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        "DelayedArray,H5ADMatrixSeed-method",
        "extractNonzeroDataByCol,H5ADMatrix-method",
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        "CSR_H5ADMatrixSeed",
        "CSR_H5ADMatrixSeed-class",
        "Dense_H5ADMatrixSeed",
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        "getHDF5DumpChunkLength",
        "getHDF5DumpChunkShape",
        "getHDF5DumpCompressionLevel",
        "getHDF5DumpDir",
        "getHDF5DumpFile",
        "getHDF5DumpName",
        "HDF5-dump-management",
        "lsHDF5DumpFile",
        "setHDF5DumpChunkLength",
        "setHDF5DumpChunkShape",
        "setHDF5DumpCompressionLevel",
        "setHDF5DumpDir",
        "setHDF5DumpFile",
        "setHDF5DumpName",
        "showHDF5DumpLog"
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    },
    {
      "page": "HDF5Array-class",
      "title": "HDF5 datasets as DelayedArray objects",
      "topics": [
        "class:HDF5Array",
        "class:HDF5Matrix",
        "coerce,ANY,HDF5Matrix-method",
        "coerce,HDF5Array,HDF5Matrix-method",
        "coerce,HDF5Matrix,HDF5Array-method",
        "DelayedArray,HDF5ArraySeed-method",
        "HDF5Array",
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        "HDF5Matrix",
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        "is_sparse<-,HDF5Array-method",
        "matrixClass,HDF5Array-method"
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    },
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      "page": "HDF5ArraySeed-class",
      "title": "HDF5ArraySeed objects",
      "topics": [
        "chunkdim,HDF5ArraySeed-method",
        "class:HDF5ArraySeed",
        "dim,HDF5ArraySeed-method",
        "dimnames,HDF5ArraySeed-method",
        "extract_array,HDF5ArraySeed-method",
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        "HDF5ArraySeed",
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        "path<-,HDF5ArraySeed-method",
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        "class:ReshapedHDF5Matrix",
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        "matrixClass,ReshapedHDF5Array-method",
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        "ReshapedHDF5Array-class",
        "ReshapedHDF5Matrix",
        "ReshapedHDF5Matrix-class"
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        "class:ReshapedHDF5ArraySeed",
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        "ReshapedHDF5ArraySeed",
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      "page": "saveHDF5SummarizedExperiment",
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      "topics": [
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        "quickResaveHDF5SummarizedExperiment",
        "saveHDF5SummarizedExperiment"
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    },
    {
      "page": "TENxMatrix-class",
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    },
    {
      "page": "writeHDF5Array",
      "title": "Write an array-like object to an HDF5 file",
      "topics": [
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        "class:HDF5RealizationSink",
        "coerce,ANY,HDF5Array-method",
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      "topics": [
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  "_readme": "https://github.com/bioc/HDF5Array/raw/RELEASE_3_23/README.md",
  "_rundeps": [
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    "BiocGenerics",
    "biocmake",
    "DelayedArray",
    "dir.expiry",
    "filelock",
    "generics",
    "h5mread",
    "IRanges",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "S4Arrays",
    "S4Vectors",
    "SparseArray",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "HDF5Array_performance.Rmd",
      "filename": "HDF5Array_performance.html",
      "title": "HDF5Array performance",
      "author": "Hervé Pagès",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Install and load the required packages",
        "The test datasets",
        "Sparse vs dense representation",
        "TENxMatrix vs HDF5Matrix objects",
        "Bring the sparse dataset in R",
        "Bring the dense dataset in R",
        "Create the test datasets",
        "Block-processed normalization and PCA",
        "Code used for normalization and PCA",
        "Block processing and block size",
        "Monitoring memory usage",
        "Normalization and PCA of the 27,998 x 12,500 test dataset",
        "Normalization",
        "TENxMatrix (sparse)",
        "HDF5Matrix (dense)",
        "HDF5Matrix as sparse",
        "On-disk realization of the normalized datasets",
        "PCA",
        "Comprehensive timings obtained on various machines",
        "Timings for DELL XPS 15 laptop",
        "Timings for Supermicro SuperServer 1029GQ-TRT",
        "Timings for Apple Silicon Mac Pro",
        "Timings for Intel Mac Pro",
        "Discussion",
        "TENxMatrix (sparse) vs HDF5Matrix (dense)",
        "Hybrid approach",
        "A note about memory usage",
        "Main takeaways",
        "Session information"
      ],
      "created": "2025-01-14 07:06:14",
      "modified": "2025-04-15 01:12:48",
      "commits": 35
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