Software

REVOLVER

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

R sources, vignettes, etc.: Github repository.

TRONCO (TRanslational ONCOlogy) / PiCnIc

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

TRONCO/PiCnIc has an official website.

https://sites.google.com/site/troncopackage

Gaussian Processes Correction Maps

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

Matlab/Python sources: Github repository.

https://github.com/caravagn/GP-correction-maps

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.

https://chaste.cs.ox.ac.uk/trac/wiki/PaperTutorials/CoGNaC

NoisySIM (Noisy Simulation)

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

Download JAVA sources and the instruction manual.

NoisySIM

pyTSA (Python Time-Series Analyzer)

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

Python package: Github repository.

pyTSA

CABERNET/ GESTODifferent

Augmented Boolean Gene Regulatory Networks.

This tool has an official website.

http://bimib.disco.unimib.it/index.php/CABERNET