hic-compartments-calling
This skill performs PCA-based A/B compartments calling on Hi-C .mcool datasets using pre-defined MCP tools from the cooler-tools, cooltools-tools, and plot-hic-tools servers.
npx skills add majiayu000/claude-skill-registry --skill 17-toolbased-hic-compartments-calling --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 Compartments Calling (MCP-based) ## Overview This skill provides an automated workflow for compartments calling on .mcool, .cool or .hic Hi-C data. Main steps 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 compartments. ~50-250 kb is recommended. 100 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. - Perform **PCA-based compartment analysis** and extract the first principal component (PC1). - **Generate compartment interaction saddle plots** and BigWig outputs for visualization. ## When to Use This Skill Use this skill when: - You want to identify A/B compartments from Hi-C `.mcool` or `.cool` files. - You need PC1 compartment scores and bigWig tracks for genome browser visualization. - You want a reproducible, normalized, automated compartment-calling workflow. ## Inputs & O
- 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 — Compute GC Track for Bins
- Step 5 — Run Expected-cis and Eigs-cis (PCA Compartment Calling)
- Step 6 — Run Saddle Analysis
- Step 7 — Plot Saddle as PDF
compartments/ plots/ # PC1 track for genome browser temp/
What does the hic-compartments-calling skill do?
This skill performs PCA-based A/B compartments calling on Hi-C .mcool datasets using pre-defined MCP tools from the cooler-tools, cooltools-tools, and plot-hic-tools servers.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 17-toolbased-hic-compartments-calling --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.