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  "Title": "Exploring Genome Scale Embeddings Parquet Files",
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  "Description": "Some explorations of the genomics embedding from the paper\n\"Incorporating LLM Embeddings for Variation Across the Human\nGenome\" <https://arxiv.org/html/2509.20702v1>",
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  "Date/Publication": "2025-11-30 12:20:16 UTC",
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    "name": "Sounkou Mahamane Toure",
    "description": "Sequences and Consequences."
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    "correlatePCWithPosition",
    "DatasetParquetUrlList",
    "embeddingSummary",
    "getPcaScores",
    "houbaPCA",
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    "OpenRemoteParquetView",
    "plotPcaDims",
    "plotPCSpatialCorrelation",
    "writeEmbeddingsHoubaFromDuckDB"
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      "page": "attachHoubaBigMatrix",
      "title": "Attach a houba file and return the bigmemory::big.matrix",
      "topics": [
        "attachHoubaBigMatrix"
      ]
    },
    {
      "page": "CopyParquetToDuckDB",
      "title": "Copy remote parquet files into a local DuckDB database file using explicit URLs",
      "topics": [
        "CopyParquetToDuckDB"
      ]
    },
    {
      "page": "correlatePCWithPosition",
      "title": "Compute correlation between PC scores and genomic position, per chromosome",
      "topics": [
        "correlatePCWithPosition"
      ]
    },
    {
      "page": "DatasetParquetUrlList",
      "title": "List of the huggingface datasets for the paper \"Incorporating LLM Embeddings for Variation Across the Human Genome\"",
      "topics": [
        "DatasetParquetUrlList"
      ]
    },
    {
      "page": "embeddingSummary",
      "title": "Quick summary for houba mmatrix",
      "topics": [
        "embeddingSummary"
      ]
    },
    {
      "page": "getPcaScores",
      "title": "Get PCA scores from houbaPCA result",
      "topics": [
        "getPcaScores"
      ]
    },
    {
      "page": "houbaPCA",
      "title": "PCA using bigPCAcpp on houba mmatrix or bigmemory::big.matrix",
      "topics": [
        "houbaPCA"
      ]
    },
    {
      "page": "infoSummary",
      "title": "Quick summary for houba info mmatrix",
      "topics": [
        "infoSummary"
      ]
    },
    {
      "page": "IterateEmbeddingsMatrixBatches",
      "title": "Iterate over embeddings as matrix batches from a local DuckDB file",
      "topics": [
        "IterateEmbeddingsMatrixBatches"
      ]
    },
    {
      "page": "OpenRemoteParquetView",
      "title": "Open remote parquet files as a DuckDB VIEW and return as tibble (minimal, http(s) only)",
      "topics": [
        "OpenRemoteParquetView"
      ]
    },
    {
      "page": "plotPcaDims",
      "title": "Plot PCA dimensions using ggplot2, colored by annotation",
      "topics": [
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    },
    {
      "page": "plotPCSpatialCorrelation",
      "title": "Plot spatial correlation between PC scores and genomic position, faceted by chromosome",
      "topics": [
        "plotPCSpatialCorrelation"
      ]
    },
    {
      "page": "writeEmbeddingsHoubaFromDuckDB",
      "title": "Write embeddings to houba mmatrix and return info as data.frame from a local DuckDB file",
      "topics": [
        "writeEmbeddingsHoubaFromDuckDB"
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