R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem

SCARLET (Single-cell Algorithm for Reconstructing Loss-supported Evolution of Tumors) is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.

Deterministic evolution and stringent selection during pre-neoplasia

R htmlwidget for Jellyfish

Simulate the evolution and treatment of tumors and generate bulk, single-cell and spatial data from them.

Jellyfish plots for integrative visualization of spatio-temporal tumor evolution and clonal dynamics

https://doi.org/10.5281/zenodo.6941367 - Spatiotemporal-Aware Glioblastoma Multiforme Tumor Growth Modeling with Deep Encoder-Decoder Networks

SIFA: identify tumor subclones and infer phylogenetic tree from WGS data

Warlock is a snakemake workflow to spawn multiple demons (deme-based oncology models) as jobs running around on a cluster environment 😈😈

Tumor Evolution Paths Project

Refined SNV calling for tumor data using perfect phylogenies and ILP

Project on ABM tumor growth for the Agent-Based Modeling course at the UvA 2023-2024

TEMA (Tumor Evolution Manager and Analyzer)

This R package computes mutation densities in a tumor's MRCA and associates the density with clinical risk. It is based on Körber et al., Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome, Nature Genetics, 2023, but is designed to accept a broader range of input formats.

Measuring a tumor's density gradient during treatment.

Comparación y análisis de la progresión de tumores en cerebros.