Links
CRC: http://www.sph.umich.edu/csg/qin/CRC/
The R Project for Statistical Computing: http://www.r-project.org/
BioConductor: http://www.bioconductor.org/
GOstats: http://bioconductor.org/packages/1.8/bioc/html/GOstats.html
Heatplus: http://bioconductor.org/packages/1.8/bioc/html/Heatplus.html
ImageMagick: http://www.imagemagick.org/script/index.php
Coefficient of variation, Wikipedia: http://en.wikipedia.org/wiki/Coefficient_of_variation
Comparsion of popular clustering programs:
| CRCView |
Model-based |
Yes |
| MCLUST |
Model-based |
No |
| GIMM |
Model-based |
No |
| GEPAS |
Self organising tree, hierarchical clustering, k-means partitioning, self-organization maps, hierarchical clustering on self-organizing map result. |
Yes |
| wCLUTO |
Classes of clustering algorithms: partitional, agglomerative, & graph-partitioning based.
Similarity/distance functions: Euclidean distance, cosine, correlation coefficient, extended Jaccard, user-defined.
|
Yes |
| GenePattern |
Supervised: classification and regression trees (CART), K-nearest neighbors (KNN), probabilistic neural network (PNN), Weighted Voting, and Support Vector Machines (SVM)
Unsupervised: consensus clustering, hierarchical clustering, and self-organizing maps (SOM clustering) |
Yes |
| Cluster(EisenLab) |
Hierarchical clustering, self-organizing maps (SOMs), k-means clustering. |
No |
| MeV |
Hierarchical clustering, support trees (bootstrapping), self-organizing trees, k-means clustering, self-organizing maps, clustering affinity search technique, qt_clust |
No |
| GeneCluster |
Deprecated |
No |
|
