analysis/main_panel/README.md

In Kalhor-Lab/QFM: Quantitative Fate Mapping with ICE-FASE and Phylotime

Analysis on the main fate map panel

1. 'construct_fate_map_panel.R': construct panel of 331 fate maps
2. 'simulate_process_evaluate.R': example to simulating, process and evaluate one replicate
3. 'figure1.R': illustration in Figure 1.
4. 'figure2and3.R': illustration in Figure 2 and Figure 3.
5. 'setup_experiment.R': set up data files for all 3,310 experiments (5 replicates) and different combinations of barcoding sites.
6. 'slurm_processing.R': simulate, process and evaluate full panel on HPC cluster.
7. 'slurm_phylotime_data.R', 'slurm_phylotime_varying_sites.R': run Phylotime n batch on HPC cluster.
8. 'evaluate_ice_fase_phylotime.R': evaluate reconstructed fate maps from Phylotime-inferred phylogenies.

Kalhor-Lab/QFM documentation built on Nov. 25, 2024, 10:18 p.m.