{
  "_id": "6a3a22266265ec60d61ff6d6",
  "Package": "HDF5Array",
  "Title": "HDF5 datasets as array-like objects in R",
  "Description": "The HDF5Array package is an HDF5 backend for DelayedArray\nobjects. It implements the HDF5Array, H5SparseMatrix,\nH5ADMatrix, and TENxMatrix classes, 4 convenient and\nmemory-efficient array-like containers for representing and\nmanipulating either: (1) a conventional (a.k.a. dense) HDF5\ndataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale\nformat), (3) the central matrix of an h5ad file (or any matrix\nin the /layers group), or (4) a 10x Genomics sparse matrix. All\nthese containers are DelayedArray extensions and thus support\nall operations (delayed or block-processed) supported by\nDelayedArray objects.",
  "biocViews": "Infrastructure, DataRepresentation, DataImport, Sequencing,\nRNASeq, Coverage, Annotation, GenomeAnnotation, SingleCell,\nImmunoOncology",
  "URL": "https://bioconductor.org/packages/HDF5Array",
  "BugReports": "https://github.com/Bioconductor/HDF5Array/issues",
  "Version": "1.41.0",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Authors@R": "person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\",\ncomment=c(ORCID=\"0009-0002-8272-4522\"))",
  "VignetteBuilder": "knitr",
  "Collate": "utils.R h5utils.R HDF5ArraySeed-class.R HDF5Array-class.R\nReshapedHDF5ArraySeed-class.R ReshapedHDF5Array-class.R\ndump-management.R writeHDF5Array.R\nsaveHDF5SummarizedExperiment.R H5SparseMatrixSeed-class.R\nH5SparseMatrix-class.R H5ADMatrixSeed-class.R\nH5ADMatrix-class.R TENxMatrixSeed-class.R TENxMatrix-class.R\nwriteTENxMatrix.R zzz.R",
  "Config/pak/sysreqs": "libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:49 UTC",
  "RemoteUrl": "https://github.com/bioc/HDF5Array",
  "RemoteRef": "HEAD",
  "RemoteSha": "e6c2cb3b95192b358931a8ed38317331faa3c550",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-22 11:53:40 UTC",
    "User": "root"
  },
  "Author": "Hervé Pagès [aut, cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>)",
  "Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>",
  "MD5sum": "3cb9d74a6dd9d5b40405e98c1559eb93",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-06-22T11:53:40.000Z",
  "_published": "2026-06-23T06:05:26.222Z",
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  "_upstream": "https://github.com/bioc/HDF5Array",
  "_commit": {
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "singlecell",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/bioconductor/hdf5array",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "appendDatasetCreationToHDF5DumpLog",
    "check_and_delete_files",
    "chunkdim",
    "close",
    "coerce",
    "create_dir",
    "DelayedArray",
    "extract_array",
    "extract_sparse_array",
    "extractNonzeroDataByCol",
    "extractNonzeroDataByRow",
    "getHDF5DumpChunkDim",
    "getHDF5DumpChunkLength",
    "getHDF5DumpChunkShape",
    "getHDF5DumpCompressionLevel",
    "getHDF5DumpDir",
    "getHDF5DumpFile",
    "getHDF5DumpName",
    "H5ADMatrix",
    "H5ADMatrixSeed",
    "H5SparseMatrix",
    "H5SparseMatrixSeed",
    "HDF5Array",
    "HDF5ArraySeed",
    "HDF5RealizationSink",
    "is_sparse",
    "is_sparse<-",
    "loadHDF5SummarizedExperiment",
    "lsHDF5DumpFile",
    "matrixClass",
    "nzcount",
    "path",
    "path<-",
    "quickResaveHDF5SummarizedExperiment",
    "replace_dir",
    "ReshapedHDF5Array",
    "ReshapedHDF5ArraySeed",
    "restore_absolute_assay2h5_links",
    "saveHDF5SummarizedExperiment",
    "setHDF5DumpChunkLength",
    "setHDF5DumpChunkShape",
    "setHDF5DumpCompressionLevel",
    "setHDF5DumpDir",
    "setHDF5DumpFile",
    "setHDF5DumpName",
    "shorten_assay2h5_links",
    "show",
    "showHDF5DumpLog",
    "stop_if_bad_dir",
    "t",
    "t.CSC_H5ADMatrixSeed",
    "t.CSC_H5SparseMatrixSeed",
    "t.CSR_H5ADMatrixSeed",
    "t.CSR_H5SparseMatrixSeed",
    "TENxMatrix",
    "TENxMatrixSeed",
    "TENxRealizationSink",
    "type",
    "updateObject",
    "validate_HDF5ArraySeed_dataset_geometry",
    "write_block",
    "write_h5_assays",
    "writeHDF5Array",
    "writeTENxMatrix"
  ],
  "_help": [
