Table 1.
TAD callers analyzed in this study
| TAD caller | Approach | # parameters | Hierarchical domains | Inter-TAD gaps |
|---|---|---|---|---|
| 3DNetMod | Network features | 18 | Overlapping | Yes |
| armatus | Linear score | 1 | Overlapping | No |
| arrowhead | Linear score | 1 | Overlapping | Yes |
| CaTCH | Linear score | 0 | Nested | No |
| CHDF | Clustering | 2 | Disjoint | No |
| chromoR | Linear score | 2 | Disjoint | No |
| ClusterTAD | Clustering | 2 | Disjoint | No |
| Directionality Index (DI) | Linear score | 3 | Disjoint | Yes |
| EAST | Linear score | 0 | Disjoint | Yes |
| GMAP | Linear score | 0 | Nested | Yes |
| HiCExplorer | Linear score | 5 | Disjoint | Yes |
| HiCseg | Statistical model | 3 | Disjoint | No |
| HiTAD | Linear score | 0 | Disjoint | Yes |
| ICFinder | Clustering | 2 | Disjoint | No |
| Insulation Score (IS) | Linear score | 5 | Disjoint | Yes |
| matryoshka | Linear score | 1 | Nested | Yes |
| MrTADFinder | Network features | 1 | Disjoint | No |
| PSYCHIC | Statistical model | 1 | Nested | No |
| spectral | Network features | 2 | Disjoint | No |
| TADbit | Statistical model | 0 | Disjoint | No |
| TADtree | Statistical model | 6 | Overlapping | No |
| TopDom | Linear score | 1 | Disjoint | Yes |