DPClus specifications

Information


Unique identifier OMICS_11245
Name DPClus
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data Associated matrix of an interaction network
Output data Protein complexes
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Md Altaf-Ul-Amin <>

Publication for DPClus

DPClus in publications

 (33)
PMCID: 5653705
PMID: 29104520
DOI: 10.1007/s11306-017-1284-x

[…] a matrix of correlation between all trait pairs was generated. initially the r-package “igraph” was used to visualize the network and then we exported the graph to a file which can be read by dpclus (altaf-ul-amin et al. ; csardi and nepusz ; fukushima and nishida ). essentially, this algorithm divides the network into modules or groups of vertices that are more connected […]

PMCID: 5657047
PMID: 29072136
DOI: 10.1186/s12859-017-1820-8

[…] in the following experiments, we use the most specific functional annotations by setting the level height to 6., we compared our method with several existing methods including mcode [], rnsc [], dpclus [], core [], clusterone [] and cpredictor []. these methods were proposed to predict protein complexes with at least three protein members, and can be tuned to predict size-two complexes. […]

PMCID: 5485287
PMID: 28691013
DOI: 10.1155/2017/1016305

[…] challenging []. a number of algorithms have been developed over the past decade to tackle this problem, including the markov cluster algorithm (mcl) [], molecular complex detection (mcode) [], dpclus [], affinity propagation clustering (apc) [], clustering based on maximal clique (cmc) [], clustermaker [], and clustering with overlapping neighborhood expansion (clusterone) []. many […]

PMCID: 5253511
PMID: 28164123
DOI: 10.1155/2017/5296729

[…] an approach for successfully classifying 216 plants based on their known incomplete metabolite content. structurally similar metabolites have been clustered using the network clustering algorithm dpclus. plants have been represented as binary vectors, implying relations with structurally similar metabolite groups, and classified using ward's method of hierarchical clustering. despite […]

PMCID: 4926396
PMID: 27258269
DOI: 10.3390/ijms17060862

[…] a comprehensive gene-level assessment to search important molecular markers and pathways of parkinson’s disease. the correlation network for parkinson’s disease was identified by applying the dpclus [] graph clustering algorithm. the densely-connected nodes of the cluster were assessed by associated go terms and kegg pathways. the approach resulted in finding significant pathways, […]


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DPClus institution(s)
Computational Systems Biology Lab, Nara Institute of Science and Technology, Ikoma, Japan
DPClus funding source(s)
Supported by National Bioscience Database Center (JST-NBDC), Japan.

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