CLI tools and notebooks for downstream analysis of Hi-C data such as creating scaling plots or calculating insulation scores.

• src/insulation/
  • insulation.py: CLI tool for computing insulation scores and plot boundary strengths as a histogram.
• src/pileups/
  • notebooks/pileups.ipynb: Jupyter notebook for creating pileups plots around centromeres.
  • pileups.py: CLI tool for creating pileups plots of a specified size around centromeres.
• src/scalings/
  • notebooks/scalings.ipynb: Jupyter notebook for creating scalings plots (contact frequency vs genomic separation).
  • notebooks/scalings_arms.ipynb: Jupyter notebook for creating scaling plots of separate chromosomal arms.
  • notebooks/scalings_asym.ipynb: Jupyter notebook for creating off-diagonal scaling plots.
  • notebooks/scalings_region.ipynb: Jupyter notebook for creating scaling plots of a specified region.
  • scalings.py: CLI tool for creating scaling plots for one or more .pairs files.

Hi-C specific libraries

• bioframe
• cooler
• cooltools
• pairlib
• pairtools