Table 1 clusterMaker algorithm implementation notes
From: clusterMaker: a multi-algorithm clustering plugin for Cytoscape
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 | Â | 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 | Â | 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 |