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  "Title": "Forge your own BSgenome data package",
  "Description": "A set of tools to forge BSgenome data packages. Supersedes\nthe old seed-based tools from the BSgenome software package.\nThis package allows the user to create a BSgenome data package\nin one function call, simplifying the old seed-based process.",
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  "Date/Publication": "2026-04-28 13:00:26 UTC",
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      "title": "The BSgenomeForge package",
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        "BSgenomeForge"
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