    {
      "page": "H5ADMatrix-class",
      "title": "h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects",
      "topics": [
        "class:H5ADMatrix",
        "DelayedArray,H5ADMatrixSeed-method",
        "extractNonzeroDataByCol,H5ADMatrix-method",
        "extractNonzeroDataByRow,H5ADMatrix-method",
        "H5ADMatrix",
        "H5ADMatrix-class",
        "nzcount,H5ADMatrix-method"
      ]
    },
    {
      "page": "H5ADMatrixSeed-class",
      "title": "H5ADMatrixSeed objects",
      "topics": [
        "class:CSC_H5ADMatrixSeed",
        "class:CSR_H5ADMatrixSeed",
        "class:Dense_H5ADMatrixSeed",
        "class:H5ADMatrixSeed",
        "CSC_H5ADMatrixSeed",
        "CSC_H5ADMatrixSeed-class",
        "CSR_H5ADMatrixSeed",
        "CSR_H5ADMatrixSeed-class",
        "Dense_H5ADMatrixSeed",
        "Dense_H5ADMatrixSeed-class",
        "dimnames,Dense_H5ADMatrixSeed-method",
        "H5ADMatrixSeed",
        "H5ADMatrixSeed-class",
        "t,CSC_H5ADMatrixSeed-method",
        "t,CSR_H5ADMatrixSeed-method",
        "t.CSC_H5ADMatrixSeed",
        "t.CSR_H5ADMatrixSeed"
      ]
    },
    {
      "page": "H5SparseMatrix-class",
      "title": "HDF5 sparse matrices as DelayedMatrix objects",
      "topics": [
        "class:H5SparseMatrix",
        "DelayedArray,H5SparseMatrixSeed-method",
        "extractNonzeroDataByCol,H5SparseMatrix-method",
        "extractNonzeroDataByRow,H5SparseMatrix-method",
        "H5SparseMatrix",
        "H5SparseMatrix-class",
        "nzcount,H5SparseMatrix-method"
      ]
    },
    {
      "page": "H5SparseMatrixSeed-class",
      "title": "H5SparseMatrixSeed objects",
      "topics": [
        "chunkdim,CSC_H5SparseMatrixSeed-method",
        "chunkdim,CSR_H5SparseMatrixSeed-method",
        "class:CSC_H5SparseMatrixSeed",
        "class:CSR_H5SparseMatrixSeed",
        "class:H5SparseMatrixSeed",
        "CSC_H5SparseMatrixSeed",
        "CSC_H5SparseMatrixSeed-class",
        "CSR_H5SparseMatrixSeed",
        "CSR_H5SparseMatrixSeed-class",
        "dim,H5SparseMatrixSeed-method",
        "dimnames,H5SparseMatrixSeed-method",
        "extractNonzeroDataByCol",
        "extractNonzeroDataByCol,CSC_H5SparseMatrixSeed-method",
        "extractNonzeroDataByRow",
        "extractNonzeroDataByRow,CSR_H5SparseMatrixSeed-method",
        "extract_array,H5SparseMatrixSeed-method",
        "extract_sparse_array,CSC_H5SparseMatrixSeed-method",
        "extract_sparse_array,CSR_H5SparseMatrixSeed-method",
        "H5SparseMatrixSeed",
        "H5SparseMatrixSeed-class",
        "is_sparse,H5SparseMatrixSeed-method",
        "nzcount,H5SparseMatrixSeed-method",
        "path,H5SparseMatrixSeed-method",
        "path<-,H5SparseMatrixSeed-method",
        "show,H5SparseMatrixSeed-method",
        "t,CSC_H5SparseMatrixSeed-method",
        "t,CSR_H5SparseMatrixSeed-method",
        "t.CSC_H5SparseMatrixSeed",
        "t.CSR_H5SparseMatrixSeed"
      ]
    },
    {
      "page": "dump-management",
      "title": "HDF5 dump management",
      "topics": [
        "appendDatasetCreationToHDF5DumpLog",
        "dump-management",
        "getHDF5DumpChunkDim",
        "getHDF5DumpChunkLength",
        "getHDF5DumpChunkShape",
        "getHDF5DumpCompressionLevel",
        "getHDF5DumpDir",
        "getHDF5DumpFile",
        "getHDF5DumpName",
        "HDF5-dump-management",
        "lsHDF5DumpFile",
        "setHDF5DumpChunkLength",
        "setHDF5DumpChunkShape",
        "setHDF5DumpCompressionLevel",
        "setHDF5DumpDir",
        "setHDF5DumpFile",
        "setHDF5DumpName",
        "showHDF5DumpLog"
      ]
    },
    {
      "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",
        "HDF5Array-class",
        "HDF5Matrix",
        "HDF5Matrix-class",
        "is_sparse<-,HDF5Array-method",
        "matrixClass,HDF5Array-method"
      ]
    },
    {
      "page": "HDF5ArraySeed-class",
      "title": "HDF5ArraySeed objects",
      "topics": [
        "chunkdim,HDF5ArraySeed-method",
        "class:HDF5ArraySeed",
        "dim,HDF5ArraySeed-method",
        "dimnames,HDF5ArraySeed-method",
        "extract_array,HDF5ArraySeed-method",
