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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)