TWIGS - Three-Way module Inference via Gibbs Sampling

TWIGS is a tool for advanced analysis of three-way data (e.g., patient-gene-time in gene expression or subject-voxel-time in fMRI). TWIGS identifies both core modules that appear in multiple patients and patient-specific augmentations of these core modules that contain additional genes.

Toy Example

The three-way data example above has a row for each gene. Each column represents a specific time point in the data of a subject. The area A represents a core module: (1) it has a set of rows that are likely to be active together across a set of subjects, and (2) it has a set of active time points in each covered subject, and these sets differ between subjects The other areas represent subject-specific augmentations of the core module.

Get the software

TWIGS is a research tool, still in the development stage.
Hence, it is not presented as error-free, accurate, complete, useful, suitable for any specific application or free from any infringement of any rights. The Software is licensed AS IS, entirely at the user's own risk.

Name (link)	Description
Gibbs sampling implementation	R implementation of TWIGS
Helper functions	Auxiliary functions, e.g., implementation of the simulations
Run commands	R commands for producing the TWIGS results on the real data (fMRI and gene expression)

Get the datasets

• Sepsis gene expression data
• fMRI data

Citing TWIGS

TWIGS can be cited as follows:

A hierarchical Bayesian model for flexible module discovery in three-way time series data,
David Amar, Daniel Yekutieli, Adi Maron-Katz, Talma Hendler, and Ron Shamir. To appear in ISMB 2015.

Get in touch

For questions or suggestions please contact David Amar.