        "extract_sparse_array,HDF5ArraySeed-method",
        "HDF5ArraySeed",
        "HDF5ArraySeed-class",
        "is_sparse,HDF5ArraySeed-method",
        "is_sparse<-,HDF5ArraySeed-method",
        "path,HDF5ArraySeed-method",
        "path<-,HDF5ArraySeed-method",
        "type,HDF5ArraySeed-method",
        "updateObject,HDF5ArraySeed-method"
      ]
    },
    {
      "page": "ReshapedHDF5Array-class",
      "title": "Virtually reshaped HDF5 datasets as DelayedArray objects",
      "topics": [
        "class:ReshapedHDF5Array",
        "class:ReshapedHDF5Matrix",
        "coerce,ANY,ReshapedHDF5Matrix-method",
        "coerce,ReshapedHDF5Array,ReshapedHDF5Matrix-method",
        "coerce,ReshapedHDF5Matrix,ReshapedHDF5Array-method",
        "DelayedArray,ReshapedHDF5ArraySeed-method",
        "matrixClass,ReshapedHDF5Array-method",
        "ReshapedHDF5Array",
        "ReshapedHDF5Array-class",
        "ReshapedHDF5Matrix",
        "ReshapedHDF5Matrix-class"
      ]
    },
    {
      "page": "ReshapedHDF5ArraySeed-class",
      "title": "ReshapedHDF5ArraySeed objects",
      "topics": [
        "chunkdim,ReshapedHDF5ArraySeed-method",
        "class:ReshapedHDF5ArraySeed",
        "dim,ReshapedHDF5ArraySeed-method",
        "extract_array,ReshapedHDF5ArraySeed-method",
        "ReshapedHDF5ArraySeed",
        "ReshapedHDF5ArraySeed-class"
      ]
    },
    {
      "page": "saveHDF5SummarizedExperiment",
      "title": "Save/load an HDF5-based SummarizedExperiment object",
      "topics": [
        "loadHDF5SummarizedExperiment",
        "quickResaveHDF5SummarizedExperiment",
        "saveHDF5SummarizedExperiment"
      ]
    },
    {
      "page": "TENxMatrix-class",
      "title": "10x Genomics datasets as DelayedMatrix objects",
      "topics": [
        "class:TENxMatrix",
        "DelayedArray,TENxMatrixSeed-method",
        "extractNonzeroDataByCol,TENxMatrix-method",
        "nzcount,TENxMatrix-method",
        "TENxMatrix",
        "TENxMatrix-class"
      ]
    },
    {
      "page": "TENxMatrixSeed-class",
      "title": "TENxMatrixSeed objects",
      "topics": [
        "class:TENxMatrixSeed",
        "TENxMatrixSeed",
        "TENxMatrixSeed-class"
      ]
    },
    {
      "page": "writeHDF5Array",
      "title": "Write an array-like object to an HDF5 file",
      "topics": [
        "chunkdim,HDF5RealizationSink-method",
        "class:HDF5RealizationSink",
        "coerce,ANY,HDF5Array-method",
        "coerce,DelayedArray,HDF5Array-method",
        "coerce,DelayedMatrix,HDF5Matrix-method",
        "coerce,HDF5RealizationSink,DelayedArray-method",
        "coerce,HDF5RealizationSink,HDF5Array-method",
        "coerce,HDF5RealizationSink,HDF5ArraySeed-method",
        "dimnames,HDF5RealizationSink-method",
        "HDF5RealizationSink",
        "HDF5RealizationSink-class",
        "is_sparse,HDF5RealizationSink-method",
        "type,HDF5RealizationSink-method",
        "writeHDF5Array",
        "write_block,HDF5RealizationSink-method"
      ]
    },
    {
      "page": "writeTENxMatrix",
      "title": "Write a matrix-like object as an HDF5-based sparse matrix",
      "topics": [
        "chunkdim,TENxRealizationSink-method",
        "class:TENxRealizationSink",
        "close,TENxRealizationSink-method",
        "coerce,ANY,TENxMatrix-method",
        "coerce,DelayedArray,TENxMatrix-method",
        "coerce,DelayedMatrix,TENxMatrix-method",
        "coerce,TENxRealizationSink,DelayedArray-method",
        "coerce,TENxRealizationSink,TENxMatrix-method",
        "coerce,TENxRealizationSink,TENxMatrixSeed-method",
        "dimnames,TENxRealizationSink-method",
        "TENxRealizationSink",
        "TENxRealizationSink-class",
        "type,TENxRealizationSink-method",
        "writeTENxMatrix",
        "write_block,TENxRealizationSink-method"
      ]
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      "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"
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      "created": "2025-01-14 07:06:14",
      "modified": "2025-04-15 01:12:48",
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