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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline John Morris

Publication for clusterMaker

clusterMaker citations

 (8)
call_split

Seasonal Succession of Free Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula

2016
Front Microbiol
PMCID: 5093341
PMID: 27857708
DOI: 10.3389/fmicb.2016.01731
call_split See protocol

[…] rence network based on Pearson’s correlation (r > 0.5) using the CoNet plugin in Cytoscape (; ). We extracted non-overlapping clusters from this network through k-means clustering using the Cytoscape clusterMaker2 plugin after first selecting a reasonable value for k through the evaluation of a scree plot of within-clusters sum of squares (Supplementary Figure ; ). The resulting network clusters w […]

library_books

Evidence for the Induction of Key Components of the NOTCH Signaling Pathway via Deltamethrin and Azamethiphos Treatment in the Sea Louse Caligus rogercresseyi

2016
Int J Mol Sci
PMCID: 4881433
PMID: 27187362
DOI: 10.3390/ijms17050304

[…] Complementary analysis was conducted with the ClusterMaker Cytoscape plugin [] using the Markov Cluster algorithm to search protein-protein interaction network modules derived from tandem affinity purification/mass spectrometry. This approach clu […]

library_books

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

2015
Genome Biol
PMCID: 4566308
PMID: 26357925
DOI: 10.1186/s13059-015-0735-9

[…] s edge weights. For clustering and visualization, edges with correlation values below 0.6 were discarded. The resulting weighted network was clustered with the Markov cluster algorithm (MCL) [] using clusterMaker version 1.10 [] with granularity (inflation) parameter 2 and default advanced parameters, and visualized in Cytoscape version 3.1.0. A circular layout was used for clusters consisting of […]

library_books

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

2015
PMCID: 4570537
PMID: 26073648
DOI: 10.1002/pro.2724

[…] Networks were created for the proteins in each superfamily using ClusterMaker, a plugin for the Cytoscape software package that has implemented the Markov clustering algorithm (MCL). The appropriate edge metric (ASP score, TM-Align score, or BLAST score) was used f […]

library_books

Systems biology analysis of the proteomic alterations induced by MPP+, a Parkinson's disease related mitochondrial toxin

2015
PMCID: 4313704
PMID: 25698928
DOI: 10.3389/fncel.2015.00014

[…] ClusterMaker Cytoscape application (http://www.cgl.ucsf.edu/cytoscape/cluster/clusterMaker.shtml) was employed to fragment the META list, PPI D2 model (Morris et al., ). In particular, the implemented […]

library_books

Genome Wide Characterization of Light Regulated Genes in Neurospora crassa

2014
PMCID: 4169166
PMID: 25053707
DOI: 10.1534/g3.114.012617

[…] ely for each time course as well as for the combined set of replicates. FPKM values across the light time course were hierarchically clustered and visualized as heat maps with Cytoscape 2.8.3 and the clusterMaker plugin (). Functional enrichments for each cluster were calculated using the FunCat database (FunCatDb) (). Gene identifiers in FunCatDb were mapped to the identifiers in the current anno […]


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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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