Version Compatibility

Reference examples tested with: BWA-MEM2 2.2.1+, cooler 0.9+, cooltools 0.6+, matplotlib 3.8+, numpy 1.26+, pairtools 1.1+, pandas 2.2+

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

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

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

Hi-C Pipeline

"Analyze my Hi-C data from FASTQ to 3D genome features" → Orchestrate read alignment, contact matrix generation, normalization, TAD calling, loop detection, compartment analysis, and differential interaction testing.

Complete workflow for Hi-C chromosome conformation capture analysis.

Workflow Overview