Table 1

clusterMaker algorithm implementation notes

Algorithm

Description

Source

Details


Hierarchical

Standard hierarchical clustering as implemented by Eisen[1]

Cluster 3.0 package from Michiel de Hoon of the University of Tokyo

Ported by clusterMaker authors from C to Java


k-means

Standard k-means clustering as implemented by Eisen[1] with the addition of silhouette estimation of k

Cluster 3.0 package from Michiel de Hoon of the University of Tokyo

Ported by clusterMaker authors from C to Java. Silhouette implemented by clusterMaker authors.


k-medoid

Modification of k-means from above to use medoid rather than means

Implemented by clusterMaker authors. Silhouette implemented by clusterMaker authors.


AutoSOME

The AutoSOME cluster algorithm [34]

The distributed AutoSOME implementation

Ported directly to clusterMaker by AutoSOME author


Affinity Propagation

The message passing-based approach to clustering by Frey and Dueck[27]

Implemented from the algorithm description in the original reference

Implemented by clusterMaker authors


Connected Components

Simple division based on connectivity

Implemented by clusterMaker authors


Community (GLay)

Newman-Girvan[32] community clustering as implemented by Su, et al.[33]

The original GLay plugin for Cytoscape

Ported by clusterMaker authors


MCODE

Bader and Hogue[4] algorithm for finding modules in PPI networks

The MCODE Cytoscape plugin

Ported by clusterMaker authors


MCL

Markov clustering algorithm from van Dongen[8,28] that uses random walks to simulate flow

Implemented from original thesis with reference to C implementation for validation of results.

Implemented by clusterMaker authors as a parallel algorithm to take advantage of multiple CPU cores.


SCPS

Spectral clustering algorithm for BLAST similarity networks[24]

Implemented from the algorithm description in the original reference using the authors' implementation to validate results

Implemented by clusterMaker authors


Transitivity Clustering

Transitivity based clustering approach from Wittkop, et al.[25]

Ported from Cytoscape TransClust plugin

Ported by original TransClust authors


Morris et al. BMC Bioinformatics 2011 12:436   doi:10.1186/1471-2105-12-436

Open Data