Version Compatibility

Reference examples tested with: cooler 0.9+, cooltools 0.6+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scipy 1.12+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Compartment Analysis

"Identify A/B compartments from my Hi-C data" → Decompose the contact matrix via eigenvector analysis to classify chromatin into active (A) and inactive (B) compartments.

• Python: cooltools.eigs_cis(clr, gc_cov) for eigenvector decomposition

Detect A/B compartments from Hi-C contact matrices.

Required Imports