Version Compatibility

Reference examples tested with: cooler 0.9+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, 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
• 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 Data I/O

"Load my Hi-C contact matrix" → Read .cool/.mcool/.hic files into Python, access contact pixels, convert between formats, and export subsets.

• Python: cooler.Cooler('file.mcool::resolutions/10000')
• CLI: cooler load, hic2cool convert

Load and manipulate Hi-C contact matrices in cooler format.