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clusterMaker specifications

Information


Unique identifier OMICS_12800
Name clusterMaker
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Other
Computer skills Medium
Version 1.10
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Documentation


Maintainer


  • person_outline John Morris <>

Publication for clusterMaker

clusterMaker in publications

 (32)
PMCID: 5928201
PMID: 29740341
DOI: 10.3389/fphys.2018.00429

[…] to generate a unique ppi network with all the interactions. only homo sapiens interactions were used to build the new network, to avoid loss of information using equine data only., the application clustermaker 2.0 (morris et al., ) with the “glay” option was used to find different clusters inside the network according to the number of connections between nodes. clusters were explored […]

PMCID: 5872385
PMID: 29589566
DOI: 10.1186/s12918-018-0551-4

[…] events linked with cell proliferation., in order to validate the components identification with our method, we compared it to two graph clustering algorithms: clusterone [] and the cytoscape plug-in clustermaker [], which is a fuzzy c-means clustering algorithm. both methods are similar to the one we propose since they do not include the geps for the clustering. we applied both methods […]

PMCID: 5624455
PMID: 29018779
DOI: 10.15430/JCP.2017.22.3.147

[…] (uhdtg, uhdt, uhdg, dhutg, dhut, and dhug) (). due to the size and complexity of the grn (427 nodes and 2,455 links), we modularized the network using the newman algorithm in the cytoscape plugin clustermaker and subsequently identified five modules. to characterize the functional annotations of the genes present in each module, we used a functional annotation tool david to perform a gene set […]

PMCID: 5540468
PMID: 28804499
DOI: 10.1155/2017/1278932

[…] cytoscape is the most successful tool for bridging the gap between analysis and visualization and it comes with a great plethora of layout, clustering, and topological network analysis algorithms. clustermaker plugin [], for example, includes attribute cluster algorithms such as autosome clustering [] and eisen's hierarchical and k-means clustering [] as well as topology-based clustering […]

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

[…] 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 of these algorithms have been implemented in various cytoscape applications (cytocluster, clusterviz [], […]


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clusterMaker institution(s)
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Max Planck Institute for Informatics, Germany; Buck Institute for Age Research, Novato, CA, USA; Bioinformatics Program, University of Michigan, Ann Arbor, MI, USA; National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI, USA; The Donnelly Centre, University of Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, ON, Canada; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
clusterMaker funding source(s)
NIH grant P41 RR001081

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