Software
Nested Effects Models
The R/Bioconductor package 'nem' reconstructs features of pathways from the nested structure of perturbation effects. It unites the software from several labs and represents the current state-of-the-art in Nested Effects Models.
HTSanalyzeR - Network analysis of high throughput screens
The R/Bioconductor package 'HTSanalyzeR' provides enrichment and network analysis of high-throughput RNAi screens.
RedeR - network analysis and visualization
A software to bridge the gap between statistical computing in R and dynamic network visualization.
CRImage - tumour image analysis
Coming soon! Image analysis for cellularity correction of tumour copy-number profiles. A preliminary developer's version is available at R-Forge.
DANCE - deregulation of copy-number and expression
Coming soon! a R/Bioconductor package for Deregulation Analysis of Copy-number and Expression data. Our approach quantifies the impact of copy-number alterations on gene expression and compares it between tumour sub-types.
lol - lots of lassos
The package contains various optimization methods for matrix-to-matrix Lasso inference, such as cross-validation, randomised lasso, subsampling lasso and others.
PAN - posterior association networks
The package implements methods to encode posteriori belief of functional association types on edges and phenotypic information on nodes.
Patient-specific data fusion
Richard Savage hosts a page to supplement our paper 'Patient-specific data fusion defines prognostic cancer subtypes' from where you can download MATLAB code implementing our clustering method.