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  "Title": "Inferring the Topology of Omics Data",
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  "Description": "Infers a topology of relationships between different\ndatasets, such as multi-omics and phenotypic data recorded on\nthe same samples. We based this methodology on the RV\ncoefficient (Robert & Escoufier, 1976, <doi:10.2307/2347233>),\na measure of matrix correlation, which we have extended for\npartial matrix correlations and binary data (Aben et al., 2018,\n<doi:10.1101/293993>).",
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  "Date/Publication": "2018-06-13 08:16:06 UTC",
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        "Statistical inference for partial matrix correlations",
        "Inferring a topology of interactions between datasets",
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