loop-annotation
This skill annotates chromatin loops, including enhancer/promoter assignments, CTCF-peak overlap. It automatically constructs enhancer and promoter sets when missing and outputs standardized loop categories.
npx skills add majiayu000/claude-skill-registry --skill 33-loop-annotation-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.
# Loop Annotation ## Overview This skill performs loop annotation for Hi-C/HiChIP/ChIA-PET interaction data. It identifies regulatory and structural loop types (E–E, E–P, P–P, CTCF-CTCF). Main steps include: - Refer to **Inputs & Outputs** to verify necessary files. - **Always prompt user** if required files are missing. - **Always prompt user** for genome assembly used. - Build enhancers.bed if absent (ATAC + H3K27ac). - Build promoters.bed if absent (.tss annotation). - **Always prompt user** for the column index of the interaction count in the raw BEDPE file. Never decide by yourself. - Standardize the format of the `.bedpe` file as the input of `annotateInteractions.pl` - Run `annotateInteractions.pl` with feature sets. - Visualization ## When to use this skill - Regulatory loop landscape analysis. - Enhancer–promoter mapping from chromatin loops. - Structural loop analysis via CTCF orientation. - Integration with ATAC/H3K27ac/TSS/CTCF datasets. - Upstream to differential loop testing or expression integration. ## Inputs & Outputs ### Inputs Required: - loops.bedpe - ctcf_peaks.bed - genome version (user must provide) Optional: - enhancers.bed - promoters.bed - ATAC_peaks.bed -
- Overview
- When to use this skill
- Inputs & Outputs
- Inputs
- Outputs
- Decision Tree
- Step 1 — Validate inputs
- Step 2 — Build enhancers.bed (if missing)
- Step 3 — Build promoters.bed (if missing)
- Step 4 — Standardize the input file
- Step 5 — Annotate the loops
- Step 6 — Classify and visualize loop types
loop_annotation/ logs/ annotateInteractions.log annotations/ interactionAnnotation.txt lengthDist.txt featureEnrichment.txt pairwiseFeatureEnrichment.txt # assign feature pairs to 0x0 0x1 and so on, represent the feature pairs like CTCF-CTCF, E-P features/ enhancers.bed
What does the loop-annotation skill do?
This skill annotates chromatin loops, including enhancer/promoter assignments, CTCF-peak overlap. It automatically constructs enhancer and promoter sets when missing and outputs standardized loop categories.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 33-loop-annotation-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.