From: A systematic comparison of genome-scale clustering algorithms
 | Small (3-10 genes) | Medium (11-100 genes) | Large (101-1000 genes) |  | |||
---|---|---|---|---|---|---|---|
Clustering Method | Param | Time (s) | Param | Time (s) | Param | Time (s) | Implementation |
K-Clique Communities | 0.80/03 | Â | 0.80/57 | Â | 0.80/48 | Â | Standalone,*** |
Maximal Clique | 0.80 | 26.510 | 0.80 | 26.510 | N/A | N/A | Standalone,*** |
Paraclique | 0.80/01 | 5.120 | 0.80/09 | 0.780 | 0.60/09 | 9.050 | Standalone,*** |
Ward (H) | N/A | 2.863 | N/A | 2.863 | N/A | 2.863 | R 2.13.0 |
CAST | 0.875 | 37.324 | 0.85 | 34.242 | 0.90 | 34.121 | MeV 4.5.1 |
QT Clust | 030 | 6 904.518 | 035 | 6 759.073 | 050 | 5 559.467 | MeV 4.5.1 |
Complete (H) | N/A | 2.721 | N/A | 2.721 | N/A | 2.721 | R 2.13.0 |
NNN | 11 | 25.550 | 24 | 30.610 | 27 | 34.370 | Standalone,*** |
K-Means | 617 | 6 711.143 | 308 | 4 060.351 | 21 | 1 068.069 | R 2.13.0 |
SOM | 25/r | 6.159 | 25/h | 6.121 | 18/r | 2.956 | MeV 4.5.1 |
WGCNA | 2/10 | 79.430 | 1/06 | 80.962 | 2/06 | 80.962 | R 2.13.0 |
Average (H) | N/A | 2.452 | N/A | 2.452 | N/A | 2.452 | R 2.13.0 |
McQuitty (H) | N/A | 2.445 | N/A | 2.445 | N/A | 2.445 | R 2.13.0 |
CLICK | 015 | 38.270 | 060 | 45.310 | 065 | 52.570 | Standalone,*** |