bio-single-cell-lineage-tracing

Cassiopeia Tree Reconstruction

Goal: Reconstruct a cell lineage tree from CRISPR barcode character matrices to reveal clonal relationships among single cells.

Approach: Load a character matrix (cells x barcode sites with mutation states), create a CassiopeiaTree object, then solve with a greedy or ILP maximum parsimony solver.

import cassiopeia as cas
import numpy as np

## Check data quality

print(f'Cells: {tree.n_cell}')
print(f'Characters: {tree.n_character}')
print(f'Missing fraction: {(char_matrix == -1).mean():.2%}')

## Reconstruct tree with greedy solver

solver = cas.solver.VanillaGreedySolver()
solver.solve(tree)