DiffHiChIP

RNA-pol-II HiChIP from HCT116 colorectal cancer cells

[Differential loops between untreated and Auxin treated conditions]

Complete background (A), FDR with BH correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background (A), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background with equal occupancy bin based distance stratification (D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background (F), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background with equal occupancy bin based distance stratification (F+D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

H3K27ac HiChIP from HaCaT cells

[Differential loops between unstimulated and IFN-gamma stimulated conditions]

Complete background (A), FDR with BH correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background (A), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background with equal occupancy bin based distance stratification (D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background (F), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background with equal occupancy bin based distance stratification (F+D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Reference results   HiCDC+

H3K27ac HiChIP from M14 Melanoma cells

[Differential loops between WT (untreated) and treated (STAG2 knockdown) conditions]

Complete background (A), FDR with BH correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background (A), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background with equal occupancy bin based distance stratification (D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background (F), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background with equal occupancy bin based distance stratification (F+D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Reference results   HiCDC+

H3K27ac HiChIP from large pre-B cells

[Differential loops between WT and IKAROS mutant]

Complete background (A), FDR with BH correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background (A), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background with equal occupancy bin based distance stratification (D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background (F), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background with equal occupancy bin based distance stratification (F+D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Reference results   HiCDC+

CTCF HiChIP from large pre-B cells

[Differential loops between WT and IKAROS mutant]

Complete background (A), FDR with BH correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background (A), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background with equal occupancy bin based distance stratification (D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background (F), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background with equal occupancy bin based distance stratification (F+D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Reference results   HiCDC+

SMC1 HiChIP from large pre-B cells

[Differential loops between WT and IKAROS mutant]

Complete background (A), FDR with BH correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background (A), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background with equal occupancy bin based distance stratification (D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background (F), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background with equal occupancy bin based distance stratification (F+D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Reference results   HiCDC+

H3K27ac HiChIP from Immune cells

[Differential loops between CD4 naive and CD8 Naive cell types]

Complete background (A), FDR with BH correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background (A), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Complete background with equal occupancy bin based distance stratification (D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background (F), FDR with IHW correction   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Filtered background with equal occupancy bin based distance stratification (F+D)   DESeq2   edgeR exactTest   edgeR glmLRT   edgeR glmQLFTest

Reference results   HiCDC+