GitHub - dekkerlab/Ozgun-ALS: ALS paper

HiC_Preliminary_analyses.ipynb: This notebook was used to perform initial HiC analysis on mcools. It includes EV track generation, saddle plots (Fig 2e, S7g), centromere-telomere plots (Fig. 3c,5g, 7d), expected calculation, and insulation track generation.
sample.py: Sample names used in the notebooks.
supp_lib.py: List of functions used in notebooks.
CentTeltrack.py: Centromere-Telomere track generation function.
Figures created in GraphPad: Fig 1-d,e,f; Fig 3-b; Fig 5-b; Fig 6-d; Fig 7-c

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Name		Name	Last commit message	Last commit date
Latest commit History 33 Commits
CentTeltrack.py		CentTeltrack.py
Fig2abc_S7de_Heatmaps_Cooler_matrices.ipynb		Fig2abc_S7de_Heatmaps_Cooler_matrices.ipynb
Fig2d_5cd_7b_Scaling_plots.ipynb		Fig2d_5cd_7b_Scaling_plots.ipynb
Fig2f_5e_S7f_Saddle-strengths-scatterplots.ipynb		Fig2f_5e_S7f_Saddle-strengths-scatterplots.ipynb
Fig2g_Saneky.ipynb		Fig2g_Saneky.ipynb
Fig2h_Compartment-transitions.ipynb		Fig2h_Compartment-transitions.ipynb
Fig2i_Violin-plots-TPMvalues-compartments.ipynb		Fig2i_Violin-plots-TPMvalues-compartments.ipynb
Fig3a_5a_heatmaps_trans_Cooler_matrices.ipynb		Fig3a_5a_heatmaps_trans_Cooler_matrices.ipynb
Fig5h_7e_Telomere-interactions.ipynb		Fig5h_7e_Telomere-interactions.ipynb
Fig6ghi_S7ijk_Insulation_pileups_unionset.ipynb		Fig6ghi_S7ijk_Insulation_pileups_unionset.ipynb
FigS6_Insulation-threshold.ipynb		FigS6_Insulation-threshold.ipynb
HiC_Preliminary_analyses.ipynb		HiC_Preliminary_analyses.ipynb
README.md		README.md
sample.py		sample.py
supp_lib.py		supp_lib.py