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.pairsfiles.