This folder contains the analysis code to reproduce the results presented in the paper "Bayesian inference of fitness landscapes via tree-structured branching processes".
The analysis code is organized to facilitate reproduction of the computational results and figures from the paper.
The analysis folder is organized into two main subfolders:
This subfolder contains data and scripts related to the simulation studies in the paper. Note that this does not contain the full workflows to generate the simulated data.
This subfolder contains data, pre-processing code, and plotting scripts for the Acute Myeloid Leukemia (AML) analysis presented in the paper. This includes data visualization code but not the complete inference pipeline.
The actual workflows for generating simulated data and inferring fitness landscapes are located in the workflows folder under the main package directory:
These workflows implement the complete pipeline for both simulation studies and real data analysis described in the paper.
All simulated data and raw results used in this analysis are available on Zenodo.