Table 1 TAD callers analyzed in this study
From: Comparison of computational methods for the identification of topologically associating domains
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 |