The cross technique integration is performed using IDR (Irreproducible Discovery Rate) analysis. IDR is well-established in DNA epigenetics and used by the ENCODE database to integrate CHIP-Seq samples. The IDR model effectively uses rank information to quantify uncertainties in overlaps between replicating omics experiments. The reproducible sites called by IDR are both highly ranked and positively correlated between paired omics assays. To measure reproducibility and eliminate spurious overlaps, IDR value is calculated using a statistical framework.

In m6AConquer, An IDR < 0.05 indicates the m⁶A site is statistically significantly reproducible across two detection techniques. A table will be returned after the query to indicate reproducible sites identified with an IDR < 0.05.

Description of Figures in IDR Analysis:

• Scatter plots of rank: The axes represent the ranks of - log FDR (BH adjusted p-values) in each technique, while the color indicates IDR values computed at the candidate m6A sites.
• Scatter plots of ratio: The axes represent the m6A level (m6A/Total Coverage) in each technique, while the color indicates IDR values computed at the candidate m6A sites.
• Distribution of IDR: The distribution of IDR values for a pair of m6A detection techniques. More IDR values will appear on the left if the techniques are significantly aligned.