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  "Title": "Set of tools to identify periodic occurrences of k-mers in DNA\nsequences",
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  "Authors@R": "c(person(given = \"Jacques\",\nfamily = \"Serizay\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jacquesserizay@gmail.com\",\ncomment = c(ORCID = \"0000-0002-4295-0624\")))",
  "Description": "This R package helps the user identify k-mers (e.g. di- or\ntri-nucleotides) present periodically in a set of genomic loci\n(typically regulatory elements). The functions of this package\nprovide a straightforward approach to find periodic occurrences\nof k-mers in DNA sequences, such as regulatory elements. It is\nnot aimed at identifying motifs separated by a conserved\ndistance; for this type of analysis, please visit MEME website.",
  "URL": "https://github.com/js2264/periodicDNA",
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  "Repository": "https://bioc.r-universe.dev",
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