hi-c-3d-genomics

Hi-C And 3D Genomics

Version Compatibility

Reference examples assume recent stable releases of the preferred tools, especially Hi-C and the other tools listed below.

Before using code or command patterns, verify installed versions match the environment:

• Python: python -c "import <module>; print(<module>.__version__)"
• CLI: <tool> --version
• If signatures differ, inspect the installed help or API and adapt the pattern instead of retrying unchanged.

Overview

Workflow for Hi-C and related 3D genomics analyses including compartments, loops, TADs, differential contacts, and visualization.

When To Use This Skill

• use when the task is Hi-C matrix analysis or 3D genome interpretation
• use when loops, compartments, or TADs must be called or compared
• use when contact-map figures or feature-level summaries are required

Quick Route

• If the input is raw or minimally processed data, start with validation and QC before any modeling.
• If the input is already processed, skip directly to the first workflow step that matches the user goal.
• If the user asks for a biological conclusion, always produce at least one QC or confidence artifact alongside the final result.

Progressive Disclosure

• Read references/technical_reference.md when you need deeper tool-selection rules, environment adaptation notes, or extra validation guidance.
• Keep SKILL.md as the main execution path and load the reference file only when the task or failure mode needs the extra detail.

Default Rules

• Prefer Python-first workflows unless the task explicitly requires something else.
• Keep intermediate and final outputs separated.
• Record software versions, reference builds, and key parameters when they affect interpretation.
• Favor reproducible tables and figures over one-off interactive-only outputs.

Expected Inputs

• Hi-C contact pairs or matrices
• genome bins
• condition metadata

Expected Outputs

• compartments
• loops and TADs
• contact maps and differential summaries