nested-TAD-detection
This skill detects hierarchical (nested) TAD structures from Hi-C contact maps (in .cool or mcool format) using OnTAD, starting from multi-resolution .mcool files. It extracts a user-specified chromosome and resolution, converts the data to a dense matrix, runs OnTAD, and organizes TAD calls and logs for downstream 3D genome analysis.
npx skills add majiayu000/claude-skill-registry --skill 31-toolbased-nested-tad-detection-bisnake2001-chromskills-2 --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Nested TAD Detection from .mcool Using OnTAD ## Overview This skill performs nested TAD (hierarchical TAD/subTAD) detection from Hi-C data using **OnTAD**, starting from a .mcool, .cool or .hic file. Main steps include: - Refer to the **Inputs & Outputs** section to verify required files and output structure. - Inspect the `.mcool` file to list available resolutions and alway remember to confirm the chromosome name and analysis resolution with the user. - Extract a **balanced or raw dense Hi-C matrix** for a selected chromosome and resolution from the `.mcool` file. - Ensure matrix quality (symmetry, no all-zero rows/columns, reasonable contact decay). - Run **OnTAD** to call TADs and nested TAD structures. - Parse and standardize OnTAD output into BED-like tables and hierarchical annotation files. --- ## When to use this skill Use this skill when you want to **identify TADs and nested sub-TADs** from high- or mid-resolution Hi-C data, especially when your contact maps are stored as **Cooler multi-resolution files (.mcool)** and you need **chromosome- and resolution-specific** OnTAD calls. Typical biological questions / use-cases: - Comparing **TAD hierarchy** between cell types
- Overview
- When to use this skill
- Inputs & Outputs
- Inputs
- Outputs
- Allowed Tools
- Decision Tree
- Step 0 — Gather Required Information from the User
- Step 1 — Initialize Project
- Step 3: Check chromosome length
- Step 4: Extract dense matrix from .mcool
- Step 5: Run OnTAD
matrices/ nested_TADs/
What does the nested-TAD-detection skill do?
This skill detects hierarchical (nested) TAD structures from Hi-C contact maps (in .cool or mcool format) using OnTAD, starting from multi-resolution .mcool files. It extracts a user-specified chromosome and resolution, converts the data to a dense matrix, runs OnTAD, and organizes TAD calls and logs for downstream 3D genome analysis.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 31-toolbased-nested-tad-detection-bisnake2001-chromskills-2 --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.