danio-2022

Notebooks (in logical order):

1. TAD_boundaries_calling.ipynb -- calling of TAD boundaries in This2022 data
2. Filtration.ipynb -- filtration of bad bins (according to the Sasha's deposited file)
3. Visual_inspection.ipynb -- visual inspection of TAD boundaries and fountains on the same Hi-C maps
4. Overlap.ipynb -- testing the 'overlapping' hypothesis (between TAD boundaries and fountains)
5. Calculate_insulation.ipynb -- calculating insulation scores for the subsequent clustering (both TAD boundaries and fountains)
6. Clustering.ipynb -- clustering of TAD boundaries and fountains in time of embryogenesis
7. Calculate_distance.ipynb -- testing the 'distance' hypothesis (TADs come after fountains) -- NOT YET FINISHED (index error)