An R tool to detected repeated evolutionary trajectories from cancer cohorts.

R sources, vignettes, etc.: Github repository.

  • Detecting repeated cancer evolution in human tumours from multi-region sequencing data. G Caravagna, Y Giarratano, D Ramazzotti, I Tomlinson, TA Graham, G Sanguinetti, A Sottoriva. Submitted.

TRONCO (TRanslational ONCOlogy) / PiCnIc

An R tool for cancer progression inference from heterogeneous genomic data.

TRONCO/PiCnIc has an official website.

Gaussian Processes Correction Maps

Statistical correction of models' outputs via heteroscedastic Gaussian Process regression.

Matlab/Python sources: Github repository.

CoGNaC (Chaste and Gene Networks for Cancer)

A Chaste plugin for the multi-scale simulation of Gene Regulatory Networks driving the spatial dynamics of tissues and cancer.

Available at Oxford's Chaste webpage.

NoisySIM (Noisy Simulation)

Simulation of chemically reacting systems with intrinsic and extrinsic bounded noises.

Download JAVA sources and the instruction manual.


pyTSA (Python Time-Series Analyzer)

A Python tool for the statistical analysis of time-series from stochastic dynamical systems.

Python package: Github repository.



Augmented Boolean Gene Regulatory Networks.

This tool has an official website.