Code & utilities for the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"
You can find notebooks, scripts, and data necessary for reproducing the results for each figure in the folder entitled reproducibility. Note that this code may not reproduce the exact figures presented in the manuscript in the future due to version updates and stochasticity in some procedures. To note, we now support several of these procedures in the Cassiopeia codebase now (e.g., fitch hartigan maximum parsimony and evolutionary coupling) and encourage interested users to use Cassiopeia. We hope that nonetheless this code is useful for other researchers who may want to use similar concepts in their analysis.
In order to reproduce our results, you can download the KP-Tracer dataset from Zenodo. Currently, this data is under general embargoed access to the public until our manuscript has been accepted, but please reach out to us if you'd like access to it.
For interactive visualization of our data (available on Zenodo), we encourage you to consider to use VISION and PhyloVision (both downloadable from https://github.com/YosefLab/VISION). We have provided instructions for how to install the software, launch existing reports, as well as create your own reports with our dataset using the vignette in here. You can check out an example PhyloVision report for one of one of our clones here.
Note: The Cassiopeia version is out of date with the main master branch in our repository and for this reason we include the Cassiopeia version used for the analysis reported in our manuscript.