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  "Title": "Datasets for benchmarking in microbiome research",
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  "Description": "The MicrobiomeBenchmarkData package provides functionality\nto access microbiome datasets suitable for benchmarking. These\ndatasets have some biological truth, which allows to have\nexpected results for comparison. The datasets come from various\npublished sources and are provided as TreeSummarizedExperiment\nobjects. Currently, only datasets suitable for benchmarking\ndifferential abundance methods are available.",
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  "Date/Publication": "2026-04-29 20:51:01 UTC",
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