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TopDom specifications


Unique identifier OMICS_16876
Name TopDom
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A Hi-C contact map.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.0.2
Stability Stable
Maintained Yes




No version available


Publication for TopDom

TopDom citations


High resolution TADs reveal DNA sequences underlying genome organization in flies

Nat Commun
PMCID: 5768762
PMID: 29335486
DOI: 10.1038/s41467-017-02525-w

[…] ing aspects: (i) we compute TAD-separation scores using a z-score matrix while TopDom uses the corrected counts matrix, (ii) we use multiple length (w) sizes to compute our TAD-separation score while TopDom uses a single-wvalue, (iii) we compute p-values using the ‘diamond’ A[αl,βl] submatrices values in contrast to the ‘diamond and triangle’ distributions used in TopDom. The triangle distribution […]


TAD free analysis of architectural proteins and insulators

Nucleic Acids Res
PMCID: 5861416
PMID: 29272504
DOI: 10.1093/nar/gkx1246

[…] pending on the TAD algorithm used in Drosophila (Figure ). For instance, GAF presented an odds ratio (OR) of 4.3 with HiCseg (), an OR of 4 with Arrowhead (), whereas it only showed an OR of 2.5 with TopDom TADs (). Conversely, dCTCF presented an OR of 3.7 with HiCseg, and ORs around 5 with Arrowhead and TopDom.Instead of testing protein enrichments at TAD borders, we used our model to directly as […]


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

PMCID: 5615356
PMID: 28885554
DOI: 10.3390/genes8090223

[…] s, 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 tackle terabase-size data for those with less informatics experience, Juicer is recommended as a one-click sy […]


Condensin mediated remodeling of the mitotic chromatin landscape in fission yeast

Nat Genet
PMCID: 5621628
PMID: 28825727
DOI: 10.1038/ng.3938

[…] Domain boundaries were determined using either the log2 directionality or the TopDom software package (version 0.0.2) from the 2 kb binned intra-arm normalized matrices. The log2 directionality values were calculated as below. A 40 kb sliding window was used to traverse the chr […]


A critical assessment of topologically associating domain prediction tools

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

[…] data, and HiCSeq, which fared somewhat better. Overall, the tool that stood out most in terms of its agreement with our manual annotation and its stability with respect to resolution and coverage was TopDom. […]


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TopDom institution(s)
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA; Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
TopDom funding source(s)
Supported by National Institutes of Health (NIH) [NHLBI MAPGEN U01HL108634, U54 DK107981]; NSF [CAREER 0747475, CAREER 1150287]; Arnold and Mabel Beckman foundation [BYI award]; Pew Charitable Trusts [Pew Scholarship].

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