TADtree specifications

Information


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

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Publication for TADtree

TADtree in publications

 (5)
PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003

[…] (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 […]

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

[…] 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 […]

PMCID: 5615356
PMID: 28885554
DOI: 10.3390/genes8090223

[…] 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 []. […]

PMCID: 5560095
PMID: 28671686
DOI: 10.1038/ng.3906

[…] reads/library, and ) showed that mutant neurons were not affected by a generalized disorganization of the 3d genome. for example, length distributions and numbers of autosomal tads, assessed by tadtree, were indistinguishable and minimally different between genotypes, with ~200kb median length as expected for mammalian genomes (, ). we then assessed longer-range chromosomal contacts, […]

PMCID: 5389712
PMID: 28334773
DOI: 10.1093/nar/gkx145

[…] used (see ). topdom produced tad annotations that divide genomic regions to ‘domain’, ‘boundaries’ and ‘gaps’. to compare with other tools, only regions labeled ‘domain’ were used in this analysis. tadtree produced different result files and a file named proportion_duplicates.txt. the authors recommend choosing the result file where duplication level is 1–2%. for simplicity, and to avoid […]


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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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