This is the repository with custom code used in Pletenev, Bazarevich, Zagirova et al., 2024

Dependencies

Create conda environment from env1.yml to run the following scripts:

• 1_merge_Hi-C.sh
• 2_Figure1_contact_scaling.ipynb
• 3_Figure1_chromatin_compartments.ipynb
• 4_Figure1_DLR.ipynb
• 10_fithic.ipynb
• 11_Figure4_polycomb_interactions.ipynb
• 12_Figure4_H3K9me3_profile.ipynb
• 13_Figure5_snm3C-seq.ipynb

Create conda environment from env2.yml to run the following scripts:

• 5_Fig1_cis_to_trans_contacts.ipynb
• 6_Fig1_tad_borders_PCA.ipynb
• 7_Fig2_tad_borders_properties_part1.ipynb
• 8_Fig2_tad_and_thier_borders_properties_part2.ipynb
• 9_Fig3_chromtain_loops_properties.ipynb