computation of information theoretic Gene Ontology similarities between terms and gene products; GO enrichment analysis
predicting KEGG Pathway membership for individual genes via protein domains signatures using hierarchical classification
reverse engineering / structure learning of biological networks from high dimensional intervention effects
patient classification using gene expression data and network information
patient classification using mRNA + optionally miRNA data and network information; some plotting functionalities
Bayesian prediction of TF and miRNA activities from joint gene and miRNA expression data.
Bayesian prediction of TF and miRNA activities from different expression data entities; interfaces nem for gene regulatory network inference.
Calculation of Steiner trees on large biological networks using several heuristic algorithms.
Algebraic method for ordering variables in biochemical networks according to velocity.