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  "Title": "Standard Input and Output for Bioconductor Packages",
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  "Description": "The `BiocIO` package contains high-level abstract classes\nand generics used by developers to build IO funcionality within\nthe Bioconductor suite of packages. Implements `import()` and\n`export()` standard generics for importing and exporting\nbiological data formats. `import()` supports whole-file as well\nas chunk-wise iterative import. The `import()` interface\noptionally provides a standard mechanism for 'lazy' access via\n`filter()` (on row or element-like components of the file\nresource), `select()` (on column-like components of the file\nresource) and `collect()`. The `import()` interface optionally\nprovides transparent access to remote (e.g. via https) as well\nas local access. Developers can register a file extension,\ne.g., `.loom` for dispatch from character-based URIs to\nspecific `import()` / `export()` methods based on classes\nrepresenting file types, e.g., `LoomFile()`.",
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  "BugReports": "https://github.com/Bioconductor/BiocIO/issues",
  "Date": "2026-04-28",
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