This is team Jasper06's submission to Allen Institute Cell Lineage Reconstruction DREAM Challenge
We used probability-based hierarchical clustering to reconstruct the cell lineage tree. In short, the transition rate of the initial state to altered states are derived using the ground truth. Next, we derived the probability of cells arising from different parents using transition rates. Then, the pairwise cell distance is calculated using the probability. Finally, we used hierarchical clustering (UPGMA) to reconstruct the cell lineage.
This repository only provides 1 example dataset from each subchallenge. Download the complete dataset from here.
Running this lineage reconstruction algorithm takes the exact 4 steps for each subchallenge.
Use Jupyter notebook to run 01_mutation_summary.ipynb
Rscript 02_mutation_rate.R
Use Jupyter notebook to run 03_probability_HC.ipynb
Rscript 04_evaluation.R