hic-loop-calling
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
npx skills add majiayu000/claude-skill-registry --skill 19-toolbased-hic-loop-calling-bisnake2001-chromskills --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.
# Hi-C Loop Calling ## Overview This skill provides a minimal and efficient workflow for detecting chromatin loops from Hi-C data stored in .mcool format and preparing results for visualization in IGV. The key steps involved include: - Refer to the **Inputs & Outputs** section to verify required files and output structure. - **Always prompt user** for genome assembly used. - **Always prompt user** for resolution used to call loops. ~2-50 kb is recommended. 5 kb is default. - **Locate the genome FASTA file** from homer genome fasta file based on user input. - **Rename chromosomes** in the .mcool or .cool file to satisfy the chromosome format with "chr". - **Generate chromosome-arm view files** for compartment calling after changing the chromosome name. - **Extract contact matrices** from .mcool files at the desired resolution. - **Detect chromatin loops**. --- ## When to Use This Skill Use this skill when: - You need to identify (in other words, call, or detect) chromatin loops from Hi-C data in .mcool format. --- ## Inputs & Outputs ### Inputs - **File format:** .mcool, .cool, or .hic (Hi-C data file). - **Genome assembly:** Prompt the user for genome assembly used. - **Resolution:
- 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 & Locate Genome FASTA
- Step 3 — Create Chromosome-Arm View File
- Step 4: Detect Chromatin Loops
loops/ temp/
What does the hic-loop-calling skill do?
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 19-toolbased-hic-loop-calling-bisnake2001-chromskills --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.