bio-workflows-hic-pipeline
OfficialHi-C end-to-end workflow for compartments and TADs.
Authorstellaromics
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This workflow automates the end-to-end Hi-C analysis from raw contact data to higher-order genome features, consolidating steps and guidance into a single reproducible process.
Core Features & Use Cases
- End-to-end pipeline: alignment, matrix generation, ICE balancing, compartment analysis, TAD detection, loop calling, and visualization.
- Compatible with cooler matrices and cooltools for downstream analysis and visualization, with example workflows and code snippets.
- Use Case: process Hi-C data to identify A/B compartments, TAD boundaries, and chromatin loops across resolutions.
Quick Start
Provide Hi-C reads and a reference, then run the complete Hi-C workflow to obtain compartments, TADs, and loops.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: bio-workflows-hic-pipeline Download link: https://github.com/stellaromics/fast-bioinfo/archive/main.zip#bio-workflows-hic-pipeline Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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