From: A systematic comparison of genome-scale clustering algorithms
 |  |  | Allows Overlapping Clusters | |||
---|---|---|---|---|---|---|
 |  |  |  | Pre-specified Number of Clusters ( k ) | ||
 |  |  |  |  | Thresholded Correlations | |
Method | Type | Result Range | Â | Â | Â | Parameters Tested |
Ward | Hierarchical | k | Â | Y | Â | Average cluster size |
Average | Hierarchical | k | Â | Y | Â | Average cluster size |
McQuitty | Hierarchical | k | Â | Y | Â | Average cluster size |
Complete | Hierarchical | k | Â | Y | Â | Average cluster size |
k-Means | Partitioning | k | Â | Y | Â | Number of clusters |
SOM | Neural network | k | Â | Y | Â | Grid size/typea |
QT Clust | Partitioning | 24-385 | Â | Â | Â | Maximum cluster diameters |
CAST | Graph-based | 1-6162 | Â | Â | Y | Threshold |
CLICK | Graph-based | 4-32 | Â | Â | Â | Cluster homogeneity |
WGCNA | Graph-based | 4-160 | Â | Â | Â | Power, Module detection method |
NNN | Graph-based | 23-52 | Yb | Â | Â | Minimum neighborhood size |
k-Cliques Communities | Graph-based | 1-68 | Y | Â | Y | Threshold, Clique size |
Maximal Clique | Graph-based | 1,000-64,000 | Y | Â | Y | Threshold |
Paraclique | Graph-based | 8-615 | Yc | Â | Y | Threshold, Glom factor |