SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information

Table 1 Properties of methods for detecting hierarchies of TADs

	SuperTAD	OnTAD	deDoc	3DNetMod	GMAP	IC-Finder	TADtree	Arrowhead
Last updated	2020	2019	2018	2018	2017	2017	2016	2014
Journal	–	Genome Biology	Nature Communications	Nature	Nature Communications	Nucleic Acids Research	Bioinformatics	Cell
Input	Raw/normalized	Raw/normalized	Raw/normalized	Normalized	Normalized	Raw/normalized	Normalized	Raw/normalized
Model	Structural information theory,	Adaptive local minimum search,	Structure information theory,	Network modularity maximization,	Gaussian mixture model,	Hierarchical clustering,	Boundary index (BI),	Arrowhead transformation
	dynamic programming	contact density signal maximization	greedy merging and combining	hierarchical spatial variance minimization	proportion test	local directionality index (DI)	dynamic programming,
							weighted interval scheduling with
							multiplicities (WISM)
Levels of TAD	Not limited	Not limited	2	Not limited	Controlled by parameter	Controlled by parameter	Not limited	Not limited
# Parameters	0	2	0	5	4	1	6	1
Reference	–	[34]	[33]	[32]	[31]	[30]	[29]	[28]

ISSN: 1474-760X