Bayesian mixture models for estimating and clustering cancer cell fractions

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

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

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.

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

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

Snakemake pipeline for running PhyloWGS on NIH Biowulf Cluster

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

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

Personalised mutual hazard networks: fixed effects in cancer progression modeling

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.

Gillespie simulations of advantageous drivers & deleterious passengers in cancer

Spatial transcriptomics of MpBC. This project analyzes spatial transcriptomics data from 15 metaplastic breast carcinoma (MpBC) samples using 10x Genomics Visium. It aims to explore tumor heterogeneity and transdifferentiation, leveraging expert-labeled cell types to identify spatial clusters and biomarkers.

Source code for "Metastatic progression of pheochromocytoma and paraganglioma occurs via parallel evolution"

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).