [
        "rc"
      ]
    },
    {
      "page": "read",
      "title": "Read FASTA and FASTQ files.",
      "topics": [
        "read",
        "readFASTA",
        "readFASTQ"
      ]
    },
    {
      "page": "replicate",
      "title": "Dereplicate and rereplicate sequence datasets.",
      "topics": [
        "dereplicate",
        "replicate",
        "rereplicate"
      ]
    },
    {
      "page": "samoa",
      "title": "Table of marine COI amplicon sequence variants from American Samoa",
      "topics": [
        "samoa"
      ]
    },
    {
      "page": "searchGB",
      "title": "Query the NCBI GenBank database.",
      "topics": [
        "searchGB"
      ]
    },
    {
      "page": "shave",
      "title": "Shave ends from DNA and amino acid sequences",
      "topics": [
        "shave"
      ]
    },
    {
      "page": "stitch",
      "title": "Paired-end read stitching.",
      "topics": [
        "stitch"
      ]
    },
    {
      "page": "taxonomy",
      "title": "Download taxonomy database.",
      "topics": [
        "taxonomy"
      ]
    },
    {
      "page": "trim",
      "title": "Trim primer and/or index sequences.",
      "topics": [
        "trim"
      ]
    },
    {
      "page": "virtualFISH",
      "title": "Virtual _in situ_ hybridization.",
      "topics": [
        "virtualFISH"
      ]
    },
    {
      "page": "virtualPCR",
      "title": "Virtual PCR.",
      "topics": [
        "virtualPCR"
      ]
    },
    {
      "page": "whale_taxonomy",
      "title": "Cetacean section of NCBI taxonomy database.",
      "topics": [
        "whale_taxonomy"
      ]
    },
    {
      "page": "whales",
      "title": "Cetacean 16S rDNA sequences.",
      "topics": [
        "whales"
      ]
    },
    {
      "page": "write",
      "title": "Write sequences to text in FASTA or FASTQ format.",
      "topics": [
        "write",
        "writeFASTA",
        "writeFASTQ"
      ]
    }
  ],
  "_readme": "https://github.com/shaunpwilkinson/insect/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "ape",
    "aphid",
    "askpass",
    "cli",
    "curl",
    "digest",
    "kmer",
    "lattice",
    "MASS",
    "nlme",
    "openssl",
    "phylogram",
    "pixmap",
    "qpdf",
    "RANN",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "segmented",
    "seqinr",
    "sp",
    "sys",
    "xml2"
  ],
  "_vignettes": [
    {
      "source": "insect-vignette.Rmd",
      "filename": "insect-vignette.html",
      "title": "The insect R package",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "The INSECT learning and classification algorithms",
        "A worked example",
        "Loading the package and data",
        "Classifying sequences",
        "Acknowledgements",
        "References"
      ],
      "created": "2018-03-08 13:19:24",
      "modified": "2025-05-24 07:30:40",
      "commits": 18
    }
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  "_nocasepkg": "insect",
  "_universes": [
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