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  "Title": "Uniform Data Model and 'Zarr' Interchange for Single-Cell Omics",
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  "Authors@R": "person(\"Peter\", \"Kharchenko\", role = c(\"aut\", \"cre\"),\nemail = \"pk.restricted@gmail.com\")",
  "Description": "A lightweight interchange layer for single-cell and\nspatial omics data, built on the L-star model of labelled axes\nand typed fields over them, serialized to the 'Zarr' format.\nProvides bidirectional converters (\"profiles\") for 'Seurat',\n'SingleCellExperiment', 'Conos', and 'pagoda2' objects,\nincluding collections of heterogeneous samples, via a shared\nC++ core ('libstar') so the same store is readable from R,\n'Python', and C++.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "URL": "https://github.com/kharchenkolab/lstar",
  "BugReports": "https://github.com/kharchenkolab/lstar/issues",
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  "Repository": "https://kharchenkolab.r-universe.dev",
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    "read_seurat_backed",
    "stream_col_stats",
    "view",
    "viewer_extend",
    "write_conos",
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      "topics": [
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      "topics": [
        "lstar_read"
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    },
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    },
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