REVOLVER - Repeated Evolution in Cancer

Bayesian mixture models for estimating and clustering cancer cell fractions

Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding

Code for "Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?", J.Diaz-Colunga, R.Diaz-Uriarte: https://doi.org/10.1371/journal.pcbi.1009055

J-SPACE is a Julia package to simulate the spatial growth and the genomic evolution of a cell population and the experiment of sequencing the genome of the sampled cells.

Datasets and analysis results released with the REVOLVER package for Cancer Evolution.

Clone trees for Cancer Evolution studies from bulk sequencing data.

Snakemake pipeline for running PhyloWGS on NIH Biowulf Cluster

Estimates the clonal population structure in a tumour sample given a cell mutation matrix

The evoverse is a package to implement cancer evolution analysis on multi-sample cancer sequecing data.

Personalised mutual hazard networks

Agent-based modelling reveals the impact of growth patterns on spatial and temporal features of clonal diversification. A GitHub repository of the Source Code for the model and Source Data for the figures of the paper.

Agent-based modelling reveals the impact of growth patterns on spatial and temporal features of clonal diversification. A GitHub repository of the Source Code for the model and Source Data for the figures of the paper.

Mutation tree from binary bulk sequencing data

Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

Gillespie simulations of advantageous drivers & deleterious passengers in cancer

Supplementary Data released with Caravagna et al. Subclonal reconstruction of tumors by using machine learning and population genetics. Nature Genetics volume 52, 898–907(2020).