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

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]