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  "Title": "de novo Annotation of Pack-TYPE Transposable Elements",
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  "Description": "Algorithm and tools for in silico pack-TYPE transposon\ndiscovery. Filters a given genome for properties unique to DNA\ntransposons and provides tools for the investigation of\nreturned matches. Sequences are input in DNAString format, and\nranges are returned as a dataframe (in the format returned by\nas.dataframe(GRanges)).",
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  "biocViews": "Genetics, SequenceMatching, Annotation",
  "Config/pak/sysreqs": "libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:38 UTC",
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    "collapseSeqs",
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    "getPacksFromCsv",
    "getPacksFromFasta",
    "getPacksFromGRanges",
    "getTsds",
    "identifyPotentialPackElements",
    "identifyTirMatches",
    "makeBlastDb",
    "packAlign",
    "packBlast",
    "packClust",
    "packSearch",
    "packsToCsv",
    "packsToFasta",
    "packsToGRanges",
    "readBlast",
    "readUc",
    "tirClust"
  ],
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      "title": "Arabidopsis thaliana Refseq Genome Chromosome 3 Subset",
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      "class": [
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      "table": false,
      "tojson": false
    },
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      "object": "packMatches",
      "file": "packMatches.rda",
      "class": [
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        "start",
        "end",
        "width",
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        "cluster"
      ],
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      "table": true,
      "tojson": true
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    {
      "page": "arabidopsisThalianaRefseq",
      "title": "Arabidopsis thaliana Refseq Genome Chromosome 3 Subset",
      "topics": [
        "arabidopsisThalianaRefseq"
      ]
    },
    {
      "page": "blastAnalysis",
      "title": "BLAST Analysis of PackTYPE Elements",
      "topics": [
        "blastAnalysis"
      ]
    },
    {
      "page": "blastAnnotate",
      "title": "Functional Annotation of PackTYPE Elements",
      "topics": [
        "blastAnnotate"
      ]
    },
    {
      "page": "collapseSeqs",
      "title": "Collapse Overlapping Sequences",
      "topics": [
        "collapseSeqs"
      ]
    },
    {
      "page": "filterWildcards",
      "title": "Remove Low Quality Sequences",
      "topics": [
        "filterWildcards"
      ]
    },
    {
      "page": "getPackSeqs",
      "title": "Extract Sequences of Pack-TYPE Elements",
      "topics": [
        "getPackSeqs"
      ]
    },
    {
      "page": "getPacksFromCsv",
      "title": "Retrieve Saved packFinder Results (.csv)",
      "topics": [
        "getPacksFromCsv"
      ]
    },
    {
      "page": "getPacksFromFasta",
      "title": "Retrieve Saved packFinder Results (.fasta)",
      "topics": [
        "getPacksFromFasta"
      ]
    },
    {
      "page": "getPacksFromGRanges",
      "title": "Retrieve packFinder Results from GRanges Object",
      "topics": [
        "getPacksFromGRanges"
      ]
    },
    {
      "page": "getTsds",
      "title": "Get Flanking Terminal Site Duplication Sequences",
      "topics": [
        "getTsds"
      ]
    },
    {
      "page": "identifyPotentialPackElements",
      "title": "Pack Element Filtering",
      "topics": [
        "identifyPotentialPackElements"
      ]
    },
    {
      "page": "identifyTirMatches",
      "title": "Identify Terminal Inverted Repeat Matches",
      "topics": [
        "identifyTirMatches"
      ]
    },
    {
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      "title": "Make Blast Database",
      "topics": [
        "makeBlastDb"
      ]
    },
    {
      "page": "packAlign",
      "title": "Global Alignment with VSEARCH",
      "topics": [
        "packAlign"
      ]
    },
    {
      "page": "packBlast",
      "title": "Pipeline for BLAST/Classification of PackTYPE Elements",
      "topics": [
        "packBlast"
      ]
    },
    {
      "page": "packClust",
      "title": "Cluster Transposons with VSEARCH",
      "topics": [
        "packClust"
      ]
    },
    {
      "page": "packFinder",
      "title": "packFinder: a package for the de novo Annotation of Pack-TYPE Transposable Elements",
      "topics": [
        "packFinder"
      ]
    },
    {
      "page": "packMatches",
      "title": "Sample packFinder Output",
      "topics": [
        "packMatches"
      ]
    },
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      "page": "packSearch",
      "title": "packFinder Algorithm Pipeline",
      "topics": [
        "packSearch"
      ]
    },
    {
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      "title": "Save packFinder Results in CSV Format (.csv)",
      "topics": [
        "packsToCsv"
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    },
    {
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      "title": "Save packFinder Results in FASTA Format (.fasta)",
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      "title": "Export packFinder Results to a GRanges Object",
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    },
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      "title": "Convert .uc Files to Dataframe",
      "topics": [
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      "title": "packFinder",
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      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting Started",
        "R Package Dependencies",
        "Command Line Dependencies",
        "Searching for Potential Transposable Elements using packFinder",
        "Getting Data",
        "Using packSearch",
        "Analysing Potential Transposable Elements using packFinder",
        "Clustering of Transposable Elements",
        "Reading VSEARCH Output Files",
        "Clustering of TIR Sequences",
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