Software

Released packages (stable)

dmt - Dependency modeling toolkit. A unified framework for probabilistic dependency models, including probabilistic versions of PCA, factor analysis and CCA and their regularized variants. (R/CRAN; Leo Lahti and Olli-Pekka Huovilainen)

pint - Genomic data integration for multi-source observations (R/BioConductor; Olli-Pekka Huovilainen and Leo Lahti)

NetResponse - Functional network analysis for modeling context-specific responses in interaction networks (R/BioConductor, Matlab; Leo Lahti, Olli-Pekka Huovilainen, António Gusmão and Juuso Parkkinen)

RPA - Probe reliability and differential gene expression analysis (R/BioConductor; Leo Lahti)

Development versions (useful and functioning alpha/beta)

DCA - discriminative component analysis (Python/C, beta-version)

drCCA data fusion package (R, BMC Bioinformatics)

dredviz - dimensionality reduction for visualization (implements Nerv and local MDS)

ICMg - Interaction component models for gene modules (R; Juuso Parkkinen, included in NetResponse as well)

multiWayCCA - Multivariate multi-way analysis of multi-source data (R, ISMB'10)

Probabilistic retrieval and visualization of biologically relevant microarray experiments (ISMB'09, supplementary material)

Treebic - Hierarchical biclustering (C++, RECOMB'10)

vbmcca - Variational Bayesian mixture of robust CCAs (MATLAB, ECML'10)

gsCCA - Bayesian CCA via group sparsity (R, ICML'11)