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  "Description": "timeOmics is a generic data-driven framework to integrate\nmulti-Omics longitudinal data measured on the same biological\nsamples and select key temporal features with strong\nassociations within the same sample group. The main steps of\ntimeOmics are: 1. Plaform and time-specific normalization and\nfiltering steps; 2. Modelling each biological into one time\nexpression profile; 3. Clustering features with the same\nexpression profile over time; 4. Post-hoc validation step.",
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