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TADtree specifications


Unique identifier OMICS_08931
Name TADtree
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for TADtree

TADtree citations


Computational Methods for Assessing Chromatin Hierarchy

Comput Struct Biotechnol J
PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003

[…] Dtool (as a Python package) enables the direct export of TADs called using a set of parameters for both directionality and insulation indices []. Other TAD callers, such as TADbit [], Armatus [], and TADtree [], exhibit balanced performance for most parameters for experimental and simulated data. Interaction callers, such as HOMER [] and HiCCUPS, [,] yield the highest proportion of biologically si […]


Stratification of TAD boundaries reveals preferential insulation of super enhancers by strong boundaries

Nat Commun
PMCID: 5803259
PMID: 29416042
DOI: 10.1038/s41467-018-03017-1

[…] g domains (TADs)– and sub-TADs, as well as gene neighborhoods. Several algorithms have been developed to reveal this hierarchical chromatin organization, including Directionality Index (DI), Armatus, TADtree, insulation index (Crane), IC-finder, and others. However, none of these studies has systematically explored the properties of TAD boundaries. Although TADs are seemingly invariant across cell […]


Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction

PMCID: 5615356
PMID: 28885554
DOI: 10.3390/genes8090223

[…] mposition) technique was proposed to identify the local chromatin states, global chromosomal interactions, and the conserved chromatin organization []. To infer the hierarchy of the nested structure, TADtree was recently introduced based on empirical distributions of contact frequencies within TADs []. TopDom is another easy-to-implement pipeline to study cross-tissue TAD conservation []. To tackl […]


Kmt1e regulates a large neuron specific topological chromatin domain

Nat Genet
PMCID: 5560095
PMID: 28671686
DOI: 10.1038/ng.3906
call_split See protocol

[…] ted interactions at each bin was then modeled using a Poisson distribution with maximum likelihood of mean (0.165) calculated from the data. Topological associating domains (TAD) were predicted using TADtree using the 20kb Hi-Cpro data as input with the following parameter settings: maximum size of TAD in bins (S) = 60; maximum number of TADs in each tad-tree (M) = 10; boundary index parameter (p) […]


A critical assessment of topologically associating domain prediction tools

Nucleic Acids Res
PMCID: 5389712
PMID: 28334773
DOI: 10.1093/nar/gkx145

[…] acting accuracy.At the complete TAD level (Figure ), the level of agreement with our manual annotation was generally lower for all tools. Front runners are TopDom, DomainCaller and TADbit, as well as TADtree, which seems to make up for its lower accuracy at boundary detection with a seemingly stronger boundary pairing approach. Because of the different levels of tolerance needed to accommodate dif […]


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TADtree institution(s)
Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI, USA
TADtree funding source(s)
A National Science Foundation (NSF) CAREER Award CCF-1053753; NIH RO1HG005690; a Career Award at the Scientific Interface from the Burroughs Wellcome Fund, an Alfred P Sloan Research Fellowship

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