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  "Title": "Copy Number Variant Annotation and Transparent Scoring",
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  "License": "GPL (>= 2)",
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  "Date/Publication": "2026-07-23 17:19:03 UTC",
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  "_created": "2026-07-23T18:54:31.000Z",
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    "cnv_2019_criteria",
    "cnv_resource_sources",
    "derive_cnv_2019_evidence",
    "load_xcnv_model",
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    "run_xcnv",
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    "validate_cnv",
    "validate_xcnv_resources",
    "write_xcnv",
    "xcnv",
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    "xcnv_fixture_resources",
    "xcnv_real_example",
    "xcnv_resource_manifest",
    "xcnv_resources"
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      "title": "Published X-CNV portable model",
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      ],
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      "page": "annotate_cnv",
      "title": "Annotate CNV records with X-CNV features",
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        "annotate_cnv"
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    },
    {
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      "title": "Convert an ACMG/ClinGen 2019 CNV score to a five-tier classification",
      "topics": [
        "classify_cnv_score"
      ]
    },
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      "page": "cnv_2019_criteria",
      "title": "ACMG/ClinGen 2019 constitutional CNV criterion contract",
      "topics": [
        "cnv_2019_criteria"
      ]
    },
    {
      "page": "cnv_resource_sources",
      "title": "Recommended source authorities for constitutional CNV annotation",
      "topics": [
        "cnv_resource_sources"
      ]
    },
    {
      "page": "derive_cnv_2019_evidence",
      "title": "Derive objective ACMG/ClinGen 2019 CNV content evidence",
      "topics": [
        "derive_cnv_2019_evidence"
      ]
    },
    {
      "page": "load_xcnv_model",
      "title": "Load an X-CNV model",
      "topics": [
        "load_xcnv_model"
      ]
    },
    {
      "page": "predict_cnv",
      "title": "Predict X-CNV MVP scores",
      "topics": [
        "predict_cnv"
      ]
    },
    {
      "page": "read_cnv",
      "title": "Read and normalize a CNV table",
      "topics": [
        "read_cnv"
      ]
    },
    {
      "page": "run_xcnv",
      "title": "Run X-CNV with a file-compatible interface",
      "topics": [
        "run_xcnv",
        "xcnv"
      ]
    },
    {
      "page": "score_cnv_2019",
      "title": "Score transparent ACMG/ClinGen 2019 constitutional CNV evidence",
      "topics": [
        "score_cnv_2019"
      ]
    },
    {
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      "title": "Validate CNV records",
      "topics": [
        "validate_cnv"
      ]
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      "title": "Validate an X-CNV resource bundle",
      "topics": [
        "validate_xcnv_resources"
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    {
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      "topics": [
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    },
    {
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      "topics": [
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    {
      "page": "xcnv_resources",
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