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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 regionsToolNormalizationDA testing
IMACS2 [27]DiffBind [29]Full library sizeDESeq2 [31]
IIMACS2 [27]DiffBind [29]Reads in peaksDESeq2 [31]
IIIMACS2 [27]csaw [28]TMM [34]edgeR [30]
IVMACS2 [27]csaw [28]LoessedgeR [30]
Vcsaw [28]csaw [28]TMM [34]edgeR [30]
VIcsaw [28]csaw [28]LoessedgeR [30]
VIIMACS2 [27]csaw [28] | voom [32]Log2cpmlimma [33]
VIIIMACS2 [27]csaw [28] | voom [32]Quantile [35]limma [33]