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ChromSDE specifications

Information


Unique identifier OMICS_06676
Name ChromSDE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for ChromSDE

ChromSDE in publications

 (4)
PMCID: 5430849
PMID: 28180292
DOI: 10.1093/nar/gkw1155

[…] \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\alpha$\end{document}., we compared our methods with four methods implemented in () and with chromsde (), shrec3d () and mogen () using the synthetic data sets. the first four methods include two classic multidimensional scaling methods (metric multidimensional scaling – mds2 and non-metric […]

PMCID: 4744395
PMID: 26852142
DOI: 10.1186/s12859-016-0894-z

[…] obtains a consensus 3d structure by minimizing some objective function, such as the total “differences” between the translated distances and those inferred from the hypothesized 3d architecture [–]. chromsde [] is an example in this category, but it also estimates the degree of the inverse relationship in addition to the 3d coordinates in the optimization step. further, the distances […]

PMCID: 4638111
PMID: 26553003
DOI: 10.1186/s12859-015-0799-2

[…] insensitive to link weighting and enjoys good overall performance speed as further described in the ‘’., an intermediary strategy is represented by the methodology of zhang et al. []. this approach, chromsde, (i) invokes a power law relationship between spatial distances and contact frequencies: d ij=(f ij)−α if f ij>0; d ij=∞ if f ij=0, (ii) uses weighted, penalized mds to obtain points […]

PMCID: 4532452
PMID: 26262780
DOI: 10.1371/journal.pcbi.1004396

[…] [], while the adaptation to 3d genome reconstruction was named shrec3d in lesne et al. []. in the following we will refer to this method simply as cmds. in addition, we present comparison with the chromsde method of zhang et al. [], which is based on semidefinite programming and is significantly more computationally demanding than both the cmds method and mbo., the structure considered […]


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ChromSDE institution(s)
1 School of Computing, National University of Singapore, Singapore, Singapore

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