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Workflow for the construction of reference datasets of cross-omics feature relationships according to the following steps: (1) identification of detectable multi-omics features and per-sample normalization; (2) intra-batch QC by filtering out features that are not detectable or have low technical reproducibility; (3) identification of cross-omics feature pairs associated with the same genes or pathways; (4) cross-batch QC by retaining reliable feature pairs identified in a sufficient number of batches; (5) calculating Pearson correlation coefficients for each feature pair in each batch combination and classifying the relationships into positive (r >= 0.5, P < 0.05) and negative (r <= –0.5, P < 0.05) categories; and (6) voting based on the direction of the correlations (negative or positive) to screen the high-confidence cross-omics feature relationships.
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