Integrative Clustering of Multiple Genomic Data Types (iCluster)

Download R package soure file

Windows and Mac compatible version available at http://cran.r-project.org/web/packages/iCluster/index.html

Reference: Shen, Olshen, and Ladanyi (2009) Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics. 25(22):2906-12.

Bayesian Cell Mixture Model (CMM)

This is a zip file containing R code to implement CMM for analyzing tissue microarray data.
Download zip file

Reference: Shen, Taylor, and Ghosh (2008) Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model. Bioinformatics. 24(24):2880-6.

Eigengene-based Linear Discriminant Analysis (ELDA)

This is a zip file containing R code to implement ELDA for tumor classification problems using gene expression microarray data. The README file describes how to use the code.
Download zip file

Reference: Shen et al. (2006) Eigengene-based linear discriminant model for tumor classification using gene expression microarray data.Bioinformatics. 22(21):2635-42.