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Codebase for "Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumour growth and metastasis"

Year: 2026
Type: software
Abstract: Code & scripts for reproducing spatial-lineage analyses in Jones, Sun et al, "Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumour growth and metastasis" 2026. Cassiopeia codebase used for processing lineage data and reconstructing trees. Code for reproducing all analyses in the study: ./utilities/: Utilities for handling spatial and phylogenetic data. ./reproducibility/: Notebooks to reproduce each figure panel. Each figure has it's own folder, and associated data and scripts are included. ./data/: General data for project. You may find the processed datasets on Zenodo (10.5281/zenodo.19771805).
DOI: 10.5281/zenodo.21263890
Authors: Jones, Matthew, Sun, Dawei, Min, Kyung Hoi (Joseph), Colgan, William, Wang, Haoyu, Torok, Tivadar, Ribeiro, Juliano, Xue, Jessie, Cardoso, Erik C., Rong, Yao, Tian, Luyi, Weir, Jackson A., Chen, Victor Z., Koblan, Luke, Yost, Kathryn E., Mathey-Andrews, Nicolas, D'Souza, Edridge, Russell, Andrew J.C., Stickels, Robert R., Balderrama, Karol S., Rideout, William, Dai, Min, Marrero, Giovanni, Kumar, Vipin, Saqi, Anjali, Herzberg, Benjamin, Izar, Benjamin, Chang, Howard, Lee, Joo-Hyeon, Jacks, Tyler, Chen, Fei, Weissman, Jonathan, Yosef, Nir, Yang, Dian
Institutions: Massachusetts Institute of Technology, Broad Institute, Whitehead Institute for Biomedical Research, Columbia University Irving Medical Center, Memorial Sloan Kettering Cancer Center, Guangzhou Laboratory, Columbia University, Stanford University, Weizmann Institute of Science
Open Access status: green
OpenAlex ID: W7167716132
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