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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:

Program Clustering Methods Web-based
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

 


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