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Table 1 Description of 8 approaches used to calculate ATAC-seq differential accessibility

From: ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation

# Genomic regions Tool Normalization DA testing
I MACS2 [27] DiffBind [29] Full library size DESeq2 [31]
II MACS2 [27] DiffBind [29] Reads in peaks DESeq2 [31]
III MACS2 [27] csaw [28] TMM [34] edgeR [30]
IV MACS2 [27] csaw [28] Loess edgeR [30]
V csaw [28] csaw [28] TMM [34] edgeR [30]
VI csaw [28] csaw [28] Loess edgeR [30]
VII MACS2 [27] csaw [28] | voom [32] Log2cpm limma [33]
VIII MACS2 [27] csaw [28] | voom [32] Quantile [35] limma [33]